Starting phenix.real_space_refine on Fri May 23 15:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd2_37122/05_2025/8kd2_37122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd2_37122/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kd2_37122/05_2025/8kd2_37122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd2_37122/05_2025/8kd2_37122.map" model { file = "/net/cci-nas-00/data/ceres_data/8kd2_37122/05_2025/8kd2_37122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd2_37122/05_2025/8kd2_37122.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.18, per 1000 atoms: 0.61 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: 6.47 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 10.29 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: 16.53 Time building geometry restraints manager: 7.45 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: 11.190 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: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 68.780 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.100 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.064 0.003 TRP B 916 HIS 0.016 0.001 HIS R 46 PHE 0.033 0.002 PHE A 160 TYR 0.029 0.002 TYR P 88 ARG 0.018 0.001 ARG O 129 Details of bonding type rmsd hydrogen bonds : bond 0.11807 ( 1198) hydrogen bonds : angle 4.90347 ( 3195) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.15635 ( 2) covalent geometry : bond 0.00354 (25898) covalent geometry : angle 0.70444 (36443) *********************** 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 : 2.160 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: 0.3210 time to fit residues: 135.5754 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 : 2.424 ------------------------------------------------------------------------------- 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 205 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN A 364 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 GLN B1254 HIS D 295 ASN E 304 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 ASN O 68 GLN ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 ASN P 75 HIS Q 82 HIS ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN S 68 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.128027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.097634 restraints weight = 58035.016| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.93 r_work: 0.3387 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.135 25899 Z= 0.412 Angle : 0.837 13.687 36445 Z= 0.458 Chirality : 0.050 0.244 4041 Planarity : 0.007 0.086 3424 Dihedral : 28.104 139.581 6166 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 7.46 % Allowed : 26.19 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2112 helix: 0.13 (0.14), residues: 1148 sheet: -0.25 (0.57), residues: 78 loop : -1.58 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP B 916 HIS 0.033 0.003 HIS D 369 PHE 0.042 0.003 PHE B 668 TYR 0.039 0.003 TYR B 755 ARG 0.009 0.001 ARG R 96 Details of bonding type rmsd hydrogen bonds : bond 0.06134 ( 1198) hydrogen bonds : angle 4.23073 ( 3195) SS BOND : bond 0.00158 ( 1) SS BOND : angle 1.79289 ( 2) covalent geometry : bond 0.00932 (25898) covalent geometry : angle 0.83643 (36443) *********************** 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 453 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 310 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7498 (tpp) cc_final: 0.7276 (tpp) REVERT: A 174 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7343 (mm) REVERT: A 346 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7686 (t80) REVERT: B 709 TYR cc_start: 0.6748 (OUTLIER) cc_final: 0.4218 (t80) REVERT: B 802 GLN cc_start: 0.6720 (tm-30) cc_final: 0.6435 (tm-30) REVERT: B 805 GLU cc_start: 0.7424 (pp20) cc_final: 0.7080 (pp20) REVERT: B 818 ASP cc_start: 0.7798 (m-30) cc_final: 0.7230 (m-30) REVERT: B 860 MET cc_start: 0.6192 (mmp) cc_final: 0.5638 (mpp) REVERT: B 868 ARG cc_start: 0.7423 (tmt-80) cc_final: 0.6880 (mtp85) REVERT: B 962 LYS cc_start: 0.5120 (OUTLIER) cc_final: 0.4278 (ptpp) REVERT: B 986 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.4981 (t80) REVERT: B 1164 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.6268 (pp-130) REVERT: B 1167 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6680 (pmt-80) REVERT: B 1248 SER cc_start: 0.8041 (t) cc_final: 0.7694 (m) REVERT: B 1284 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.7002 (pp) REVERT: D 220 ILE cc_start: 0.5793 (mt) cc_final: 0.5374 (mm) REVERT: D 222 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7333 (pp) REVERT: D 261 TYR cc_start: 0.6373 (OUTLIER) cc_final: 0.5259 (t80) REVERT: D 386 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7549 (pt) REVERT: E 35 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6322 (mpp80) REVERT: E 365 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8697 (ptmm) REVERT: E 472 THR cc_start: 0.7028 (OUTLIER) cc_final: 0.6731 (p) REVERT: E 511 LYS cc_start: 0.3060 (mmtt) cc_final: 0.2348 (mptt) REVERT: E 514 TYR cc_start: 0.6993 (t80) cc_final: 0.6554 (t80) REVERT: O 42 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8196 (mmm-85) REVERT: P 80 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8987 (m) REVERT: P 88 TYR cc_start: 0.8822 (m-10) cc_final: 0.8548 (m-80) REVERT: P 92 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7187 (ptp-170) REVERT: Q 36 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7918 (pttp) REVERT: Q 56 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: Q 74 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8344 (mptp) REVERT: Q 91 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: R 73 GLU cc_start: 0.8704 (tp30) cc_final: 0.8281 (tp30) REVERT: R 90 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: S 57 SER cc_start: 0.8001 (p) cc_final: 0.7672 (p) REVERT: S 59 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: S 109 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9168 (mp) REVERT: U 51 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9034 (tp) REVERT: U 56 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: V 105 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8500 (mtpt) outliers start: 143 outliers final: 54 residues processed: 419 average time/residue: 0.3725 time to fit residues: 239.3378 Evaluate side-chains 341 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 260 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 174 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 250 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1250 VAL 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 222 LEU Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 LEU 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 423 THR Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 57 VAL 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 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 48 ASP Chi-restraints excluded: chain R residue 60 ASN 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 103 LEU Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 93 GLN 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 71 ARG 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 113 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 GLN B1173 ASN B1233 ASN ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN O 125 GLN Q 104 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN U 73 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.129154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.098926 restraints weight = 57471.348| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.76 r_work: 0.3458 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25899 Z= 0.181 Angle : 0.596 8.583 36445 Z= 0.329 Chirality : 0.039 0.200 4041 Planarity : 0.004 0.046 3424 Dihedral : 27.980 140.461 6159 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.59 % Allowed : 27.60 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2112 helix: 0.66 (0.15), residues: 1161 sheet: -0.36 (0.54), residues: 84 loop : -1.47 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 916 HIS 0.006 0.001 HIS A 150 PHE 0.029 0.002 PHE A 160 TYR 0.020 0.002 TYR A 198 ARG 0.005 0.000 ARG O 131 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 1198) hydrogen bonds : angle 3.74305 ( 3195) SS BOND : bond 0.00111 ( 1) SS BOND : angle 1.06768 ( 2) covalent geometry : bond 0.00410 (25898) covalent geometry : angle 0.59563 (36443) *********************** 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 364 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 276 time to evaluate : 2.311 Fit side-chains revert: symmetry clash REVERT: A 40 MET cc_start: 0.7358 (tpp) cc_final: 0.6593 (tpp) REVERT: A 46 ARG cc_start: 0.8122 (ttp-170) cc_final: 0.7912 (ttp-110) REVERT: A 313 TYR cc_start: 0.7050 (m-80) cc_final: 0.6533 (m-80) REVERT: A 373 MET cc_start: 0.7468 (mmp) cc_final: 0.7182 (mmt) REVERT: B 709 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.4313 (t80) REVERT: B 802 GLN cc_start: 0.6730 (tm-30) cc_final: 0.6525 (tm-30) REVERT: B 818 ASP cc_start: 0.7789 (m-30) cc_final: 0.7412 (m-30) REVERT: B 860 MET cc_start: 0.6195 (mmp) cc_final: 0.5663 (mpp) REVERT: B 868 ARG cc_start: 0.7378 (tmt-80) cc_final: 0.6878 (mtp85) REVERT: B 912 TRP cc_start: 0.7724 (OUTLIER) cc_final: 0.6990 (t-100) REVERT: B 986 TYR cc_start: 0.6238 (OUTLIER) cc_final: 0.4991 (t80) REVERT: B 1164 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.6296 (pp-130) REVERT: B 1167 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6996 (pmt-80) REVERT: B 1248 SER cc_start: 0.8108 (t) cc_final: 0.7770 (m) REVERT: B 1284 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6833 (pp) REVERT: D 220 ILE cc_start: 0.5778 (mt) cc_final: 0.5324 (mm) REVERT: D 223 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: D 300 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7934 (ttt90) REVERT: D 347 MET cc_start: 0.5745 (tmt) cc_final: 0.4924 (tpt) REVERT: E 35 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6245 (mpp80) REVERT: E 465 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8578 (ttmt) REVERT: E 472 THR cc_start: 0.7047 (OUTLIER) cc_final: 0.6693 (p) REVERT: P 25 ASN cc_start: 0.8725 (m-40) cc_final: 0.8411 (m110) REVERT: Q 56 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: Q 74 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8331 (mptp) REVERT: R 68 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: R 90 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: R 102 GLU cc_start: 0.8044 (tp30) cc_final: 0.7844 (mm-30) REVERT: S 57 SER cc_start: 0.8226 (p) cc_final: 0.7924 (p) REVERT: S 59 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: T 88 TYR cc_start: 0.8806 (m-10) cc_final: 0.8458 (m-10) outliers start: 88 outliers final: 39 residues processed: 342 average time/residue: 0.3732 time to fit residues: 199.1598 Evaluate side-chains 310 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 2.176 ------------------------------------------------------------------------------- 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 83 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 709 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 986 TYR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1266 MET Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1322 LEU Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 300 ARG 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 E residue 35 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain E residue 498 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 68 GLU 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 96 THR 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 141 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 ASN B1254 HIS D 369 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 HIS ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 HIS O 68 GLN O 108 ASN O 125 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 81 ASN R 92 GLN U 73 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.123480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.092630 restraints weight = 57538.963| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.78 r_work: 0.3324 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 25899 Z= 0.256 Angle : 0.650 10.602 36445 Z= 0.356 Chirality : 0.041 0.185 4041 Planarity : 0.005 0.061 3424 Dihedral : 27.840 140.901 6159 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 6.78 % Allowed : 25.09 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2112 helix: 0.72 (0.15), residues: 1170 sheet: -0.85 (0.54), residues: 86 loop : -1.49 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 301 HIS 0.025 0.002 HIS A 38 PHE 0.033 0.002 PHE A 160 TYR 0.021 0.002 TYR A 198 ARG 0.005 0.001 ARG B1209 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 1198) hydrogen bonds : angle 3.74180 ( 3195) SS BOND : bond 0.00186 ( 1) SS BOND : angle 1.22703 ( 2) covalent geometry : bond 0.00587 (25898) covalent geometry : angle 0.64949 (36443) *********************** 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 423 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 293 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7219 (tpp) cc_final: 0.6926 (tpp) REVERT: A 72 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6783 (pt0) REVERT: A 172 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: A 174 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7585 (mm) REVERT: A 305 MET cc_start: 0.8205 (ttt) cc_final: 0.7946 (ttt) REVERT: B 671 LYS cc_start: 0.8294 (mttm) cc_final: 0.7902 (mttm) REVERT: B 802 GLN cc_start: 0.7424 (tm-30) cc_final: 0.7150 (tm-30) REVERT: B 812 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7883 (tp30) REVERT: B 817 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8355 (t80) REVERT: B 818 ASP cc_start: 0.7845 (m-30) cc_final: 0.7491 (m-30) REVERT: B 860 MET cc_start: 0.6139 (mmp) cc_final: 0.5650 (mpp) REVERT: B 868 ARG cc_start: 0.7401 (tmt-80) cc_final: 0.6919 (mtp85) REVERT: B 912 TRP cc_start: 0.7867 (OUTLIER) cc_final: 0.7647 (t-100) REVERT: B 917 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7845 (ttm170) REVERT: B 962 LYS cc_start: 0.5065 (OUTLIER) cc_final: 0.4179 (ptpp) REVERT: B 986 TYR cc_start: 0.6373 (OUTLIER) cc_final: 0.5303 (t80) REVERT: B 989 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7562 (mm) REVERT: B 1164 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.6662 (pp-130) REVERT: B 1167 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7072 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.5823 (ptt180) REVERT: B 1248 SER cc_start: 0.8196 (t) cc_final: 0.7863 (m) REVERT: B 1284 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.7007 (pp) REVERT: D 220 ILE cc_start: 0.5982 (mt) cc_final: 0.5530 (mm) REVERT: D 300 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7886 (ttt90) REVERT: D 347 MET cc_start: 0.5756 (tmt) cc_final: 0.4857 (tpt) REVERT: E 340 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9138 (mm) REVERT: E 401 TYR cc_start: 0.6124 (m-10) cc_final: 0.5868 (m-80) REVERT: E 463 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7438 (mmpt) REVERT: E 472 THR cc_start: 0.7258 (OUTLIER) cc_final: 0.6876 (p) REVERT: O 59 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7772 (pp20) REVERT: Q 11 ARG cc_start: 0.1311 (OUTLIER) cc_final: -0.3122 (mtm-85) REVERT: Q 74 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8109 (mptp) REVERT: Q 91 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: R 68 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: R 90 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: S 59 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: U 56 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: V 102 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7889 (mm-30) REVERT: V 105 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8317 (pttp) outliers start: 130 outliers final: 57 residues processed: 394 average time/residue: 0.3976 time to fit residues: 239.8748 Evaluate side-chains 346 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 263 time to evaluate : 2.393 ------------------------------------------------------------------------------- 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 172 GLU 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 703 VAL Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 898 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 934 THR Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1243 ASP Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1286 TYR Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 300 ARG Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 371 ASP 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 452 VAL Chi-restraints excluded: chain E residue 463 LYS 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 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 96 THR Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 68 GLU 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 92 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 77 LYS Chi-restraints excluded: chain T residue 93 GLN 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 105 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 65 optimal weight: 0.6980 chunk 189 optimal weight: 0.0570 chunk 68 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 341 ASN B 983 ASN D 389 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 HIS ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 92 GLN S 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.125548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.094624 restraints weight = 57885.098| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.84 r_work: 0.3372 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25899 Z= 0.150 Angle : 0.571 10.421 36445 Z= 0.316 Chirality : 0.037 0.171 4041 Planarity : 0.004 0.049 3424 Dihedral : 27.782 141.916 6159 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.17 % Allowed : 27.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.18), residues: 2112 helix: 1.02 (0.15), residues: 1173 sheet: -0.92 (0.55), residues: 85 loop : -1.39 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 301 HIS 0.012 0.001 HIS E 346 PHE 0.027 0.001 PHE A 160 TYR 0.022 0.001 TYR A 198 ARG 0.006 0.000 ARG D 381 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 1198) hydrogen bonds : angle 3.57241 ( 3195) SS BOND : bond 0.00276 ( 1) SS BOND : angle 1.18151 ( 2) covalent geometry : bond 0.00334 (25898) covalent geometry : angle 0.57063 (36443) *********************** 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 363 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 283 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6926 (pm20) cc_final: 0.6611 (pt0) REVERT: A 120 CYS cc_start: 0.8536 (m) cc_final: 0.8334 (m) REVERT: A 145 TYR cc_start: 0.8529 (m-80) cc_final: 0.8282 (m-80) REVERT: A 172 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7113 (tm-30) REVERT: A 305 MET cc_start: 0.8122 (ttt) cc_final: 0.7888 (ttt) REVERT: B 671 LYS cc_start: 0.8246 (mttm) cc_final: 0.7765 (mttm) REVERT: B 756 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7042 (pttm) REVERT: B 802 GLN cc_start: 0.7374 (tm-30) cc_final: 0.7111 (tm-30) REVERT: B 860 MET cc_start: 0.6121 (mmp) cc_final: 0.5643 (mpp) REVERT: B 868 ARG cc_start: 0.7334 (tmt-80) cc_final: 0.6906 (mtp85) REVERT: B 917 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7805 (ttm170) REVERT: B 986 TYR cc_start: 0.6287 (OUTLIER) cc_final: 0.5179 (t80) REVERT: B 989 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7540 (mm) REVERT: B 1164 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6626 (pp-130) REVERT: B 1167 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7050 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6644 (ptp-170) REVERT: B 1248 SER cc_start: 0.8179 (t) cc_final: 0.7850 (m) REVERT: B 1284 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6930 (pp) REVERT: D 220 ILE cc_start: 0.5978 (mt) cc_final: 0.5518 (mm) REVERT: D 347 MET cc_start: 0.5871 (tmt) cc_final: 0.5072 (tpt) REVERT: E 340 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9020 (mm) REVERT: E 401 TYR cc_start: 0.6051 (m-10) cc_final: 0.5791 (m-80) REVERT: E 472 THR cc_start: 0.7159 (OUTLIER) cc_final: 0.6789 (p) REVERT: P 93 GLN cc_start: 0.8308 (mt0) cc_final: 0.8063 (mt0) REVERT: R 90 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: U 56 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: V 102 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7652 (mm-30) REVERT: V 105 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8186 (pttp) outliers start: 80 outliers final: 39 residues processed: 349 average time/residue: 0.3797 time to fit residues: 205.2325 Evaluate side-chains 323 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 270 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU 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 699 LEU Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 989 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 1229 ARG Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1286 TYR Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 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 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 436 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain 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 103 LEU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 100 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 144 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS B1293 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN O 68 GLN P 93 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.122182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.091618 restraints weight = 57384.558| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.97 r_work: 0.3280 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25899 Z= 0.232 Angle : 0.621 10.051 36445 Z= 0.341 Chirality : 0.040 0.270 4041 Planarity : 0.004 0.049 3424 Dihedral : 27.767 142.147 6159 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.64 % Allowed : 26.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2112 helix: 0.95 (0.15), residues: 1168 sheet: -1.04 (0.57), residues: 84 loop : -1.34 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 301 HIS 0.018 0.002 HIS B1293 PHE 0.026 0.002 PHE A 160 TYR 0.027 0.002 TYR A 198 ARG 0.008 0.001 ARG D 300 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 1198) hydrogen bonds : angle 3.63314 ( 3195) SS BOND : bond 0.00196 ( 1) SS BOND : angle 1.15011 ( 2) covalent geometry : bond 0.00535 (25898) covalent geometry : angle 0.62142 (36443) *********************** 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 369 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 280 time to evaluate : 2.405 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6850 (pt0) REVERT: A 120 CYS cc_start: 0.8703 (m) cc_final: 0.8502 (m) REVERT: A 160 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7199 (t80) REVERT: A 172 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: A 189 HIS cc_start: 0.6640 (OUTLIER) cc_final: 0.6169 (p90) REVERT: A 191 ASP cc_start: 0.8268 (p0) cc_final: 0.8012 (p0) REVERT: A 347 TYR cc_start: 0.8100 (m-80) cc_final: 0.7884 (m-80) REVERT: B 671 LYS cc_start: 0.8287 (mttm) cc_final: 0.7841 (mttm) REVERT: B 756 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7006 (pttp) REVERT: B 802 GLN cc_start: 0.7459 (tm-30) cc_final: 0.7146 (tm-30) REVERT: B 818 ASP cc_start: 0.7757 (m-30) cc_final: 0.7424 (m-30) REVERT: B 860 MET cc_start: 0.6216 (mmp) cc_final: 0.5772 (mpp) REVERT: B 868 ARG cc_start: 0.7400 (tmt-80) cc_final: 0.6955 (mtp85) REVERT: B 917 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7872 (ttm170) REVERT: B 986 TYR cc_start: 0.6442 (OUTLIER) cc_final: 0.5367 (t80) REVERT: B 1164 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.6726 (pp-130) REVERT: B 1167 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7179 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6768 (ptp-170) REVERT: B 1248 SER cc_start: 0.8234 (t) cc_final: 0.7878 (m) REVERT: B 1284 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6978 (pp) REVERT: D 220 ILE cc_start: 0.5924 (mt) cc_final: 0.5463 (mm) REVERT: D 347 MET cc_start: 0.6158 (tmt) cc_final: 0.5221 (tpp) REVERT: E 49 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8496 (tptp) REVERT: E 340 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9032 (mm) REVERT: E 401 TYR cc_start: 0.6231 (m-10) cc_final: 0.5950 (m-80) REVERT: E 544 GLU cc_start: 0.7784 (pp20) cc_final: 0.7514 (tt0) REVERT: O 59 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7787 (pp20) REVERT: Q 11 ARG cc_start: 0.1929 (OUTLIER) cc_final: -0.2475 (mtm-85) REVERT: Q 56 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: Q 74 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8152 (mptp) REVERT: R 90 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: R 102 GLU cc_start: 0.8056 (tp30) cc_final: 0.7802 (tp30) REVERT: U 17 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.6644 (ttp80) REVERT: U 56 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: V 105 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8401 (mtpt) outliers start: 89 outliers final: 49 residues processed: 353 average time/residue: 0.3691 time to fit residues: 201.7649 Evaluate side-chains 335 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 266 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 189 HIS 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 778 LEU Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 986 TYR 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 1219 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1243 ASP Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1284 ILE 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 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 344 SER 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 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 80 THR 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 74 LYS Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 242 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 132 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS B1293 HIS D 263 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 92 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.123758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.092874 restraints weight = 57326.256| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.92 r_work: 0.3328 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25899 Z= 0.166 Angle : 0.582 9.626 36445 Z= 0.320 Chirality : 0.037 0.183 4041 Planarity : 0.004 0.052 3424 Dihedral : 27.740 142.903 6159 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.28 % Allowed : 26.86 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2112 helix: 1.05 (0.15), residues: 1176 sheet: -1.20 (0.56), residues: 85 loop : -1.33 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 301 HIS 0.007 0.001 HIS B 815 PHE 0.028 0.001 PHE A 160 TYR 0.032 0.002 TYR P 88 ARG 0.007 0.000 ARG B1302 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 1198) hydrogen bonds : angle 3.55501 ( 3195) SS BOND : bond 0.00235 ( 1) SS BOND : angle 1.11471 ( 2) covalent geometry : bond 0.00377 (25898) covalent geometry : angle 0.58219 (36443) *********************** 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 367 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 285 time to evaluate : 2.444 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6714 (pt0) REVERT: A 120 CYS cc_start: 0.8620 (m) cc_final: 0.8398 (m) REVERT: A 172 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: A 191 ASP cc_start: 0.8288 (p0) cc_final: 0.8038 (p0) REVERT: A 373 MET cc_start: 0.7759 (mmp) cc_final: 0.7338 (mmt) REVERT: B 671 LYS cc_start: 0.8275 (mttm) cc_final: 0.7794 (mttm) REVERT: B 756 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.6823 (pttm) REVERT: B 818 ASP cc_start: 0.7704 (m-30) cc_final: 0.7337 (m-30) REVERT: B 821 ILE cc_start: 0.8745 (mm) cc_final: 0.8477 (mm) REVERT: B 860 MET cc_start: 0.6212 (mmp) cc_final: 0.5753 (mpp) REVERT: B 868 ARG cc_start: 0.7406 (tmt-80) cc_final: 0.6939 (mtp85) REVERT: B 917 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7811 (ttm170) REVERT: B 986 TYR cc_start: 0.6372 (OUTLIER) cc_final: 0.5325 (t80) REVERT: B 993 ASP cc_start: 0.6902 (OUTLIER) cc_final: 0.6669 (t0) REVERT: B 1164 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.6667 (pp-130) REVERT: B 1167 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7185 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7145 (ptp90) REVERT: B 1248 SER cc_start: 0.8197 (t) cc_final: 0.7844 (m) REVERT: B 1284 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.7016 (pp) REVERT: D 220 ILE cc_start: 0.5922 (mt) cc_final: 0.5461 (mm) REVERT: D 347 MET cc_start: 0.6274 (tmt) cc_final: 0.5457 (tpp) REVERT: E 340 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8995 (mm) REVERT: E 401 TYR cc_start: 0.6148 (m-10) cc_final: 0.5855 (m-80) REVERT: E 544 GLU cc_start: 0.7726 (pp20) cc_final: 0.7386 (tt0) REVERT: O 59 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7743 (pp20) REVERT: Q 11 ARG cc_start: 0.1983 (OUTLIER) cc_final: -0.2443 (mtm-85) REVERT: Q 56 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: Q 74 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8096 (mptp) REVERT: R 90 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: R 102 GLU cc_start: 0.8000 (tp30) cc_final: 0.7733 (tp30) REVERT: U 17 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.6822 (ttp80) REVERT: U 56 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: V 90 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: V 105 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8371 (mtpt) outliers start: 82 outliers final: 48 residues processed: 351 average time/residue: 0.3729 time to fit residues: 203.1459 Evaluate side-chains 340 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 272 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 699 LEU Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 993 ASP 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 1229 ARG 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 337 VAL Chi-restraints excluded: chain D residue 344 SER 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 436 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 11 ARG 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 R residue 109 SER Chi-restraints excluded: chain S residue 92 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 125 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 0.0010 chunk 66 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 193 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 81 ASN R 92 GLN V 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.121614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.091542 restraints weight = 57367.443| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.87 r_work: 0.3266 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25899 Z= 0.224 Angle : 0.623 12.499 36445 Z= 0.339 Chirality : 0.039 0.182 4041 Planarity : 0.004 0.047 3424 Dihedral : 27.769 142.996 6159 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.59 % Allowed : 26.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2112 helix: 0.97 (0.15), residues: 1168 sheet: -1.47 (0.55), residues: 83 loop : -1.31 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 492 HIS 0.007 0.001 HIS B 815 PHE 0.031 0.002 PHE A 160 TYR 0.032 0.002 TYR B1204 ARG 0.011 0.000 ARG E 50 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 1198) hydrogen bonds : angle 3.63510 ( 3195) SS BOND : bond 0.00193 ( 1) SS BOND : angle 1.15085 ( 2) covalent geometry : bond 0.00511 (25898) covalent geometry : angle 0.62341 (36443) *********************** 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 358 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 270 time to evaluate : 2.208 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6913 (pt0) REVERT: A 120 CYS cc_start: 0.8660 (m) cc_final: 0.8450 (m) REVERT: A 172 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: A 189 HIS cc_start: 0.6634 (OUTLIER) cc_final: 0.6157 (p90) REVERT: A 191 ASP cc_start: 0.8304 (p0) cc_final: 0.8038 (p0) REVERT: B 671 LYS cc_start: 0.8250 (mttm) cc_final: 0.7780 (mttm) REVERT: B 756 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7031 (pttm) REVERT: B 818 ASP cc_start: 0.7779 (m-30) cc_final: 0.7411 (m-30) REVERT: B 860 MET cc_start: 0.6313 (mmp) cc_final: 0.5850 (mpp) REVERT: B 868 ARG cc_start: 0.7496 (tmt-80) cc_final: 0.7033 (mtp85) REVERT: B 917 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7887 (ttm170) REVERT: B 962 LYS cc_start: 0.4982 (OUTLIER) cc_final: 0.4192 (ptpp) REVERT: B 986 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.5410 (t80) REVERT: B 993 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6702 (t0) REVERT: B 1164 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.6779 (pp-130) REVERT: B 1167 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7188 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6218 (ptt180) REVERT: B 1248 SER cc_start: 0.8294 (t) cc_final: 0.7940 (m) REVERT: B 1284 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7033 (pp) REVERT: D 220 ILE cc_start: 0.6045 (mt) cc_final: 0.5582 (mm) REVERT: D 235 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8080 (t0) REVERT: D 347 MET cc_start: 0.6258 (tmt) cc_final: 0.5431 (tpp) REVERT: E 340 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8967 (mm) REVERT: E 401 TYR cc_start: 0.6182 (m-10) cc_final: 0.5893 (m-80) REVERT: E 544 GLU cc_start: 0.7701 (pp20) cc_final: 0.7408 (tt0) REVERT: O 59 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7787 (pp20) REVERT: Q 11 ARG cc_start: 0.2247 (OUTLIER) cc_final: -0.1798 (mtm-85) REVERT: Q 56 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: Q 74 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8119 (mptp) REVERT: Q 91 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: R 90 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: U 17 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.6857 (ttp80) REVERT: U 56 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: V 105 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8426 (mtpt) outliers start: 88 outliers final: 50 residues processed: 343 average time/residue: 0.3751 time to fit residues: 197.3598 Evaluate side-chains 332 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 259 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 181 LEU Chi-restraints excluded: chain A residue 189 HIS 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 718 THR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 993 ASP 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 1229 ARG Chi-restraints excluded: chain B residue 1243 ASP 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 235 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 344 SER 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 430 HIS 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 O residue 92 LEU 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 74 LYS Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain 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 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 105 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 181 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** 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** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.121205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.090496 restraints weight = 57739.497| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.91 r_work: 0.3281 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25899 Z= 0.214 Angle : 0.624 11.041 36445 Z= 0.339 Chirality : 0.039 0.197 4041 Planarity : 0.004 0.053 3424 Dihedral : 27.803 144.078 6159 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.17 % Allowed : 27.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2112 helix: 0.96 (0.15), residues: 1174 sheet: -1.55 (0.55), residues: 83 loop : -1.32 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 492 HIS 0.011 0.001 HIS B1293 PHE 0.022 0.002 PHE A 160 TYR 0.031 0.002 TYR B1204 ARG 0.010 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 1198) hydrogen bonds : angle 3.63187 ( 3195) SS BOND : bond 0.00166 ( 1) SS BOND : angle 1.18098 ( 2) covalent geometry : bond 0.00492 (25898) covalent geometry : angle 0.62346 (36443) *********************** 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 347 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 267 time to evaluate : 2.353 Fit side-chains REVERT: A 72 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6875 (pt0) REVERT: A 105 ASN cc_start: 0.8530 (t0) cc_final: 0.8294 (t0) REVERT: A 120 CYS cc_start: 0.8671 (m) cc_final: 0.8460 (m) REVERT: A 172 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: B 671 LYS cc_start: 0.8235 (mttm) cc_final: 0.7739 (mttm) REVERT: B 756 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7036 (pttm) REVERT: B 818 ASP cc_start: 0.7773 (m-30) cc_final: 0.7401 (m-30) REVERT: B 860 MET cc_start: 0.6343 (mmp) cc_final: 0.5852 (mpp) REVERT: B 868 ARG cc_start: 0.7499 (tmt-80) cc_final: 0.7061 (mtp85) REVERT: B 917 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7809 (ttm170) REVERT: B 986 TYR cc_start: 0.6523 (OUTLIER) cc_final: 0.5497 (t80) REVERT: B 989 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7593 (mm) REVERT: B 993 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6696 (t0) REVERT: B 1008 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: B 1164 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.6874 (pp-130) REVERT: B 1167 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7279 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6556 (ptp-170) REVERT: B 1248 SER cc_start: 0.8270 (t) cc_final: 0.7914 (m) REVERT: B 1284 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.7033 (pp) REVERT: D 220 ILE cc_start: 0.5997 (mt) cc_final: 0.5514 (mm) REVERT: D 235 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8035 (t0) REVERT: D 347 MET cc_start: 0.6393 (tmt) cc_final: 0.5729 (tpp) REVERT: E 35 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6596 (ttm170) REVERT: E 61 ARG cc_start: 0.5968 (mmm-85) cc_final: 0.5499 (mmm160) REVERT: E 340 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8953 (mm) REVERT: E 401 TYR cc_start: 0.6271 (m-10) cc_final: 0.5977 (m-80) REVERT: E 544 GLU cc_start: 0.7666 (pp20) cc_final: 0.7338 (tt0) REVERT: O 59 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7648 (pp20) REVERT: Q 11 ARG cc_start: 0.2352 (OUTLIER) cc_final: -0.1744 (mtm-85) REVERT: Q 56 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: Q 74 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8092 (mptp) REVERT: Q 91 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: R 90 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: T 88 TYR cc_start: 0.8649 (m-10) cc_final: 0.8376 (m-80) REVERT: U 17 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.7037 (ttp80) REVERT: U 56 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: V 105 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8410 (mtpt) outliers start: 80 outliers final: 49 residues processed: 330 average time/residue: 0.3768 time to fit residues: 192.9631 Evaluate side-chains 332 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 259 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 718 THR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 993 ASP 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 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 1219 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1243 ASP 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 235 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 344 SER 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 E residue 498 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 11 ARG 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 48 ASP Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain 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 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 105 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 183 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 195 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.122379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.092460 restraints weight = 57489.401| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.79 r_work: 0.3305 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25899 Z= 0.164 Angle : 0.605 13.632 36445 Z= 0.328 Chirality : 0.037 0.165 4041 Planarity : 0.004 0.046 3424 Dihedral : 27.741 144.107 6159 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.86 % Allowed : 27.75 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2112 helix: 1.06 (0.15), residues: 1174 sheet: -1.51 (0.56), residues: 83 loop : -1.28 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 301 HIS 0.007 0.001 HIS B1293 PHE 0.017 0.001 PHE A 160 TYR 0.028 0.002 TYR B1204 ARG 0.008 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 1198) hydrogen bonds : angle 3.56968 ( 3195) SS BOND : bond 0.00202 ( 1) SS BOND : angle 1.18435 ( 2) covalent geometry : bond 0.00374 (25898) covalent geometry : angle 0.60511 (36443) ********************** 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 353 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 279 time to evaluate : 2.173 Fit side-chains REVERT: A 40 MET cc_start: 0.7250 (tpp) cc_final: 0.6561 (tpp) REVERT: A 72 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6862 (pt0) REVERT: A 105 ASN cc_start: 0.8521 (t0) cc_final: 0.8307 (t0) REVERT: A 120 CYS cc_start: 0.8639 (m) cc_final: 0.8425 (m) REVERT: A 172 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7210 (tm-30) REVERT: A 373 MET cc_start: 0.7887 (mmp) cc_final: 0.7426 (mmt) REVERT: B 671 LYS cc_start: 0.8230 (mttm) cc_final: 0.7750 (mttm) REVERT: B 756 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7000 (pttm) REVERT: B 818 ASP cc_start: 0.7685 (m-30) cc_final: 0.7350 (m-30) REVERT: B 860 MET cc_start: 0.6259 (mmp) cc_final: 0.5780 (mpp) REVERT: B 868 ARG cc_start: 0.7429 (tmt-80) cc_final: 0.7007 (mtp85) REVERT: B 917 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7878 (ttm170) REVERT: B 951 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6636 (mt-10) REVERT: B 986 TYR cc_start: 0.6476 (OUTLIER) cc_final: 0.5432 (t80) REVERT: B 989 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7580 (mm) REVERT: B 993 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6604 (t0) REVERT: B 1008 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: B 1164 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.6839 (pp-130) REVERT: B 1167 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7231 (pmt-80) REVERT: B 1229 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7003 (ptp-170) REVERT: B 1248 SER cc_start: 0.8274 (t) cc_final: 0.7929 (m) REVERT: B 1284 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7045 (pp) REVERT: D 220 ILE cc_start: 0.6017 (mt) cc_final: 0.5525 (mm) REVERT: D 235 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8039 (t0) REVERT: D 347 MET cc_start: 0.6303 (tmt) cc_final: 0.5643 (tpp) REVERT: E 35 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6609 (ttm170) REVERT: E 61 ARG cc_start: 0.5943 (mmm-85) cc_final: 0.5514 (mmm160) REVERT: E 340 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8912 (mm) REVERT: E 401 TYR cc_start: 0.6142 (m-10) cc_final: 0.5871 (m-80) REVERT: O 59 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7744 (pp20) REVERT: Q 11 ARG cc_start: 0.2281 (OUTLIER) cc_final: -0.1739 (mtm-85) REVERT: Q 56 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: Q 91 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: R 90 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: U 17 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.6996 (ttp80) REVERT: U 56 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: V 105 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8391 (mtpt) outliers start: 74 outliers final: 42 residues processed: 339 average time/residue: 0.3652 time to fit residues: 194.0063 Evaluate side-chains 340 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 275 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 993 ASP 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 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 1219 LEU Chi-restraints excluded: chain B residue 1229 ARG Chi-restraints excluded: chain B residue 1243 ASP 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 344 SER 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 E residue 498 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 56 GLU 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 92 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 133 optimal weight: 6.9990 chunk 187 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 108 optimal weight: 0.0670 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.122546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092744 restraints weight = 57747.045| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.79 r_work: 0.3311 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.6194 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= 0.162 Angle : 0.596 12.101 36445 Z= 0.325 Chirality : 0.037 0.163 4041 Planarity : 0.004 0.046 3424 Dihedral : 27.674 143.636 6159 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.76 % Allowed : 27.75 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.18), residues: 2112 helix: 1.12 (0.15), residues: 1168 sheet: -1.58 (0.53), residues: 95 loop : -1.29 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 301 HIS 0.006 0.001 HIS B 998 PHE 0.032 0.001 PHE B 708 TYR 0.028 0.002 TYR B1204 ARG 0.009 0.000 ARG R 83 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1198) hydrogen bonds : angle 3.54427 ( 3195) SS BOND : bond 0.00211 ( 1) SS BOND : angle 1.19722 ( 2) covalent geometry : bond 0.00370 (25898) covalent geometry : angle 0.59572 (36443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14742.50 seconds wall clock time: 256 minutes 39.41 seconds (15399.41 seconds total)