Starting phenix.real_space_refine on Mon Aug 25 01:30:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd2_37122/08_2025/8kd2_37122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd2_37122/08_2025/8kd2_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_37122/08_2025/8kd2_37122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd2_37122/08_2025/8kd2_37122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kd2_37122/08_2025/8kd2_37122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd2_37122/08_2025/8kd2_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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24694 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3097 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 15, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4361 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 12, 'TRANS': 506} Chain breaks: 4 Chain: "D" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1474 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "E" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2399 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 17, 'TRANS': 272} Chain breaks: 5 Chain: "F" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 146 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain breaks: 1 Chain: "G" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 160 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain breaks: 1 Chain: "O" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "P" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "Q" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "S" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "T" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 618 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "X" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3590 Classifications: {'DNA': 174} Link IDs: {'rna3p': 173} Chain: "Y" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3544 Classifications: {'DNA': 174} Link IDs: {'rna3p': 173} Time building chain proxies: 4.88, per 1000 atoms: 0.20 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: 1.75 Conformation dependent library (CDL) restraints added in 705.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.23 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: 6.16 Time building geometry restraints manager: 2.28 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=" N ASN E 45 " pdb=" CA ASN E 45 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.25e+00 bond pdb=" N TYR E 46 " pdb=" CA TYR E 46 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.26e-02 6.30e+03 6.62e+00 bond pdb=" N LEU E 48 " pdb=" CA LEU E 48 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.55e+00 bond pdb=" N LYS E 49 " pdb=" CA LYS E 49 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.34e-02 5.57e+03 5.27e+00 bond pdb=" N LEU B 883 " pdb=" CA LEU B 883 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.23e-02 6.61e+03 4.72e+00 ... (remaining 25893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 35954 2.38 - 4.75: 387 4.75 - 7.13: 76 7.13 - 9.50: 21 9.50 - 11.88: 5 Bond angle restraints: 36443 Sorted by residual: angle pdb=" CA LEU D 248 " pdb=" C LEU D 248 " pdb=" N PRO D 249 " ideal model delta sigma weight residual 120.58 117.53 3.05 7.40e-01 1.83e+00 1.70e+01 angle pdb=" C ASN E 516 " pdb=" N ASN E 517 " pdb=" CA ASN E 517 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CB MET A 373 " pdb=" CG MET A 373 " pdb=" SD MET A 373 " ideal model delta sigma weight residual 112.70 124.58 -11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CB ILE E 523 " pdb=" CG1 ILE E 523 " pdb=" CD1 ILE E 523 " ideal model delta sigma weight residual 113.80 121.72 -7.92 2.10e+00 2.27e-01 1.42e+01 angle pdb=" CG ARG D 247 " pdb=" CD ARG D 247 " pdb=" NE ARG D 247 " ideal model delta sigma weight residual 112.00 120.24 -8.24 2.20e+00 2.07e-01 1.40e+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: 3535 0.060 - 0.120: 467 0.120 - 0.181: 35 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: 10.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.570 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25899 Z= 0.172 Angle : 0.704 11.877 36445 Z= 0.384 Chirality : 0.041 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 aren 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 covalent geometry : bond 0.00354 (25898) covalent geometry : angle 0.70444 (36443) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.15635 ( 2) hydrogen bonds : bond 0.11807 ( 1198) hydrogen bonds : angle 4.90347 ( 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 : 0.834 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: 0.1397 time to fit residues: 59.5563 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 : 0.721 ------------------------------------------------------------------------------- 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: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 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: 1.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 ASN B1254 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 510 GLN G 331 ASN O 68 GLN ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 ASN P 75 HIS ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 92 GLN U 38 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.136444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.106287 restraints weight = 59425.976| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.95 r_work: 0.3575 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 25899 Z= 0.245 Angle : 0.666 14.394 36445 Z= 0.365 Chirality : 0.042 0.243 4041 Planarity : 0.005 0.058 3424 Dihedral : 27.620 138.596 6166 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 6.57 % Allowed : 27.44 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.18), residues: 2112 helix: 0.76 (0.15), residues: 1160 sheet: 0.56 (0.60), residues: 82 loop : -1.49 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 247 TYR 0.030 0.002 TYR B 755 PHE 0.023 0.002 PHE E 262 TRP 0.042 0.002 TRP B 916 HIS 0.020 0.002 HIS D 369 Details of bonding type rmsd covalent geometry : bond 0.00563 (25898) covalent geometry : angle 0.66607 (36443) SS BOND : bond 0.00103 ( 1) SS BOND : angle 1.39258 ( 2) hydrogen bonds : bond 0.04881 ( 1198) hydrogen bonds : angle 3.72882 ( 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 411 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 285 time to evaluate : 0.884 Fit side-chains REVERT: A 346 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7645 (t80) REVERT: B 709 TYR cc_start: 0.6391 (OUTLIER) cc_final: 0.3939 (t80) REVERT: B 805 GLU cc_start: 0.7099 (pp20) cc_final: 0.6784 (pp20) REVERT: B 860 MET cc_start: 0.5822 (mmp) cc_final: 0.5398 (mpp) REVERT: B 868 ARG cc_start: 0.7192 (tmt-80) cc_final: 0.6678 (mtp85) REVERT: B 962 LYS cc_start: 0.5131 (OUTLIER) cc_final: 0.4413 (ptpp) REVERT: B 986 TYR cc_start: 0.6031 (OUTLIER) cc_final: 0.4689 (t80) REVERT: B 1164 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.5686 (pp-130) REVERT: B 1167 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6587 (pmt-80) REVERT: B 1248 SER cc_start: 0.7867 (t) cc_final: 0.7371 (m) REVERT: B 1284 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6824 (pp) REVERT: D 220 ILE cc_start: 0.5674 (mt) cc_final: 0.5271 (mm) REVERT: D 275 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: D 354 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7036 (pp) REVERT: D 394 TYR cc_start: 0.7965 (t80) cc_final: 0.7752 (t80) REVERT: E 35 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6251 (mpp80) REVERT: E 46 TYR cc_start: 0.6387 (p90) cc_final: 0.6129 (p90) REVERT: E 365 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8358 (ptpp) REVERT: E 472 THR cc_start: 0.6457 (OUTLIER) cc_final: 0.6165 (p) REVERT: E 511 LYS cc_start: 0.2604 (mmtt) cc_final: 0.2334 (mptt) REVERT: Q 36 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7425 (pptt) REVERT: Q 56 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: Q 74 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8286 (mptp) REVERT: Q 91 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: R 90 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: S 59 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: S 109 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9087 (mp) REVERT: T 50 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8491 (tt) REVERT: U 56 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: V 102 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7565 (mm-30) REVERT: V 105 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7836 (pttp) outliers start: 126 outliers final: 43 residues processed: 379 average time/residue: 0.1743 time to fit residues: 104.0586 Evaluate side-chains 319 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 254 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 334 LEU Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 376 ILE 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 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 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 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 1228 LEU Chi-restraints excluded: chain B residue 1266 MET 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 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 354 LEU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 415 LEU 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 E residue 542 ILE Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 91 GLU 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 96 THR Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 133 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 193 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS A 341 ASN 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 R 92 GLN U 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.135150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.104599 restraints weight = 59308.338| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.95 r_work: 0.3565 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25899 Z= 0.167 Angle : 0.563 9.813 36445 Z= 0.311 Chirality : 0.037 0.231 4041 Planarity : 0.004 0.064 3424 Dihedral : 27.655 139.088 6159 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.01 % Allowed : 27.86 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.18), residues: 2112 helix: 0.99 (0.15), residues: 1166 sheet: 0.17 (0.57), residues: 83 loop : -1.43 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1149 TYR 0.017 0.002 TYR E 401 PHE 0.023 0.001 PHE A 160 TRP 0.017 0.001 TRP E 301 HIS 0.006 0.001 HIS B 815 Details of bonding type rmsd covalent geometry : bond 0.00377 (25898) covalent geometry : angle 0.56265 (36443) SS BOND : bond 0.00192 ( 1) SS BOND : angle 0.97450 ( 2) hydrogen bonds : bond 0.03788 ( 1198) hydrogen bonds : angle 3.58722 ( 3195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 277 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 347 TYR cc_start: 0.7575 (m-80) cc_final: 0.7367 (m-80) REVERT: B 671 LYS cc_start: 0.8060 (mttm) cc_final: 0.7666 (mttm) REVERT: B 709 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.3925 (t80) REVERT: B 756 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.5942 (pttm) REVERT: B 805 GLU cc_start: 0.7156 (pp20) cc_final: 0.6823 (pp20) REVERT: B 817 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8497 (t80) REVERT: B 818 ASP cc_start: 0.7384 (m-30) cc_final: 0.7104 (m-30) REVERT: B 860 MET cc_start: 0.5853 (mmp) cc_final: 0.5403 (mpp) REVERT: B 868 ARG cc_start: 0.7209 (tmt-80) cc_final: 0.6686 (mtp85) REVERT: B 986 TYR cc_start: 0.6043 (OUTLIER) cc_final: 0.4775 (t80) REVERT: B 1136 PHE cc_start: 0.3855 (OUTLIER) cc_final: 0.3114 (m-10) REVERT: B 1164 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.5898 (pp-130) REVERT: B 1167 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6708 (pmt-80) REVERT: B 1248 SER cc_start: 0.7886 (t) cc_final: 0.7387 (m) REVERT: B 1284 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6741 (pp) REVERT: D 220 ILE cc_start: 0.5754 (mt) cc_final: 0.5293 (mm) REVERT: D 347 MET cc_start: 0.5611 (tmt) cc_final: 0.4649 (tpt) REVERT: D 354 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7012 (pp) REVERT: D 386 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7021 (pt) REVERT: E 511 LYS cc_start: 0.2636 (mmtt) cc_final: 0.2328 (mptt) REVERT: Q 56 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: Q 74 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8244 (mptp) REVERT: R 68 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: R 90 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: R 113 LYS cc_start: 0.8127 (ptmm) cc_final: 0.7780 (ttpp) REVERT: T 50 ILE cc_start: 0.8545 (tt) cc_final: 0.8244 (tt) REVERT: U 56 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8120 (tm-30) outliers start: 96 outliers final: 47 residues processed: 350 average time/residue: 0.1711 time to fit residues: 93.4793 Evaluate side-chains 310 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 248 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 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 A residue 376 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 779 ASN 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 956 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1266 MET Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 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 D residue 386 LEU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 346 HIS 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 E residue 542 ILE 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 60 ASN Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 42 ARG Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain V residue 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 115 optimal weight: 0.0010 chunk 203 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 829 GLN B1254 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 HIS P 25 ASN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 106 HIS U 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.134692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.104571 restraints weight = 59307.942| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.91 r_work: 0.3548 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25899 Z= 0.146 Angle : 0.533 9.665 36445 Z= 0.296 Chirality : 0.036 0.169 4041 Planarity : 0.004 0.048 3424 Dihedral : 27.513 139.610 6159 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.59 % Allowed : 27.07 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.18), residues: 2112 helix: 1.26 (0.15), residues: 1156 sheet: 0.09 (0.58), residues: 83 loop : -1.36 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 316 TYR 0.020 0.001 TYR B 755 PHE 0.019 0.001 PHE A 160 TRP 0.019 0.001 TRP E 301 HIS 0.007 0.001 HIS E 346 Details of bonding type rmsd covalent geometry : bond 0.00316 (25898) covalent geometry : angle 0.53266 (36443) SS BOND : bond 0.00296 ( 1) SS BOND : angle 1.11532 ( 2) hydrogen bonds : bond 0.03456 ( 1198) hydrogen bonds : angle 3.44727 ( 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 353 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 265 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 120 CYS cc_start: 0.8121 (m) cc_final: 0.7913 (m) REVERT: B 671 LYS cc_start: 0.8074 (mttm) cc_final: 0.7614 (mttm) REVERT: B 709 TYR cc_start: 0.6443 (OUTLIER) cc_final: 0.3967 (t80) REVERT: B 756 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.5960 (pttm) REVERT: B 791 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7846 (mp0) REVERT: B 805 GLU cc_start: 0.7200 (pp20) cc_final: 0.6853 (pp20) REVERT: B 817 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8492 (t80) REVERT: B 818 ASP cc_start: 0.7441 (m-30) cc_final: 0.7109 (m-30) REVERT: B 860 MET cc_start: 0.5872 (mmp) cc_final: 0.5409 (mpp) REVERT: B 868 ARG cc_start: 0.7199 (tmt-80) cc_final: 0.6694 (mtp85) REVERT: B 912 TRP cc_start: 0.7552 (OUTLIER) cc_final: 0.6719 (t-100) REVERT: B 917 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7303 (ttm170) REVERT: B 951 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7459 (tt0) REVERT: B 956 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7762 (ttmt) REVERT: B 986 TYR cc_start: 0.6053 (OUTLIER) cc_final: 0.4803 (t80) REVERT: B 1164 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.5934 (pp-130) REVERT: B 1167 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6830 (pmt-80) REVERT: B 1248 SER cc_start: 0.7907 (t) cc_final: 0.7622 (m) REVERT: B 1284 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6755 (pp) REVERT: D 220 ILE cc_start: 0.5886 (mt) cc_final: 0.5403 (mm) REVERT: D 347 MET cc_start: 0.5662 (tmt) cc_final: 0.4631 (tpt) REVERT: D 354 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6990 (pp) REVERT: D 386 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7077 (pt) REVERT: E 472 THR cc_start: 0.6558 (OUTLIER) cc_final: 0.6246 (p) REVERT: E 511 LYS cc_start: 0.2762 (mmtt) cc_final: 0.2504 (mptt) REVERT: Q 56 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: R 90 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: R 113 LYS cc_start: 0.8149 (ptmm) cc_final: 0.7819 (ttpp) REVERT: S 59 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6949 (pm20) REVERT: S 133 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7232 (mt-10) REVERT: T 50 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8187 (tt) REVERT: U 56 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: V 90 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8129 (mp0) outliers start: 88 outliers final: 39 residues processed: 334 average time/residue: 0.1861 time to fit residues: 96.6201 Evaluate side-chains 312 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 253 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 86 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 314 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 779 ASN 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 956 LYS 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 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 1228 LEU Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 346 HIS 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 R residue 61 SER 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 103 LEU Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 232 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 210 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 341 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 GLN ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 HIS ** 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 P 25 ASN Q 82 HIS ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 81 ASN R 92 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.124552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.094171 restraints weight = 57512.927| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.77 r_work: 0.3352 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 25899 Z= 0.306 Angle : 0.701 12.950 36445 Z= 0.381 Chirality : 0.043 0.290 4041 Planarity : 0.005 0.062 3424 Dihedral : 27.805 140.058 6159 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.89 % Allowed : 26.03 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.18), residues: 2112 helix: 0.72 (0.15), residues: 1161 sheet: -0.43 (0.55), residues: 85 loop : -1.46 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 50 TYR 0.032 0.002 TYR B 755 PHE 0.019 0.002 PHE A 97 TRP 0.021 0.002 TRP E 301 HIS 0.083 0.003 HIS E 346 Details of bonding type rmsd covalent geometry : bond 0.00683 (25898) covalent geometry : angle 0.70046 (36443) SS BOND : bond 0.00253 ( 1) SS BOND : angle 1.33045 ( 2) hydrogen bonds : bond 0.04907 ( 1198) hydrogen bonds : angle 3.83020 ( 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 413 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 300 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6802 (pt0) REVERT: A 172 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: A 174 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7589 (mm) REVERT: A 305 MET cc_start: 0.8488 (ttt) cc_final: 0.8171 (ttt) REVERT: A 377 PHE cc_start: 0.7137 (m-10) cc_final: 0.6836 (m-10) REVERT: B 670 GLU cc_start: 0.8237 (pm20) cc_final: 0.8001 (pm20) REVERT: B 709 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.4456 (t80) REVERT: B 802 GLN cc_start: 0.7273 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 817 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8625 (t80) REVERT: B 818 ASP cc_start: 0.7966 (m-30) cc_final: 0.7472 (m-30) REVERT: B 860 MET cc_start: 0.6320 (mmp) cc_final: 0.5804 (mpp) REVERT: B 868 ARG cc_start: 0.7443 (tmt-80) cc_final: 0.6950 (mtp85) REVERT: B 911 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7462 (pm20) REVERT: B 912 TRP cc_start: 0.7896 (OUTLIER) cc_final: 0.7321 (t-100) REVERT: B 917 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7697 (ttm170) REVERT: B 951 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7677 (tt0) REVERT: B 956 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8587 (tttt) REVERT: B 962 LYS cc_start: 0.5298 (OUTLIER) cc_final: 0.4536 (ptpp) REVERT: B 986 TYR cc_start: 0.6412 (OUTLIER) cc_final: 0.5130 (t80) REVERT: B 1164 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.6655 (pp-130) REVERT: B 1167 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7045 (pmt-80) REVERT: B 1248 SER cc_start: 0.8256 (t) cc_final: 0.7914 (m) REVERT: B 1284 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6928 (pp) REVERT: D 220 ILE cc_start: 0.6017 (mt) cc_final: 0.5505 (mm) REVERT: D 263 HIS cc_start: 0.6472 (t-170) cc_final: 0.6157 (t-170) REVERT: D 269 LEU cc_start: 0.4775 (OUTLIER) cc_final: 0.4528 (pp) REVERT: D 275 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: D 347 MET cc_start: 0.5886 (tmt) cc_final: 0.4873 (tpt) REVERT: E 365 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8715 (ptmm) REVERT: E 472 THR cc_start: 0.7259 (OUTLIER) cc_final: 0.6891 (p) REVERT: E 489 TYR cc_start: 0.6080 (p90) cc_final: 0.5857 (p90) REVERT: O 59 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7919 (pp20) REVERT: P 25 ASN cc_start: 0.8761 (m-40) cc_final: 0.8429 (m110) REVERT: P 88 TYR cc_start: 0.9019 (m-10) cc_final: 0.8767 (m-80) REVERT: P 93 GLN cc_start: 0.8691 (mt0) cc_final: 0.8437 (mt0) REVERT: Q 74 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8392 (mptp) REVERT: Q 91 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: T 50 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8660 (tt) REVERT: T 88 TYR cc_start: 0.8879 (m-10) cc_final: 0.8493 (m-10) REVERT: U 56 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: V 105 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8515 (mtpt) outliers start: 113 outliers final: 57 residues processed: 389 average time/residue: 0.1925 time to fit residues: 115.8200 Evaluate side-chains 348 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 267 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 110 CYS Chi-restraints excluded: chain A residue 172 GLU 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 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 817 TYR 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 956 LYS Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 996 ILE 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 1228 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1322 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 253 THR 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 298 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 415 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 E residue 498 ILE Chi-restraints excluded: chain O residue 45 THR 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 80 THR Chi-restraints excluded: chain P residue 92 ARG 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 61 SER Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 76 ARG Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 188 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 67 optimal weight: 0.2980 chunk 197 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 296 ASN A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN O 68 GLN O 108 ASN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN R 106 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.126347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.096236 restraints weight = 57415.369| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.87 r_work: 0.3372 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25899 Z= 0.164 Angle : 0.585 10.989 36445 Z= 0.321 Chirality : 0.037 0.187 4041 Planarity : 0.004 0.052 3424 Dihedral : 27.742 141.251 6159 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.12 % Allowed : 27.07 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.18), residues: 2112 helix: 1.01 (0.15), residues: 1169 sheet: -0.58 (0.55), residues: 83 loop : -1.41 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 83 TYR 0.027 0.002 TYR B 755 PHE 0.025 0.001 PHE A 160 TRP 0.021 0.001 TRP E 301 HIS 0.020 0.001 HIS B1293 Details of bonding type rmsd covalent geometry : bond 0.00371 (25898) covalent geometry : angle 0.58515 (36443) SS BOND : bond 0.00267 ( 1) SS BOND : angle 1.28775 ( 2) hydrogen bonds : bond 0.03675 ( 1198) hydrogen bonds : angle 3.58567 ( 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 367 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 288 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6654 (pt0) REVERT: A 120 CYS cc_start: 0.8550 (m) cc_final: 0.8259 (m) REVERT: A 174 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7690 (mm) REVERT: A 305 MET cc_start: 0.8245 (ttt) cc_final: 0.7912 (ttt) REVERT: A 313 TYR cc_start: 0.7290 (m-80) cc_final: 0.6918 (m-80) REVERT: A 377 PHE cc_start: 0.7005 (m-10) cc_final: 0.6769 (m-10) REVERT: B 671 LYS cc_start: 0.8143 (mttm) cc_final: 0.7675 (mttm) REVERT: B 709 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.4240 (t80) REVERT: B 756 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.6506 (pttm) REVERT: B 791 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8095 (mp0) REVERT: B 817 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.8402 (t80) REVERT: B 818 ASP cc_start: 0.7642 (m-30) cc_final: 0.7392 (m-30) REVERT: B 860 MET cc_start: 0.6139 (mmp) cc_final: 0.5642 (mpp) REVERT: B 868 ARG cc_start: 0.7357 (tmt-80) cc_final: 0.6859 (mtp85) REVERT: B 912 TRP cc_start: 0.7849 (OUTLIER) cc_final: 0.7341 (t-100) REVERT: B 916 TRP cc_start: 0.8207 (m-10) cc_final: 0.7825 (m-10) REVERT: B 917 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7512 (ttm170) REVERT: B 951 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7582 (tt0) REVERT: B 986 TYR cc_start: 0.6374 (OUTLIER) cc_final: 0.5272 (t80) REVERT: B 1164 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6522 (pp-130) REVERT: B 1167 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7044 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7211 (ptp90) REVERT: B 1248 SER cc_start: 0.8125 (t) cc_final: 0.7785 (m) REVERT: B 1284 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6932 (pp) REVERT: D 220 ILE cc_start: 0.6049 (mt) cc_final: 0.5570 (mm) REVERT: D 235 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8100 (t0) REVERT: D 247 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7489 (mtm-85) REVERT: D 263 HIS cc_start: 0.6293 (t-170) cc_final: 0.5973 (t-170) REVERT: D 347 MET cc_start: 0.5677 (tmt) cc_final: 0.4832 (tpt) REVERT: E 340 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9023 (mm) REVERT: E 472 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6750 (p) REVERT: P 25 ASN cc_start: 0.8684 (m-40) cc_final: 0.8417 (m-40) REVERT: Q 56 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: Q 74 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8150 (mptp) REVERT: R 90 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: T 50 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8358 (tt) REVERT: T 88 TYR cc_start: 0.8556 (m-10) cc_final: 0.8248 (m-10) REVERT: U 56 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: V 105 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8254 (pttp) outliers start: 79 outliers final: 43 residues processed: 348 average time/residue: 0.1896 time to fit residues: 102.7700 Evaluate side-chains 336 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 272 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 110 CYS Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 SER 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 703 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 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 1228 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1266 MET Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP 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 360 GLU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 415 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 74 LYS Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 76 ARG Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 223 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 204 optimal weight: 0.7980 chunk 187 optimal weight: 0.5980 chunk 233 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** O 68 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.123970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.093418 restraints weight = 57281.958| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.89 r_work: 0.3323 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25899 Z= 0.215 Angle : 0.614 10.070 36445 Z= 0.335 Chirality : 0.039 0.246 4041 Planarity : 0.004 0.048 3424 Dihedral : 27.661 141.287 6159 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.43 % Allowed : 27.02 % 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 aren not related in a simple way. whole: -0.02 (0.18), residues: 2112 helix: 1.00 (0.15), residues: 1165 sheet: -0.89 (0.55), residues: 84 loop : -1.33 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 248 TYR 0.031 0.002 TYR B 755 PHE 0.015 0.002 PHE B 935 TRP 0.028 0.001 TRP E 301 HIS 0.013 0.001 HIS B1293 Details of bonding type rmsd covalent geometry : bond 0.00493 (25898) covalent geometry : angle 0.61415 (36443) SS BOND : bond 0.00204 ( 1) SS BOND : angle 1.18314 ( 2) hydrogen bonds : bond 0.04190 ( 1198) hydrogen bonds : angle 3.61846 ( 3195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 281 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6835 (pt0) REVERT: A 120 CYS cc_start: 0.8619 (m) cc_final: 0.8351 (m) REVERT: A 305 MET cc_start: 0.8222 (ttt) cc_final: 0.7930 (ttt) REVERT: A 377 PHE cc_start: 0.7292 (m-10) cc_final: 0.7028 (m-10) REVERT: B 670 GLU cc_start: 0.8186 (pm20) cc_final: 0.7965 (pm20) REVERT: B 671 LYS cc_start: 0.8194 (mttm) cc_final: 0.7671 (mttm) REVERT: B 817 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8453 (t80) REVERT: B 818 ASP cc_start: 0.7654 (m-30) cc_final: 0.7343 (m-30) REVERT: B 821 ILE cc_start: 0.8763 (mm) cc_final: 0.8498 (mm) REVERT: B 860 MET cc_start: 0.6196 (mmp) cc_final: 0.5704 (mpp) REVERT: B 868 ARG cc_start: 0.7429 (tmt-80) cc_final: 0.6941 (mtp85) REVERT: B 912 TRP cc_start: 0.7954 (OUTLIER) cc_final: 0.7430 (t-100) REVERT: B 916 TRP cc_start: 0.8179 (m-10) cc_final: 0.7766 (m-10) REVERT: B 917 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7584 (ttm170) REVERT: B 951 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7642 (tt0) REVERT: B 986 TYR cc_start: 0.6490 (OUTLIER) cc_final: 0.5374 (t80) REVERT: B 1164 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.6581 (pp-130) REVERT: B 1167 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7146 (pmt-80) REVERT: B 1248 SER cc_start: 0.8217 (t) cc_final: 0.7882 (m) REVERT: B 1284 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6990 (pp) REVERT: D 220 ILE cc_start: 0.5992 (mt) cc_final: 0.5364 (mm) REVERT: D 235 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8168 (t0) REVERT: D 263 HIS cc_start: 0.6433 (t-170) cc_final: 0.6091 (t-170) REVERT: D 347 MET cc_start: 0.5942 (tmt) cc_final: 0.5038 (tpt) REVERT: E 340 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9034 (mm) REVERT: E 543 ASP cc_start: 0.7298 (t0) cc_final: 0.7073 (t0) REVERT: O 59 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7771 (pp20) REVERT: P 25 ASN cc_start: 0.8754 (m-40) cc_final: 0.8487 (m-40) REVERT: Q 11 ARG cc_start: 0.1422 (OUTLIER) cc_final: -0.3029 (mtm-85) REVERT: Q 74 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8152 (mptp) REVERT: R 90 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: T 50 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8483 (tt) REVERT: T 88 TYR cc_start: 0.8714 (m-10) cc_final: 0.8353 (m-10) REVERT: U 17 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.6818 (ttp80) REVERT: U 56 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: V 90 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: V 105 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8412 (mtpt) outliers start: 85 outliers final: 47 residues processed: 344 average time/residue: 0.1925 time to fit residues: 102.3227 Evaluate side-chains 338 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 272 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 SER 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 703 VAL Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 11 ARG 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 90 GLU 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 50 ILE 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 76 ARG 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: 0.7980 chunk 83 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.124892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.094041 restraints weight = 57445.310| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.85 r_work: 0.3359 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5320 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= 0.164 Angle : 0.581 10.320 36445 Z= 0.316 Chirality : 0.037 0.161 4041 Planarity : 0.004 0.053 3424 Dihedral : 27.626 142.015 6159 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.12 % Allowed : 26.97 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.18), residues: 2112 helix: 1.11 (0.15), residues: 1177 sheet: -0.95 (0.55), residues: 84 loop : -1.34 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1302 TYR 0.022 0.002 TYR B 755 PHE 0.014 0.001 PHE B 668 TRP 0.023 0.001 TRP E 301 HIS 0.007 0.001 HIS B 815 Details of bonding type rmsd covalent geometry : bond 0.00375 (25898) covalent geometry : angle 0.58084 (36443) SS BOND : bond 0.00209 ( 1) SS BOND : angle 1.23371 ( 2) hydrogen bonds : bond 0.03509 ( 1198) hydrogen bonds : angle 3.51360 ( 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 359 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 280 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6763 (pt0) REVERT: A 120 CYS cc_start: 0.8586 (m) cc_final: 0.8293 (m) REVERT: A 305 MET cc_start: 0.8118 (ttt) cc_final: 0.7787 (ttt) REVERT: A 373 MET cc_start: 0.7695 (mmt) cc_final: 0.7339 (mmp) REVERT: B 671 LYS cc_start: 0.8097 (mttm) cc_final: 0.7671 (mttm) REVERT: B 756 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6401 (pttm) REVERT: B 805 GLU cc_start: 0.7532 (pp20) cc_final: 0.7175 (pp20) REVERT: B 812 GLU cc_start: 0.8161 (tp30) cc_final: 0.7958 (tp30) REVERT: B 817 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8409 (t80) REVERT: B 818 ASP cc_start: 0.7588 (m-30) cc_final: 0.7269 (m-30) REVERT: B 821 ILE cc_start: 0.8753 (mm) cc_final: 0.8497 (mm) REVERT: B 860 MET cc_start: 0.6144 (mmp) cc_final: 0.5662 (mpp) REVERT: B 868 ARG cc_start: 0.7344 (tmt-80) cc_final: 0.6898 (mtp85) REVERT: B 912 TRP cc_start: 0.7922 (OUTLIER) cc_final: 0.7413 (t-100) REVERT: B 916 TRP cc_start: 0.8162 (m-10) cc_final: 0.7751 (m-10) REVERT: B 917 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7556 (ttm170) REVERT: B 951 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7636 (tt0) REVERT: B 986 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.5284 (t80) REVERT: B 1164 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6510 (pp-130) REVERT: B 1167 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7139 (pmt-80) REVERT: B 1220 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.7002 (mt-10) REVERT: B 1229 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7139 (ptp90) REVERT: B 1248 SER cc_start: 0.8210 (t) cc_final: 0.7873 (m) REVERT: B 1284 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6949 (pp) REVERT: D 220 ILE cc_start: 0.5950 (mt) cc_final: 0.5610 (mm) REVERT: D 235 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8092 (t0) REVERT: D 247 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7546 (mtm-85) REVERT: D 263 HIS cc_start: 0.6398 (t-170) cc_final: 0.6046 (t-170) REVERT: D 347 MET cc_start: 0.5951 (tmt) cc_final: 0.5133 (tpt) REVERT: E 340 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9050 (mm) REVERT: E 544 GLU cc_start: 0.7892 (pp20) cc_final: 0.7368 (tt0) REVERT: O 59 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7603 (pp20) REVERT: P 25 ASN cc_start: 0.8705 (m-40) cc_final: 0.8472 (m-40) REVERT: Q 11 ARG cc_start: 0.1803 (OUTLIER) cc_final: -0.2589 (mtm-85) REVERT: Q 91 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: R 90 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: T 50 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8300 (tt) REVERT: T 88 TYR cc_start: 0.8629 (m-10) cc_final: 0.8348 (m-10) REVERT: U 17 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.6978 (ttp80) REVERT: U 56 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: V 90 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: V 105 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8200 (pttp) outliers start: 79 outliers final: 49 residues processed: 338 average time/residue: 0.1904 time to fit residues: 99.6405 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 : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 SER 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 703 VAL Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 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 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1266 MET Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 371 ASP 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 340 LEU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 50 ILE 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 76 ARG Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 19 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 156 optimal weight: 0.0980 chunk 46 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 47 optimal weight: 0.0270 chunk 65 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 HIS O 125 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN R 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.125130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.094281 restraints weight = 57696.879| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.87 r_work: 0.3377 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25899 Z= 0.152 Angle : 0.578 9.468 36445 Z= 0.315 Chirality : 0.037 0.158 4041 Planarity : 0.004 0.055 3424 Dihedral : 27.558 141.981 6159 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.65 % Allowed : 27.75 % 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 aren not related in a simple way. whole: 0.12 (0.18), residues: 2112 helix: 1.21 (0.15), residues: 1168 sheet: -1.19 (0.52), residues: 95 loop : -1.38 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 381 TYR 0.024 0.002 TYR B 755 PHE 0.021 0.001 PHE A 160 TRP 0.024 0.001 TRP E 301 HIS 0.010 0.001 HIS R 106 Details of bonding type rmsd covalent geometry : bond 0.00342 (25898) covalent geometry : angle 0.57815 (36443) SS BOND : bond 0.00215 ( 1) SS BOND : angle 1.19475 ( 2) hydrogen bonds : bond 0.03485 ( 1198) hydrogen bonds : angle 3.49685 ( 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 343 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 273 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6733 (pt0) REVERT: A 120 CYS cc_start: 0.8556 (m) cc_final: 0.8279 (m) REVERT: A 129 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7487 (mt-10) REVERT: A 305 MET cc_start: 0.8156 (ttt) cc_final: 0.7841 (ttt) REVERT: A 313 TYR cc_start: 0.6880 (m-80) cc_final: 0.6246 (m-80) REVERT: A 373 MET cc_start: 0.7674 (mmt) cc_final: 0.7433 (mmp) REVERT: B 670 GLU cc_start: 0.8076 (pm20) cc_final: 0.7833 (pm20) REVERT: B 671 LYS cc_start: 0.8085 (mttm) cc_final: 0.7611 (mttm) REVERT: B 756 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6343 (pttm) REVERT: B 805 GLU cc_start: 0.7461 (pp20) cc_final: 0.7060 (pp20) REVERT: B 812 GLU cc_start: 0.8135 (tp30) cc_final: 0.7897 (tp30) REVERT: B 817 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8395 (t80) REVERT: B 818 ASP cc_start: 0.7635 (m-30) cc_final: 0.7305 (m-30) REVERT: B 860 MET cc_start: 0.6154 (mmp) cc_final: 0.5670 (mpp) REVERT: B 868 ARG cc_start: 0.7328 (tmt-80) cc_final: 0.6896 (mtp85) REVERT: B 912 TRP cc_start: 0.7920 (OUTLIER) cc_final: 0.7483 (t-100) REVERT: B 916 TRP cc_start: 0.8150 (m-10) cc_final: 0.7705 (m-10) REVERT: B 917 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7580 (ttm170) REVERT: B 951 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7609 (tt0) REVERT: B 986 TYR cc_start: 0.6332 (OUTLIER) cc_final: 0.5249 (t80) REVERT: B 1164 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.6431 (pp-130) REVERT: B 1167 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7136 (pmt-80) REVERT: B 1220 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: B 1248 SER cc_start: 0.8208 (t) cc_final: 0.7879 (m) REVERT: B 1284 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6986 (pp) REVERT: D 220 ILE cc_start: 0.6105 (mt) cc_final: 0.5450 (mm) REVERT: D 235 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8098 (t0) REVERT: D 263 HIS cc_start: 0.6366 (t-170) cc_final: 0.6022 (t-170) REVERT: D 347 MET cc_start: 0.5982 (tmt) cc_final: 0.5091 (tpt) REVERT: E 340 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9037 (mm) REVERT: E 544 GLU cc_start: 0.7814 (pp20) cc_final: 0.7432 (tt0) REVERT: P 25 ASN cc_start: 0.8702 (m-40) cc_final: 0.8462 (m-40) REVERT: Q 11 ARG cc_start: 0.1728 (OUTLIER) cc_final: -0.2601 (mtm-85) REVERT: Q 56 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: Q 91 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: R 90 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: T 50 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8297 (tt) REVERT: T 88 TYR cc_start: 0.8601 (m-10) cc_final: 0.8326 (m-10) REVERT: U 17 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.6936 (ttp80) REVERT: U 56 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: V 90 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: V 105 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8197 (pttp) outliers start: 70 outliers final: 44 residues processed: 326 average time/residue: 0.1888 time to fit residues: 95.4157 Evaluate side-chains 323 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 258 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 83 ILE 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 232 TYR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1266 MET Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL 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 11 ARG Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 50 ILE 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: 2.9990 chunk 143 optimal weight: 0.1980 chunk 150 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 164 optimal weight: 0.0270 chunk 200 optimal weight: 2.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN ** E 325 ASN ** 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 = 0.4137 r_free = 0.4137 target = 0.124874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.094712 restraints weight = 58156.869| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.92 r_work: 0.3342 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25899 Z= 0.170 Angle : 0.586 9.605 36445 Z= 0.318 Chirality : 0.038 0.256 4041 Planarity : 0.004 0.052 3424 Dihedral : 27.537 141.895 6159 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.55 % Allowed : 27.75 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 2112 helix: 1.20 (0.15), residues: 1169 sheet: -1.26 (0.52), residues: 95 loop : -1.35 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1302 TYR 0.027 0.002 TYR R 80 PHE 0.017 0.001 PHE B 720 TRP 0.039 0.002 TRP E 492 HIS 0.006 0.001 HIS B 815 Details of bonding type rmsd covalent geometry : bond 0.00388 (25898) covalent geometry : angle 0.58576 (36443) SS BOND : bond 0.00205 ( 1) SS BOND : angle 1.21731 ( 2) hydrogen bonds : bond 0.03583 ( 1198) hydrogen bonds : angle 3.50913 ( 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 335 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 267 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6779 (pt0) REVERT: A 120 CYS cc_start: 0.8653 (m) cc_final: 0.8374 (m) REVERT: A 129 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7559 (mt-10) REVERT: A 305 MET cc_start: 0.8236 (ttt) cc_final: 0.7926 (ttt) REVERT: A 315 MET cc_start: 0.8543 (mpp) cc_final: 0.7974 (mtp) REVERT: A 373 MET cc_start: 0.7688 (mmt) cc_final: 0.7459 (mmp) REVERT: B 671 LYS cc_start: 0.8080 (mttm) cc_final: 0.7661 (mttm) REVERT: B 756 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6504 (pttm) REVERT: B 805 GLU cc_start: 0.7490 (pp20) cc_final: 0.7081 (pp20) REVERT: B 812 GLU cc_start: 0.8155 (tp30) cc_final: 0.7910 (tp30) REVERT: B 817 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8429 (t80) REVERT: B 818 ASP cc_start: 0.7631 (m-30) cc_final: 0.7287 (m-30) REVERT: B 860 MET cc_start: 0.6198 (mmp) cc_final: 0.5706 (mpp) REVERT: B 868 ARG cc_start: 0.7348 (tmt-80) cc_final: 0.6922 (mtp85) REVERT: B 912 TRP cc_start: 0.7941 (OUTLIER) cc_final: 0.7506 (t-100) REVERT: B 916 TRP cc_start: 0.8197 (m-10) cc_final: 0.7763 (m-10) REVERT: B 917 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: B 951 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7640 (tt0) REVERT: B 986 TYR cc_start: 0.6380 (OUTLIER) cc_final: 0.5291 (t80) REVERT: B 1164 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.6503 (pp-130) REVERT: B 1167 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7122 (pmt-80) REVERT: B 1220 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6983 (mt-10) REVERT: B 1248 SER cc_start: 0.8251 (t) cc_final: 0.7919 (m) REVERT: B 1271 LYS cc_start: 0.8815 (tptp) cc_final: 0.8347 (ttpt) REVERT: B 1284 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.7011 (pp) REVERT: D 220 ILE cc_start: 0.5979 (mt) cc_final: 0.5650 (mm) REVERT: D 263 HIS cc_start: 0.6441 (t-170) cc_final: 0.6105 (t-170) REVERT: D 347 MET cc_start: 0.6011 (tmt) cc_final: 0.5121 (tpt) REVERT: E 340 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9016 (mm) REVERT: E 544 GLU cc_start: 0.7813 (pp20) cc_final: 0.7279 (tt0) REVERT: P 25 ASN cc_start: 0.8741 (m-40) cc_final: 0.8496 (m-40) REVERT: Q 11 ARG cc_start: 0.1859 (OUTLIER) cc_final: -0.2474 (mtm-85) REVERT: Q 56 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: Q 91 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: R 90 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: T 50 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8357 (tt) REVERT: U 17 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.6972 (ttp80) REVERT: U 56 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: V 90 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: V 105 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8237 (pttp) outliers start: 68 outliers final: 44 residues processed: 318 average time/residue: 0.1819 time to fit residues: 90.4067 Evaluate side-chains 325 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 83 ILE 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 232 TYR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 SER 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 756 LYS Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL 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 11 ARG Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 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 76 ARG Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 176 optimal weight: 0.7980 chunk 177 optimal weight: 0.5980 chunk 241 optimal weight: 7.9990 chunk 226 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** O 125 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN R 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.121258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.090311 restraints weight = 57484.231| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.89 r_work: 0.3268 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.6062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25899 Z= 0.245 Angle : 0.650 13.392 36445 Z= 0.351 Chirality : 0.041 0.314 4041 Planarity : 0.005 0.072 3424 Dihedral : 27.746 142.259 6159 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.96 % Allowed : 27.70 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.18), residues: 2112 helix: 0.92 (0.15), residues: 1169 sheet: -1.38 (0.54), residues: 85 loop : -1.26 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG V 89 TYR 0.035 0.002 TYR T 88 PHE 0.023 0.002 PHE A 160 TRP 0.022 0.002 TRP E 301 HIS 0.007 0.001 HIS T 75 Details of bonding type rmsd covalent geometry : bond 0.00563 (25898) covalent geometry : angle 0.65013 (36443) SS BOND : bond 0.00116 ( 1) SS BOND : angle 1.23761 ( 2) hydrogen bonds : bond 0.04455 ( 1198) hydrogen bonds : angle 3.69758 ( 3195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7439.97 seconds wall clock time: 128 minutes 19.76 seconds (7699.76 seconds total)