Starting phenix.real_space_refine on Sun Jul 5 00:05:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd2_37122/07_2026/8kd2_37122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd2_37122/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8kd2_37122/07_2026/8kd2_37122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd2_37122/07_2026/8kd2_37122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kd2_37122/07_2026/8kd2_37122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd2_37122/07_2026/8kd2_37122.map" } 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-dev-6108/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: 5.14, per 1000 atoms: 0.21 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: 1.87 Conformation dependent library (CDL) restraints added in 757.5 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: 3.19 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: 7.63 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 35702 2.38 - 4.75: 639 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: 14.960 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: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.680 Find NCS groups from input model: 0.180 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: 43.880 ------------------------------------------------------------------------------- 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= 0.407 Angle : 0.798 11.877 36445 Z= 0.584 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 0.79845 / 0.58 (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 : 0.754 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: 0.1540 time to fit residues: 65.4779 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 : 0.793 ------------------------------------------------------------------------------- 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: 4.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 30.0000 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: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.139637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.110412 restraints weight = 60376.435| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.90 r_work: 0.3663 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 25899 Z= 0.251 Angle : 0.732 19.700 36445 Z= 0.393 Chirality : 0.048 0.310 4041 Planarity : 0.006 0.053 3424 Dihedral : 27.960 139.787 6166 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 6.73 % Allowed : 28.27 % Favored : 65.00 % 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: -0.20 (0.18), residues: 2112 helix: 0.84 (0.15), residues: 1156 sheet: 0.44 (0.60), residues: 81 loop : -1.53 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O 129 TYR 0.031 0.002 TYR B 755 PHE 0.017 0.002 PHE A 160 TRP 0.041 0.003 TRP B 916 HIS 0.010 0.002 HIS B 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 (25898) covalent geometry : angle 0.73236 / 0.39 (36443) SS BOND : bond 0.00012 / 0.01 ( 1) SS BOND : angle 1.08342 / 0.63 ( 2) hydrogen bonds : bond 0.05424 / 3.67 ( 1198) hydrogen bonds : angle 3.80001 / 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 394 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 265 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8144 (t0) cc_final: 0.7866 (t0) REVERT: A 204 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7106 (ttp) REVERT: B 708 PHE cc_start: 0.5122 (t80) cc_final: 0.4872 (t80) REVERT: B 709 TYR cc_start: 0.6230 (OUTLIER) cc_final: 0.3990 (t80) REVERT: B 860 MET cc_start: 0.5801 (mmp) cc_final: 0.5305 (mpp) REVERT: B 962 LYS cc_start: 0.5100 (OUTLIER) cc_final: 0.4362 (ptpp) REVERT: B 1136 PHE cc_start: 0.3438 (OUTLIER) cc_final: 0.2842 (m-10) REVERT: B 1164 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.5509 (pp-130) REVERT: B 1167 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6594 (pmt-80) REVERT: B 1220 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5788 (mt-10) REVERT: B 1284 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6792 (pp) REVERT: D 220 ILE cc_start: 0.5525 (mt) cc_final: 0.5173 (mm) REVERT: D 269 LEU cc_start: 0.3992 (OUTLIER) cc_final: 0.3780 (pp) REVERT: D 275 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: D 354 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6926 (pp) REVERT: E 305 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6618 (pt0) REVERT: E 369 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7602 (ptt180) REVERT: E 432 GLU cc_start: 0.8047 (pm20) cc_final: 0.7805 (pm20) REVERT: E 472 THR cc_start: 0.6323 (OUTLIER) cc_final: 0.6038 (p) REVERT: E 511 LYS cc_start: 0.2604 (mmtt) cc_final: 0.1746 (mptt) REVERT: O 42 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7929 (mmm-85) REVERT: P 85 ASP cc_start: 0.8367 (p0) cc_final: 0.8128 (p0) REVERT: P 91 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8301 (ttpt) REVERT: Q 36 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7148 (pptt) REVERT: Q 56 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: Q 91 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: R 90 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: S 59 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6904 (pm20) REVERT: S 109 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9019 (mp) REVERT: T 50 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8406 (tt) REVERT: U 56 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8019 (tm-30) outliers start: 129 outliers final: 50 residues processed: 364 average time/residue: 0.1714 time to fit residues: 98.2562 Evaluate side-chains 310 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 237 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 42 ARG Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 49 LEU 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: 5.9990 chunk 62 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 193 optimal weight: 0.3980 chunk 160 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 HIS A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 GLN B 974 GLN B1254 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 HIS Q 104 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN T 25 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.139674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.110357 restraints weight = 60442.123| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.92 r_work: 0.3661 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2163 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= 0.139 Angle : 0.565 10.273 36445 Z= 0.314 Chirality : 0.041 0.265 4041 Planarity : 0.004 0.076 3424 Dihedral : 27.916 139.477 6159 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.54 % Allowed : 28.69 % Favored : 66.77 % 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: 1.12 (0.15), residues: 1157 sheet: 0.43 (0.59), residues: 82 loop : -1.47 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 50 TYR 0.019 0.001 TYR B 755 PHE 0.024 0.001 PHE B 977 TRP 0.019 0.001 TRP E 301 HIS 0.008 0.001 HIS B 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (25898) covalent geometry : angle 0.56449 / 0.31 (36443) SS BOND : bond 0.00047 / 0.02 ( 1) SS BOND : angle 0.83935 / 0.47 ( 2) hydrogen bonds : bond 0.04122 / 2.77 ( 1198) hydrogen bonds : angle 3.58116 / 2.53 ( 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 341 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 254 time to evaluate : 0.804 Fit side-chains REVERT: A 105 ASN cc_start: 0.8238 (t0) cc_final: 0.7973 (t0) REVERT: B 709 TYR cc_start: 0.6248 (OUTLIER) cc_final: 0.3938 (t80) REVERT: B 818 ASP cc_start: 0.7456 (m-30) cc_final: 0.7222 (m-30) REVERT: B 860 MET cc_start: 0.5762 (mmp) cc_final: 0.5260 (mpp) REVERT: B 986 TYR cc_start: 0.5953 (OUTLIER) cc_final: 0.4633 (t80) REVERT: B 1164 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.5646 (pp-130) REVERT: B 1167 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6666 (pmt-80) REVERT: B 1284 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6776 (pp) REVERT: D 220 ILE cc_start: 0.5684 (mt) cc_final: 0.5268 (mm) REVERT: D 354 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6971 (pp) REVERT: E 35 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6193 (mpp80) REVERT: E 49 LYS cc_start: 0.8339 (tptp) cc_final: 0.8033 (tptp) REVERT: E 472 THR cc_start: 0.6344 (OUTLIER) cc_final: 0.6056 (p) REVERT: P 85 ASP cc_start: 0.8274 (p0) cc_final: 0.8028 (p0) REVERT: P 91 LYS cc_start: 0.8495 (ttmt) cc_final: 0.8289 (ttmt) REVERT: Q 56 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: Q 74 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8271 (mptp) REVERT: R 31 LYS cc_start: 0.5948 (ttpp) cc_final: 0.5668 (ttpt) REVERT: R 68 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: R 90 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: S 59 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6834 (pm20) REVERT: S 109 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8767 (mp) REVERT: U 56 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: V 90 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8090 (mp0) outliers start: 87 outliers final: 40 residues processed: 320 average time/residue: 0.1684 time to fit residues: 85.6225 Evaluate side-chains 301 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 245 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 250 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 815 HIS Chi-restraints excluded: chain B residue 883 LEU 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 1138 LEU 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 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 D residue 360 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 35 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 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 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 44 LYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 115 optimal weight: 20.0000 chunk 203 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 ASN A 105 ASN ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 341 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 829 GLN ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1173 ASN B1254 HIS B1311 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 ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN P 75 HIS Q 104 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 92 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.127688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.097546 restraints weight = 58057.392| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.97 r_work: 0.3372 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.130 25899 Z= 0.327 Angle : 0.787 12.780 36445 Z= 0.418 Chirality : 0.051 0.294 4041 Planarity : 0.006 0.055 3424 Dihedral : 28.253 138.567 6159 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.99 % Allowed : 26.13 % Favored : 66.88 % 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: -0.59 (0.17), residues: 2112 helix: 0.45 (0.15), residues: 1158 sheet: -0.27 (0.57), residues: 84 loop : -1.53 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG U 17 TYR 0.038 0.003 TYR B 755 PHE 0.039 0.002 PHE A 160 TRP 0.021 0.002 TRP B1151 HIS 0.058 0.003 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.33 (25898) covalent geometry : angle 0.78665 / 0.42 (36443) SS BOND : bond 0.00093 / 0.05 ( 1) SS BOND : angle 1.16307 / 0.66 ( 2) hydrogen bonds : bond 0.05830 / 3.94 ( 1198) hydrogen bonds : angle 3.96762 / 2.81 ( 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 418 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 284 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7408 (tpp) cc_final: 0.6195 (tpp) REVERT: A 74 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7273 (ttp) REVERT: A 105 ASN cc_start: 0.8551 (t0) cc_final: 0.8246 (t0) REVERT: A 163 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7066 (mp) REVERT: A 174 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7500 (mm) REVERT: A 305 MET cc_start: 0.8376 (ttt) cc_final: 0.8125 (ttt) REVERT: A 346 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.8143 (t80) REVERT: B 709 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.4376 (t80) REVERT: B 802 GLN cc_start: 0.6901 (tm-30) cc_final: 0.6512 (tm-30) REVERT: B 805 GLU cc_start: 0.7427 (pp20) cc_final: 0.7016 (pp20) REVERT: B 818 ASP cc_start: 0.7754 (m-30) cc_final: 0.7270 (m-30) REVERT: B 860 MET cc_start: 0.6182 (mmp) cc_final: 0.5638 (mpp) REVERT: B 868 ARG cc_start: 0.7414 (tmt-80) cc_final: 0.6891 (mtp85) REVERT: B 911 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7090 (pm20) REVERT: B 912 TRP cc_start: 0.7676 (OUTLIER) cc_final: 0.6663 (t-100) REVERT: B 917 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7276 (ttm170) REVERT: B 962 LYS cc_start: 0.5163 (OUTLIER) cc_final: 0.4337 (ptpp) REVERT: B 986 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.4901 (t80) REVERT: B 989 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7413 (mm) REVERT: B 1164 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6504 (pp-130) REVERT: B 1167 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6850 (pmt-80) REVERT: B 1220 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6723 (mt-10) REVERT: B 1248 SER cc_start: 0.8036 (t) cc_final: 0.7525 (m) REVERT: B 1284 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6924 (pp) REVERT: D 220 ILE cc_start: 0.5914 (mt) cc_final: 0.5490 (mm) REVERT: D 223 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: D 347 MET cc_start: 0.5684 (tmt) cc_final: 0.4696 (tpt) REVERT: D 354 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7012 (pp) REVERT: E 49 LYS cc_start: 0.8494 (tptp) cc_final: 0.8195 (tptp) REVERT: E 465 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8559 (ttmt) REVERT: E 472 THR cc_start: 0.7035 (OUTLIER) cc_final: 0.6711 (p) REVERT: E 511 LYS cc_start: 0.3150 (mmtt) cc_final: 0.2564 (mptt) REVERT: O 59 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7745 (pp20) REVERT: O 60 LEU cc_start: 0.8560 (mt) cc_final: 0.7878 (mt) REVERT: P 88 TYR cc_start: 0.8790 (m-10) cc_final: 0.8455 (m-80) REVERT: Q 74 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8348 (mptp) REVERT: Q 91 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: R 90 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: R 113 LYS cc_start: 0.8423 (ptmm) cc_final: 0.8222 (ttpp) REVERT: S 56 LYS cc_start: 0.8221 (ptpt) cc_final: 0.8019 (ptmm) REVERT: S 79 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7576 (tmtt) REVERT: S 109 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9144 (mp) REVERT: T 79 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8527 (tppt) REVERT: U 56 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: V 90 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: V 105 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8495 (mmtt) outliers start: 134 outliers final: 60 residues processed: 387 average time/residue: 0.1777 time to fit residues: 107.0049 Evaluate side-chains 346 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 257 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 163 LEU Chi-restraints excluded: chain A residue 174 LEU 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 A residue 345 GLU Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 668 PHE 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 883 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 911 GLU 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 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 989 LEU 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 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 223 GLN 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 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 D residue 360 GLU Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 452 VAL 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 E residue 493 LYS 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 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 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 79 LYS 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 49 LEU Chi-restraints excluded: chain T residue 79 LYS 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 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: 0.6980 chunk 221 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 232 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 210 optimal weight: 40.0000 chunk 179 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 76 GLN A 341 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 HIS B1173 ASN 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** O 68 GLN O 125 GLN P 25 ASN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 92 GLN U 73 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.129453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.099090 restraints weight = 57936.427| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.75 r_work: 0.3450 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4071 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= 0.156 Angle : 0.604 10.341 36445 Z= 0.331 Chirality : 0.043 0.260 4041 Planarity : 0.004 0.049 3424 Dihedral : 28.187 139.658 6159 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.69 % Allowed : 27.80 % Favored : 67.50 % 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: -0.23 (0.18), residues: 2112 helix: 0.82 (0.15), residues: 1159 sheet: -0.56 (0.56), residues: 83 loop : -1.45 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 20 TYR 0.032 0.002 TYR B 755 PHE 0.037 0.001 PHE A 160 TRP 0.026 0.001 TRP E 301 HIS 0.014 0.001 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (25898) covalent geometry : angle 0.60383 / 0.33 (36443) SS BOND : bond 0.00189 / 0.10 ( 1) SS BOND : angle 1.15474 / 0.63 ( 2) hydrogen bonds : bond 0.04113 / 2.75 ( 1198) hydrogen bonds : angle 3.69399 / 2.61 ( 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 377 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 287 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8454 (t0) cc_final: 0.8149 (t0) REVERT: A 313 TYR cc_start: 0.6789 (m-80) cc_final: 0.6576 (m-80) REVERT: A 373 MET cc_start: 0.7386 (mmt) cc_final: 0.7182 (mmp) REVERT: B 671 LYS cc_start: 0.8177 (mttm) cc_final: 0.7646 (mtmt) REVERT: B 709 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.4239 (t80) REVERT: B 802 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6646 (tm-30) REVERT: B 818 ASP cc_start: 0.7555 (m-30) cc_final: 0.7272 (m-30) REVERT: B 860 MET cc_start: 0.6004 (mmp) cc_final: 0.5515 (mpp) REVERT: B 868 ARG cc_start: 0.7331 (tmt-80) cc_final: 0.6855 (mtp85) REVERT: B 912 TRP cc_start: 0.7702 (OUTLIER) cc_final: 0.6978 (t-100) REVERT: B 917 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7352 (ttm170) REVERT: B 986 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.4826 (t80) REVERT: B 1164 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6445 (pp-130) REVERT: B 1167 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6915 (pmt-80) REVERT: B 1220 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6756 (mt-10) REVERT: B 1248 SER cc_start: 0.7960 (t) cc_final: 0.7660 (m) REVERT: B 1284 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6883 (pp) REVERT: D 220 ILE cc_start: 0.5893 (mt) cc_final: 0.5464 (mm) REVERT: D 347 MET cc_start: 0.5602 (tmt) cc_final: 0.4649 (tpp) REVERT: D 354 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6984 (pp) REVERT: E 35 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6273 (mpp80) REVERT: E 49 LYS cc_start: 0.8499 (tptp) cc_final: 0.8196 (tptp) REVERT: E 432 GLU cc_start: 0.8190 (pm20) cc_final: 0.7969 (pm20) REVERT: E 472 THR cc_start: 0.7005 (OUTLIER) cc_final: 0.6645 (p) REVERT: E 509 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.5946 (mt) REVERT: P 25 ASN cc_start: 0.8598 (m-40) cc_final: 0.8389 (m110) REVERT: Q 56 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: Q 74 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8200 (mptp) REVERT: R 113 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8077 (ttpp) REVERT: U 56 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: V 90 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: V 102 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7874 (mm-30) REVERT: V 105 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8355 (pttp) outliers start: 90 outliers final: 41 residues processed: 357 average time/residue: 0.1613 time to fit residues: 90.2684 Evaluate side-chains 330 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 271 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 815 HIS 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 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 1286 TYR Chi-restraints excluded: chain B residue 1312 VAL 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 354 LEU Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain E residue 35 ARG 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 493 LYS Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 509 LEU 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 61 SER Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain S residue 59 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 U residue 71 ARG Chi-restraints excluded: chain V residue 90 GLU 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: 0.3980 chunk 118 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 197 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 127 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 959 GLN B1254 HIS B1293 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** O 68 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.129684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.099856 restraints weight = 57830.416| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.71 r_work: 0.3477 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25899 Z= 0.138 Angle : 0.580 9.576 36445 Z= 0.318 Chirality : 0.041 0.254 4041 Planarity : 0.004 0.049 3424 Dihedral : 28.073 140.587 6159 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.64 % Allowed : 27.18 % Favored : 68.18 % 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: -0.01 (0.18), residues: 2112 helix: 1.04 (0.15), residues: 1158 sheet: -0.60 (0.57), residues: 83 loop : -1.38 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 46 TYR 0.023 0.001 TYR B 755 PHE 0.033 0.001 PHE A 160 TRP 0.026 0.001 TRP E 301 HIS 0.029 0.001 HIS B 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (25898) covalent geometry : angle 0.57962 / 0.32 (36443) SS BOND : bond 0.00178 / 0.09 ( 1) SS BOND : angle 1.00871 / 0.56 ( 2) hydrogen bonds : bond 0.03920 / 2.61 ( 1198) hydrogen bonds : angle 3.58877 / 2.54 ( 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 374 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 285 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7163 (ttp) REVERT: A 105 ASN cc_start: 0.8589 (t0) cc_final: 0.8285 (t0) REVERT: B 671 LYS cc_start: 0.8072 (mttm) cc_final: 0.7698 (mtmt) REVERT: B 709 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.4300 (t80) REVERT: B 756 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.6553 (pttm) REVERT: B 802 GLN cc_start: 0.6799 (tm-30) cc_final: 0.6571 (tm-30) REVERT: B 860 MET cc_start: 0.6122 (mmp) cc_final: 0.5581 (mpp) REVERT: B 868 ARG cc_start: 0.7362 (tmt-80) cc_final: 0.6883 (mtp85) REVERT: B 912 TRP cc_start: 0.7844 (OUTLIER) cc_final: 0.7046 (t-100) REVERT: B 917 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7446 (ttm170) REVERT: B 986 TYR cc_start: 0.6194 (OUTLIER) cc_final: 0.5120 (t80) REVERT: B 1164 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6281 (pp-130) REVERT: B 1167 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.6962 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7250 (ptp90) REVERT: B 1248 SER cc_start: 0.8086 (t) cc_final: 0.7783 (m) REVERT: B 1284 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6907 (pp) REVERT: D 220 ILE cc_start: 0.6007 (mt) cc_final: 0.5476 (mm) REVERT: D 223 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7706 (pt0) REVERT: D 347 MET cc_start: 0.5756 (tmt) cc_final: 0.4784 (tpp) REVERT: D 354 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7025 (pp) REVERT: E 35 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6230 (mpp80) REVERT: E 432 GLU cc_start: 0.8263 (pm20) cc_final: 0.8034 (pm20) REVERT: E 544 GLU cc_start: 0.7843 (pp20) cc_final: 0.7194 (tt0) REVERT: O 129 ARG cc_start: 0.8565 (tpt90) cc_final: 0.8352 (tpt90) REVERT: P 25 ASN cc_start: 0.8733 (m-40) cc_final: 0.8427 (m110) REVERT: Q 56 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: Q 74 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8296 (mptp) REVERT: U 17 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.6467 (ttp80) REVERT: U 56 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8481 (tm-30) REVERT: V 90 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8358 (mp0) REVERT: V 105 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8608 (pttp) outliers start: 89 outliers final: 52 residues processed: 353 average time/residue: 0.1713 time to fit residues: 94.2719 Evaluate side-chains 340 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 269 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 61 MET 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 314 THR Chi-restraints excluded: chain B residue 684 GLU 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 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 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 1207 VAL Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1255 THR Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1286 TYR Chi-restraints excluded: chain D residue 223 GLN 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 344 SER Chi-restraints excluded: chain D residue 354 LEU 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 423 THR Chi-restraints excluded: chain E residue 436 LEU 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 62 ILE Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain T residue 44 LYS 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 49 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 105 LYS Chi-restraints excluded: chain V residue 117 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 223 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 9 optimal weight: 0.3980 chunk 115 optimal weight: 0.9980 chunk 204 optimal weight: 0.5980 chunk 187 optimal weight: 0.5980 chunk 233 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN B1254 HIS B1293 HIS D 389 ASN ** 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 422 GLN O 108 ASN 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 U 73 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.129468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.099300 restraints weight = 58048.194| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.79 r_work: 0.3452 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25899 Z= 0.139 Angle : 0.579 10.344 36445 Z= 0.314 Chirality : 0.041 0.249 4041 Planarity : 0.004 0.049 3424 Dihedral : 28.025 140.627 6159 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.80 % Allowed : 26.76 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.18), residues: 2112 helix: 1.15 (0.15), residues: 1155 sheet: -0.90 (0.53), residues: 94 loop : -1.40 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 46 TYR 0.022 0.001 TYR R 37 PHE 0.025 0.001 PHE A 160 TRP 0.028 0.001 TRP E 301 HIS 0.005 0.001 HIS B 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (25898) covalent geometry : angle 0.57907 / 0.31 (36443) SS BOND : bond 0.00159 / 0.08 ( 1) SS BOND : angle 0.93788 / 0.52 ( 2) hydrogen bonds : bond 0.03859 / 2.57 ( 1198) hydrogen bonds : angle 3.54423 / 2.51 ( 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 371 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 279 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7383 (tpp) cc_final: 0.6156 (tpp) REVERT: A 74 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7107 (ttp) REVERT: A 105 ASN cc_start: 0.8479 (t0) cc_final: 0.8183 (t0) REVERT: A 120 CYS cc_start: 0.8430 (m) cc_final: 0.8132 (m) REVERT: A 305 MET cc_start: 0.8213 (ttt) cc_final: 0.7932 (ttt) REVERT: B 671 LYS cc_start: 0.8072 (mttm) cc_final: 0.7699 (mtmt) REVERT: B 709 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.4218 (t80) REVERT: B 756 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.6450 (pttm) REVERT: B 802 GLN cc_start: 0.6942 (tm-30) cc_final: 0.6649 (tm-30) REVERT: B 805 GLU cc_start: 0.7363 (pp20) cc_final: 0.6970 (pp20) REVERT: B 818 ASP cc_start: 0.7345 (m-30) cc_final: 0.7052 (m-30) REVERT: B 860 MET cc_start: 0.5958 (mmp) cc_final: 0.5504 (mpp) REVERT: B 868 ARG cc_start: 0.7329 (tmt-80) cc_final: 0.6856 (mtp85) REVERT: B 912 TRP cc_start: 0.7768 (OUTLIER) cc_final: 0.6576 (t-100) REVERT: B 916 TRP cc_start: 0.8186 (m-10) cc_final: 0.7656 (m-10) REVERT: B 917 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7541 (ttm170) REVERT: B 986 TYR cc_start: 0.6163 (OUTLIER) cc_final: 0.5070 (t80) REVERT: B 1164 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.6209 (pp-130) REVERT: B 1167 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6940 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7228 (ptp90) REVERT: B 1248 SER cc_start: 0.8002 (t) cc_final: 0.7699 (m) REVERT: B 1284 ILE cc_start: 0.7138 (OUTLIER) cc_final: 0.6896 (pp) REVERT: D 220 ILE cc_start: 0.6052 (mt) cc_final: 0.5547 (mm) REVERT: D 347 MET cc_start: 0.5670 (tmt) cc_final: 0.4783 (tpt) REVERT: D 354 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7000 (pp) REVERT: E 35 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6258 (mpp80) REVERT: E 432 GLU cc_start: 0.8212 (pm20) cc_final: 0.7999 (pm20) REVERT: E 472 THR cc_start: 0.6953 (OUTLIER) cc_final: 0.6588 (p) REVERT: E 544 GLU cc_start: 0.7837 (pp20) cc_final: 0.7213 (tt0) REVERT: Q 15 LYS cc_start: 0.7171 (tptt) cc_final: 0.6935 (tptt) REVERT: Q 56 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: Q 74 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8113 (mptp) REVERT: Q 91 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: U 17 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.6440 (ttp80) REVERT: U 56 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: V 90 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: V 102 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7536 (mm-30) REVERT: V 105 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8164 (pttp) outliers start: 92 outliers final: 52 residues processed: 347 average time/residue: 0.1715 time to fit residues: 93.0330 Evaluate side-chains 341 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 269 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 110 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 221 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 684 GLU 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 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 1207 VAL Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1255 THR Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1286 TYR 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 354 LEU Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 389 ASN 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 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 62 ILE Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 59 GLU 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 77 LYS 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 49 THR 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: 0.8980 chunk 83 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 143 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 93 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN B1254 HIS D 389 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.129398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.099398 restraints weight = 57965.498| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.82 r_work: 0.3456 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4287 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= 0.137 Angle : 0.577 9.450 36445 Z= 0.312 Chirality : 0.040 0.246 4041 Planarity : 0.004 0.049 3424 Dihedral : 27.994 140.622 6159 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.64 % Allowed : 26.92 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 2112 helix: 1.21 (0.15), residues: 1154 sheet: -1.02 (0.52), residues: 95 loop : -1.39 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 46 TYR 0.022 0.001 TYR R 37 PHE 0.038 0.001 PHE A 160 TRP 0.029 0.001 TRP E 301 HIS 0.005 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (25898) covalent geometry : angle 0.57662 / 0.31 (36443) SS BOND : bond 0.00156 / 0.08 ( 1) SS BOND : angle 0.92304 / 0.52 ( 2) hydrogen bonds : bond 0.03773 / 2.51 ( 1198) hydrogen bonds : angle 3.51941 / 2.49 ( 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 366 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 277 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7810 (mmm) cc_final: 0.7608 (mmt) REVERT: A 72 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.6364 (pt0) REVERT: A 74 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7175 (ttp) REVERT: A 105 ASN cc_start: 0.8525 (t0) cc_final: 0.8212 (t0) REVERT: A 120 CYS cc_start: 0.8483 (m) cc_final: 0.8162 (m) REVERT: A 305 MET cc_start: 0.8219 (ttt) cc_final: 0.7949 (ttt) REVERT: A 347 TYR cc_start: 0.7874 (m-80) cc_final: 0.7623 (m-80) REVERT: B 671 LYS cc_start: 0.8040 (mttm) cc_final: 0.7677 (mtmt) REVERT: B 709 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.4254 (t80) REVERT: B 756 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.6568 (pttm) REVERT: B 802 GLN cc_start: 0.6872 (tm-30) cc_final: 0.6568 (tm-30) REVERT: B 805 GLU cc_start: 0.7397 (pp20) cc_final: 0.6979 (pp20) REVERT: B 818 ASP cc_start: 0.7315 (m-30) cc_final: 0.7058 (m-30) REVERT: B 860 MET cc_start: 0.6035 (mmp) cc_final: 0.5555 (mpp) REVERT: B 868 ARG cc_start: 0.7305 (tmt-80) cc_final: 0.6877 (mtp85) REVERT: B 912 TRP cc_start: 0.7790 (OUTLIER) cc_final: 0.6487 (t-100) REVERT: B 916 TRP cc_start: 0.8200 (m-10) cc_final: 0.7642 (m-10) REVERT: B 917 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7510 (ttm170) REVERT: B 986 TYR cc_start: 0.6110 (OUTLIER) cc_final: 0.5009 (t80) REVERT: B 1164 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6189 (pp-130) REVERT: B 1167 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6971 (pmt-80) REVERT: B 1248 SER cc_start: 0.8007 (t) cc_final: 0.7699 (m) REVERT: B 1284 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6858 (pp) REVERT: D 220 ILE cc_start: 0.5977 (mt) cc_final: 0.5471 (mm) REVERT: D 347 MET cc_start: 0.5774 (tmt) cc_final: 0.4807 (tpp) REVERT: D 354 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7049 (pp) REVERT: E 432 GLU cc_start: 0.8244 (pm20) cc_final: 0.8009 (pm20) REVERT: E 472 THR cc_start: 0.6973 (OUTLIER) cc_final: 0.6594 (p) REVERT: E 544 GLU cc_start: 0.7811 (pp20) cc_final: 0.7354 (tt0) REVERT: Q 15 LYS cc_start: 0.7168 (tptt) cc_final: 0.6942 (tptt) REVERT: Q 56 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: Q 74 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8089 (mptp) REVERT: U 56 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: V 90 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: V 105 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8389 (mtpt) outliers start: 89 outliers final: 54 residues processed: 344 average time/residue: 0.1691 time to fit residues: 92.1834 Evaluate side-chains 340 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 269 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 221 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 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 1207 VAL 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 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 354 LEU Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 389 ASN 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 423 THR 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 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 R residue 48 ASP Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 77 LYS 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 49 THR 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: 2.9990 chunk 125 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 210 optimal weight: 40.0000 chunk 47 optimal weight: 0.0040 chunk 65 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN B1254 HIS D 389 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN ** 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 = 0.4203 r_free = 0.4203 target = 0.129342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098719 restraints weight = 58346.567| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.89 r_work: 0.3452 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25899 Z= 0.132 Angle : 0.577 9.364 36445 Z= 0.312 Chirality : 0.040 0.257 4041 Planarity : 0.004 0.049 3424 Dihedral : 27.961 140.604 6159 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.33 % Allowed : 27.07 % 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: 0.17 (0.18), residues: 2112 helix: 1.28 (0.15), residues: 1154 sheet: -1.05 (0.52), residues: 95 loop : -1.39 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 46 TYR 0.023 0.001 TYR R 37 PHE 0.036 0.001 PHE A 160 TRP 0.034 0.001 TRP E 301 HIS 0.005 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (25898) covalent geometry : angle 0.57742 / 0.31 (36443) SS BOND : bond 0.00171 / 0.09 ( 1) SS BOND : angle 0.92956 / 0.52 ( 2) hydrogen bonds : bond 0.03721 / 2.47 ( 1198) hydrogen bonds : angle 3.49510 / 2.47 ( 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 353 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 270 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7401 (tpp) cc_final: 0.6487 (tpp) REVERT: A 53 MET cc_start: 0.7828 (mmm) cc_final: 0.7622 (mmt) REVERT: A 72 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6373 (pt0) REVERT: A 74 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7209 (ttp) REVERT: A 105 ASN cc_start: 0.8515 (t0) cc_final: 0.8207 (t0) REVERT: A 120 CYS cc_start: 0.8454 (m) cc_final: 0.8139 (m) REVERT: A 305 MET cc_start: 0.8216 (ttt) cc_final: 0.7954 (ttt) REVERT: A 347 TYR cc_start: 0.7857 (m-80) cc_final: 0.7620 (m-80) REVERT: B 671 LYS cc_start: 0.8038 (mttm) cc_final: 0.7681 (mtmt) REVERT: B 709 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.4222 (t80) REVERT: B 756 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.6193 (pttp) REVERT: B 805 GLU cc_start: 0.7399 (pp20) cc_final: 0.7039 (pp20) REVERT: B 818 ASP cc_start: 0.7329 (m-30) cc_final: 0.7048 (m-30) REVERT: B 860 MET cc_start: 0.5987 (mmp) cc_final: 0.5534 (mpp) REVERT: B 868 ARG cc_start: 0.7299 (tmt-80) cc_final: 0.6855 (mtp85) REVERT: B 912 TRP cc_start: 0.7809 (OUTLIER) cc_final: 0.6562 (t-100) REVERT: B 916 TRP cc_start: 0.8178 (m-10) cc_final: 0.7635 (m-10) REVERT: B 917 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7405 (ttm170) REVERT: B 986 TYR cc_start: 0.6145 (OUTLIER) cc_final: 0.5076 (t80) REVERT: B 1164 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6252 (pp-130) REVERT: B 1167 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6967 (pmt-80) REVERT: B 1220 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6780 (mt-10) REVERT: B 1248 SER cc_start: 0.8025 (t) cc_final: 0.7715 (m) REVERT: B 1284 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6891 (pp) REVERT: D 220 ILE cc_start: 0.6002 (mt) cc_final: 0.5499 (mm) REVERT: D 347 MET cc_start: 0.5738 (tmt) cc_final: 0.4791 (tpp) REVERT: D 354 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6997 (pp) REVERT: D 389 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8229 (m110) REVERT: E 472 THR cc_start: 0.6987 (OUTLIER) cc_final: 0.6600 (p) REVERT: Q 15 LYS cc_start: 0.7192 (tptt) cc_final: 0.6978 (tptt) REVERT: Q 56 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: Q 74 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8067 (mptp) REVERT: Q 91 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: U 17 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.6321 (ttp80) REVERT: U 51 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8954 (tp) REVERT: U 56 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: V 90 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: V 105 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8366 (mtpt) outliers start: 83 outliers final: 52 residues processed: 330 average time/residue: 0.1492 time to fit residues: 77.6407 Evaluate side-chains 336 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 262 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 221 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 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 1207 VAL 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 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 354 LEU Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 389 ASN 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 423 THR 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 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 109 SER Chi-restraints excluded: chain S residue 59 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 77 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 231 optimal weight: 9.9990 chunk 143 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 148 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS D 389 ASN ** 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** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.127133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.097442 restraints weight = 58070.678| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.99 r_work: 0.3376 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25899 Z= 0.183 Angle : 0.610 9.666 36445 Z= 0.328 Chirality : 0.041 0.237 4041 Planarity : 0.004 0.065 3424 Dihedral : 27.994 140.218 6159 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.28 % Allowed : 27.18 % Favored : 68.54 % 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: 1.21 (0.15), residues: 1156 sheet: -1.09 (0.52), residues: 95 loop : -1.39 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 83 TYR 0.023 0.002 TYR A 34 PHE 0.033 0.002 PHE A 160 TRP 0.036 0.002 TRP E 301 HIS 0.007 0.001 HIS R 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (25898) covalent geometry : angle 0.61030 / 0.33 (36443) SS BOND : bond 0.00152 / 0.08 ( 1) SS BOND : angle 0.93360 / 0.53 ( 2) hydrogen bonds : bond 0.04072 / 2.72 ( 1198) hydrogen bonds : angle 3.56504 / 2.52 ( 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 345 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 263 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6544 (pt0) REVERT: A 74 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7443 (ttp) REVERT: A 105 ASN cc_start: 0.8594 (t0) cc_final: 0.8280 (t0) REVERT: A 305 MET cc_start: 0.8315 (ttt) cc_final: 0.8058 (ttt) REVERT: A 313 TYR cc_start: 0.7070 (m-80) cc_final: 0.6723 (m-80) REVERT: B 671 LYS cc_start: 0.8056 (mttm) cc_final: 0.7693 (mtmt) REVERT: B 709 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.4297 (t80) REVERT: B 756 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.6477 (pttm) REVERT: B 802 GLN cc_start: 0.7194 (tm-30) cc_final: 0.6936 (tm-30) REVERT: B 805 GLU cc_start: 0.7482 (pp20) cc_final: 0.7125 (pp20) REVERT: B 818 ASP cc_start: 0.7397 (m-30) cc_final: 0.7083 (m-30) REVERT: B 860 MET cc_start: 0.6140 (mmp) cc_final: 0.5652 (mpp) REVERT: B 868 ARG cc_start: 0.7351 (tmt-80) cc_final: 0.6870 (mtp85) REVERT: B 912 TRP cc_start: 0.7852 (OUTLIER) cc_final: 0.6790 (t-100) REVERT: B 916 TRP cc_start: 0.8203 (m-10) cc_final: 0.7672 (m-10) REVERT: B 917 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7468 (ttm170) REVERT: B 986 TYR cc_start: 0.6291 (OUTLIER) cc_final: 0.5196 (t80) REVERT: B 1164 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.6511 (pp-130) REVERT: B 1167 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6994 (pmt-80) REVERT: B 1220 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: B 1248 SER cc_start: 0.8089 (t) cc_final: 0.7773 (m) REVERT: B 1284 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6952 (pp) REVERT: D 220 ILE cc_start: 0.6022 (mt) cc_final: 0.5525 (mm) REVERT: D 347 MET cc_start: 0.5771 (tmt) cc_final: 0.4746 (tpp) REVERT: D 354 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6971 (pp) REVERT: D 389 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8330 (m110) REVERT: E 472 THR cc_start: 0.7100 (OUTLIER) cc_final: 0.6715 (p) REVERT: E 544 GLU cc_start: 0.7917 (pp20) cc_final: 0.7485 (tt0) REVERT: O 59 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7733 (pp20) REVERT: Q 15 LYS cc_start: 0.7232 (tptt) cc_final: 0.7005 (tptt) REVERT: Q 74 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8109 (mptp) REVERT: Q 91 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: U 17 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.6499 (ttp80) REVERT: U 51 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8969 (tp) REVERT: U 56 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: V 90 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: V 105 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8417 (mtpt) outliers start: 82 outliers final: 55 residues processed: 324 average time/residue: 0.1648 time to fit residues: 84.1144 Evaluate side-chains 338 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 261 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL 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 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 221 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 A residue 345 GLU 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 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 1207 VAL 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 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 265 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 354 LEU Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 389 ASN 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 423 THR 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 O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER 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 81 ASN Chi-restraints excluded: chain R residue 84 SER 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 96 THR Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 176 optimal weight: 0.0270 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: 0.6980 chunk 221 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 220 optimal weight: 8.9990 overall best weight: 1.0640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN E 304 ASN ** 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 125 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.126552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.096282 restraints weight = 57831.125| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.86 r_work: 0.3384 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25899 Z= 0.170 Angle : 0.609 9.585 36445 Z= 0.326 Chirality : 0.041 0.232 4041 Planarity : 0.004 0.048 3424 Dihedral : 28.030 140.542 6159 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.17 % Allowed : 27.07 % Favored : 68.75 % 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: 0.07 (0.18), residues: 2112 helix: 1.19 (0.15), residues: 1163 sheet: -1.16 (0.52), residues: 94 loop : -1.43 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG V 89 TYR 0.024 0.002 TYR A 34 PHE 0.037 0.001 PHE A 160 TRP 0.033 0.001 TRP E 301 HIS 0.007 0.001 HIS B 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (25898) covalent geometry : angle 0.60942 / 0.33 (36443) SS BOND : bond 0.00136 / 0.07 ( 1) SS BOND : angle 0.97614 / 0.55 ( 2) hydrogen bonds : bond 0.03905 / 2.60 ( 1198) hydrogen bonds : angle 3.56622 / 2.52 ( 3195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7089.38 seconds wall clock time: 122 minutes 10.97 seconds (7330.97 seconds total)