Starting phenix.real_space_refine on Wed Aug 27 02:14:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3v_34475/08_2025/8h3v_34475_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3v_34475/08_2025/8h3v_34475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h3v_34475/08_2025/8h3v_34475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3v_34475/08_2025/8h3v_34475.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3v_34475/08_2025/8h3v_34475_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3v_34475/08_2025/8h3v_34475_neut.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.055 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 208 5.49 5 S 149 5.16 5 C 28368 2.51 5 N 8180 2.21 5 O 9143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46048 Number of models: 1 Model: "" Number of chains: 15 Chain: "1" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2302 Classifications: {'DNA': 112} Link IDs: {'rna3p': 111} Chain: "2" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1967 Classifications: {'DNA': 96} Link IDs: {'rna3p': 95} Chain breaks: 1 Chain: "A" Number of atoms: 8473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8473 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 61, 'TRANS': 1015} Chain: "B" Number of atoms: 9292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 9292 Classifications: {'peptide': 1217} Link IDs: {'PTRANS': 52, 'TRANS': 1164} Chain breaks: 3 Chain: "C" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1762 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1762 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "E" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4918 Classifications: {'peptide': 619} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 585} Chain: "F" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 474 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "G" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2600 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "S" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2389 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 17, 'TRANS': 286} Chain: "T" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2320 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 16, 'TRANS': 277} Chain breaks: 1 Chain: "U" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2320 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 16, 'TRANS': 277} Chain breaks: 1 Chain: "V" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2389 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 17, 'TRANS': 286} Chain: "X" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1540 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "Y" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1540 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Time building chain proxies: 10.58, per 1000 atoms: 0.23 Number of scatterers: 46048 At special positions: 0 Unit cell: (194.74, 218.28, 162.64, 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 149 16.00 P 208 15.00 O 9143 8.00 N 8180 7.00 C 28368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 295 " distance=2.92 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 295 " distance=1.94 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.00 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 73 " distance=1.81 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 86 " distance=2.20 Simple disulfide: pdb=" SG CYS E 73 " - pdb=" SG CYS E 86 " distance=2.05 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9902 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 42 sheets defined 32.3% alpha, 3.0% beta 66 base pairs and 148 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 4.003A pdb=" N LEU A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.536A pdb=" N SER A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 293 through 309 removed outlier: 3.945A pdb=" N ILE A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.070A pdb=" N GLN A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 378 removed outlier: 3.656A pdb=" N VAL A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 400 removed outlier: 3.521A pdb=" N ARG A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.844A pdb=" N ARG A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 554 through 560 removed outlier: 4.057A pdb=" N GLN A 560 " --> pdb=" O GLY A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 579 through 587 Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 706 through 711 removed outlier: 3.554A pdb=" N GLN A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 784 through 793 Processing helix chain 'A' and resid 821 through 825 removed outlier: 3.641A pdb=" N GLN A 824 " --> pdb=" O THR A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 911 Processing helix chain 'A' and resid 926 through 943 removed outlier: 3.757A pdb=" N ARG A 930 " --> pdb=" O GLU A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1032 through 1040 Processing helix chain 'A' and resid 1044 through 1057 removed outlier: 3.515A pdb=" N VAL A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1082 Processing helix chain 'B' and resid 9 through 22 removed outlier: 3.726A pdb=" N LEU B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 Processing helix chain 'B' and resid 34 through 48 Processing helix chain 'B' and resid 60 through 81 removed outlier: 4.336A pdb=" N SER B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 115 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 168 through 196 removed outlier: 3.999A pdb=" N TYR B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 265 through 275 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.727A pdb=" N ILE B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 696 through 703 removed outlier: 3.744A pdb=" N VAL B 700 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 703 " --> pdb=" O VAL B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 813 Processing helix chain 'B' and resid 1011 through 1019 removed outlier: 4.166A pdb=" N GLU B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B1017 " --> pdb=" O ARG B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1026 removed outlier: 4.112A pdb=" N ALA B1026 " --> pdb=" O PRO B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1101 Processing helix chain 'B' and resid 1106 through 1132 removed outlier: 3.909A pdb=" N VAL B1128 " --> pdb=" O GLU B1124 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1149 removed outlier: 3.647A pdb=" N THR B1149 " --> pdb=" O VAL B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1156 through 1161 Processing helix chain 'B' and resid 1170 through 1180 Processing helix chain 'B' and resid 1196 through 1204 removed outlier: 4.148A pdb=" N LEU B1202 " --> pdb=" O THR B1198 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B1203 " --> pdb=" O LYS B1199 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1222 removed outlier: 3.959A pdb=" N THR B1221 " --> pdb=" O THR B1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1223 through 1227 Processing helix chain 'B' and resid 1234 through 1240 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 33 through 47 removed outlier: 3.627A pdb=" N ASN C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'C' and resid 205 through 208 Processing helix chain 'C' and resid 209 through 222 removed outlier: 3.972A pdb=" N GLY C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP C 219 " --> pdb=" O GLY C 215 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 44 removed outlier: 3.759A pdb=" N VAL D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 81 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 209 through 222 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.617A pdb=" N ARG E 102 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 132 through 140 Processing helix chain 'E' and resid 164 through 169 removed outlier: 4.469A pdb=" N GLU E 169 " --> pdb=" O ASP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 176 removed outlier: 4.027A pdb=" N GLN E 173 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 3.740A pdb=" N LEU E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 215 removed outlier: 4.059A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 236 removed outlier: 3.643A pdb=" N PHE E 234 " --> pdb=" O VAL E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 244 Processing helix chain 'E' and resid 253 through 257 removed outlier: 3.799A pdb=" N LEU E 256 " --> pdb=" O PRO E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 288 removed outlier: 3.753A pdb=" N LEU E 286 " --> pdb=" O ARG E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 293 Processing helix chain 'E' and resid 299 through 308 removed outlier: 3.923A pdb=" N ARG E 304 " --> pdb=" O ARG E 300 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 315 Processing helix chain 'E' and resid 333 through 337 removed outlier: 3.703A pdb=" N ILE E 337 " --> pdb=" O LEU E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 349 Processing helix chain 'E' and resid 376 through 380 Processing helix chain 'E' and resid 381 through 383 No H-bonds generated for 'chain 'E' and resid 381 through 383' Processing helix chain 'E' and resid 384 through 395 removed outlier: 3.812A pdb=" N ARG E 391 " --> pdb=" O PHE E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 411 Processing helix chain 'E' and resid 412 through 422 removed outlier: 4.622A pdb=" N TRP E 416 " --> pdb=" O ASP E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 441 Processing helix chain 'E' and resid 480 through 489 removed outlier: 3.625A pdb=" N GLN E 484 " --> pdb=" O SER E 480 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 485 " --> pdb=" O LEU E 481 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 489 " --> pdb=" O ALA E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 522 Processing helix chain 'E' and resid 538 through 547 removed outlier: 4.183A pdb=" N ILE E 542 " --> pdb=" O LEU E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 609 through 616 Processing helix chain 'E' and resid 617 through 625 removed outlier: 4.156A pdb=" N GLU E 621 " --> pdb=" O LYS E 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 20 removed outlier: 3.700A pdb=" N ASP F 20 " --> pdb=" O ARG F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 45 Processing helix chain 'F' and resid 50 through 55 removed outlier: 3.961A pdb=" N MET F 55 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 67 removed outlier: 3.725A pdb=" N ARG F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 98 through 124 removed outlier: 4.091A pdb=" N GLU G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 135 Processing helix chain 'G' and resid 140 through 162 removed outlier: 4.316A pdb=" N HIS G 149 " --> pdb=" O ARG G 145 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL G 159 " --> pdb=" O LYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 Processing helix chain 'G' and resid 181 through 196 removed outlier: 4.490A pdb=" N GLY G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 225 removed outlier: 3.541A pdb=" N THR G 219 " --> pdb=" O ARG G 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG G 220 " --> pdb=" O GLN G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 237 Processing helix chain 'G' and resid 238 through 240 No H-bonds generated for 'chain 'G' and resid 238 through 240' Processing helix chain 'G' and resid 241 through 250 Processing helix chain 'G' and resid 260 through 266 Processing helix chain 'G' and resid 269 through 279 Processing helix chain 'G' and resid 311 through 325 removed outlier: 3.600A pdb=" N ASN G 316 " --> pdb=" O GLN G 312 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU G 317 " --> pdb=" O VAL G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 335 Processing helix chain 'G' and resid 336 through 340 removed outlier: 3.603A pdb=" N LEU G 339 " --> pdb=" O VAL G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 358 Processing helix chain 'G' and resid 362 through 375 removed outlier: 4.694A pdb=" N ARG G 366 " --> pdb=" O ARG G 362 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN G 367 " --> pdb=" O GLU G 363 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 15 Processing helix chain 'S' and resid 18 through 23 Processing helix chain 'S' and resid 32 through 40 removed outlier: 3.694A pdb=" N SER S 38 " --> pdb=" O ARG S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 80 removed outlier: 3.610A pdb=" N CYS S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU S 80 " --> pdb=" O THR S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 116 Processing helix chain 'S' and resid 128 through 136 Processing helix chain 'S' and resid 185 through 190 removed outlier: 3.548A pdb=" N VAL S 189 " --> pdb=" O TRP S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 212 removed outlier: 3.905A pdb=" N GLU S 208 " --> pdb=" O ARG S 204 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 230 Processing helix chain 'S' and resid 287 through 298 Processing helix chain 'T' and resid 4 through 13 removed outlier: 4.011A pdb=" N ALA T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA T 11 " --> pdb=" O GLN T 7 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 43 removed outlier: 4.026A pdb=" N GLN T 37 " --> pdb=" O SER T 33 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER T 38 " --> pdb=" O ARG T 34 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP T 42 " --> pdb=" O SER T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 64 Processing helix chain 'T' and resid 64 through 84 removed outlier: 3.765A pdb=" N LEU T 81 " --> pdb=" O ALA T 77 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLY T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 115 Processing helix chain 'T' and resid 130 through 138 Processing helix chain 'T' and resid 175 through 182 removed outlier: 4.207A pdb=" N ALA T 178 " --> pdb=" O HIS T 175 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG T 182 " --> pdb=" O ALA T 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 200 through 211 Processing helix chain 'T' and resid 225 through 235 Processing helix chain 'T' and resid 246 through 251 Processing helix chain 'T' and resid 287 through 299 removed outlier: 3.553A pdb=" N PHE T 293 " --> pdb=" O PRO T 289 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 14 removed outlier: 4.018A pdb=" N ALA U 11 " --> pdb=" O GLN U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 23 Processing helix chain 'U' and resid 31 through 41 removed outlier: 5.035A pdb=" N GLN U 37 " --> pdb=" O SER U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 64 Processing helix chain 'U' and resid 64 through 84 removed outlier: 4.787A pdb=" N GLY U 82 " --> pdb=" O THR U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 111 Processing helix chain 'U' and resid 129 through 134 Processing helix chain 'U' and resid 175 through 180 removed outlier: 3.520A pdb=" N ALA U 179 " --> pdb=" O HIS U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 191 removed outlier: 4.008A pdb=" N ARG U 190 " --> pdb=" O GLU U 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 211 Processing helix chain 'U' and resid 225 through 230 Processing helix chain 'U' and resid 281 through 285 Processing helix chain 'U' and resid 287 through 296 Processing helix chain 'V' and resid 2 through 11 Processing helix chain 'V' and resid 11 through 16 Processing helix chain 'V' and resid 19 through 25 Processing helix chain 'V' and resid 32 through 44 removed outlier: 3.711A pdb=" N SER V 38 " --> pdb=" O ARG V 34 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP V 42 " --> pdb=" O SER V 38 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY V 44 " --> pdb=" O GLU V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 78 removed outlier: 3.966A pdb=" N ALA V 77 " --> pdb=" O GLU V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 104 through 110 Processing helix chain 'V' and resid 128 through 135 Processing helix chain 'V' and resid 175 through 179 Processing helix chain 'V' and resid 200 through 208 Processing helix chain 'V' and resid 227 through 232 Processing helix chain 'V' and resid 243 through 251 removed outlier: 3.899A pdb=" N GLU V 249 " --> pdb=" O SER V 245 " (cutoff:3.500A) Processing helix chain 'V' and resid 287 through 292 Processing helix chain 'V' and resid 292 through 301 removed outlier: 3.970A pdb=" N ARG V 298 " --> pdb=" O TRP V 294 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU V 299 " --> pdb=" O GLN V 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 77 through 81 Processing helix chain 'X' and resid 104 through 114 removed outlier: 4.554A pdb=" N VAL X 108 " --> pdb=" O PRO X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 129 Processing helix chain 'X' and resid 129 through 141 removed outlier: 3.517A pdb=" N MET X 136 " --> pdb=" O GLN X 132 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA X 141 " --> pdb=" O ILE X 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 155 Processing helix chain 'X' and resid 177 through 182 Processing helix chain 'X' and resid 191 through 200 Processing helix chain 'X' and resid 205 through 209 Processing helix chain 'X' and resid 215 through 220 removed outlier: 3.710A pdb=" N SER X 219 " --> pdb=" O PRO X 215 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 81 Processing helix chain 'Y' and resid 104 through 114 removed outlier: 4.320A pdb=" N VAL Y 108 " --> pdb=" O PRO Y 104 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 141 removed outlier: 3.575A pdb=" N ARG Y 124 " --> pdb=" O MET Y 120 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N MET Y 135 " --> pdb=" O LEU Y 131 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA Y 141 " --> pdb=" O ILE Y 137 " (cutoff:3.500A) Processing helix chain 'Y' and resid 145 through 160 removed outlier: 3.922A pdb=" N ARG Y 158 " --> pdb=" O LEU Y 154 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE Y 160 " --> pdb=" O LEU Y 156 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 182 removed outlier: 3.589A pdb=" N GLU Y 181 " --> pdb=" O GLN Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 199 removed outlier: 3.706A pdb=" N GLU Y 199 " --> pdb=" O GLY Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 220 removed outlier: 3.812A pdb=" N LEU Y 218 " --> pdb=" O LYS Y 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.751A pdb=" N VAL A 136 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA5, first strand: chain 'A' and resid 149 through 152 removed outlier: 4.015A pdb=" N GLU A 152 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 509 Processing sheet with id=AA8, first strand: chain 'A' and resid 608 through 610 removed outlier: 4.538A pdb=" N VAL A 608 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AB2, first strand: chain 'A' and resid 715 through 720 removed outlier: 4.338A pdb=" N VAL A 840 " --> pdb=" O GLU A 720 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 736 through 737 removed outlier: 3.715A pdb=" N GLY A 771 " --> pdb=" O THR A 737 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 818 through 820 removed outlier: 3.592A pdb=" N ARG A 818 " --> pdb=" O ARG A 837 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 837 " --> pdb=" O ARG A 818 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 820 " --> pdb=" O VAL A 835 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 992 through 993 removed outlier: 3.692A pdb=" N ARG A 993 " --> pdb=" O SER E 357 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER E 357 " --> pdb=" O ARG A 993 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 3 through 4 removed outlier: 6.846A pdb=" N PHE B 3 " --> pdb=" O GLU E 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 439 through 443 Processing sheet with id=AB8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AB9, first strand: chain 'B' and resid 461 through 462 Processing sheet with id=AC1, first strand: chain 'B' and resid 502 through 504 Processing sheet with id=AC2, first strand: chain 'B' and resid 512 through 513 removed outlier: 3.612A pdb=" N THR B 513 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 551 through 552 Processing sheet with id=AC4, first strand: chain 'B' and resid 635 through 642 removed outlier: 4.678A pdb=" N ARG B 682 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LYS B 641 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE B 680 " --> pdb=" O LYS B 641 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 660 through 661 Processing sheet with id=AC6, first strand: chain 'B' and resid 765 through 766 removed outlier: 3.677A pdb=" N SER B 765 " --> pdb=" O GLU B 800 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1152 through 1154 Processing sheet with id=AC8, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AC9, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AD1, first strand: chain 'C' and resid 176 through 177 Processing sheet with id=AD2, first strand: chain 'C' and resid 180 through 182 Processing sheet with id=AD3, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.769A pdb=" N ILE D 24 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 25 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 194 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP D 192 " --> pdb=" O PRO D 27 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=AD5, first strand: chain 'E' and resid 428 through 429 Processing sheet with id=AD6, first strand: chain 'E' and resid 431 through 432 Processing sheet with id=AD7, first strand: chain 'E' and resid 556 through 558 Processing sheet with id=AD8, first strand: chain 'S' and resid 93 through 94 removed outlier: 7.856A pdb=" N LEU S 121 " --> pdb=" O GLU U 222 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 161 through 163 removed outlier: 3.531A pdb=" N TYR S 163 " --> pdb=" O VAL S 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 163 through 165 removed outlier: 4.259A pdb=" N ARG U 274 " --> pdb=" O GLU U 165 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 145 through 146 removed outlier: 3.561A pdb=" N VAL V 145 " --> pdb=" O VAL V 277 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 263 through 264 removed outlier: 5.053A pdb=" N ASN V 263 " --> pdb=" O GLY V 271 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 51 through 54 Processing sheet with id=AE5, first strand: chain 'Y' and resid 26 through 27 Processing sheet with id=AE6, first strand: chain 'Y' and resid 51 through 54 1028 hydrogen bonds defined for protein. 2802 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 153 hydrogen bonds 298 hydrogen bond angles 0 basepair planarities 66 basepair parallelities 148 stacking parallelities Total time for adding SS restraints: 11.37 Time building geometry restraints manager: 6.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.38: 18033 1.38 - 1.78: 29001 1.78 - 2.17: 205 2.17 - 2.56: 0 2.56 - 2.95: 1 Bond restraints: 47240 Sorted by residual: bond pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " ideal model delta sigma weight residual 1.607 2.949 -1.342 1.50e-02 4.44e+03 8.00e+03 bond pdb=" C GLY U 154 " pdb=" N ARG U 155 " ideal model delta sigma weight residual 1.332 1.733 -0.401 1.40e-02 5.10e+03 8.19e+02 bond pdb=" CA GLN G 87 " pdb=" C GLN G 87 " ideal model delta sigma weight residual 1.524 1.132 0.393 1.48e-02 4.57e+03 7.03e+02 bond pdb=" N PRO E 150 " pdb=" CD PRO E 150 " ideal model delta sigma weight residual 1.473 1.148 0.325 1.40e-02 5.10e+03 5.39e+02 bond pdb=" N PRO U 176 " pdb=" CD PRO U 176 " ideal model delta sigma weight residual 1.473 1.148 0.325 1.40e-02 5.10e+03 5.37e+02 ... (remaining 47235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.70: 64662 15.70 - 31.39: 170 31.39 - 47.09: 14 47.09 - 62.79: 2 62.79 - 78.49: 2 Bond angle restraints: 64850 Sorted by residual: angle pdb=" C3' DC 1 45 " pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " ideal model delta sigma weight residual 120.20 41.71 78.49 1.50e+00 4.44e-01 2.74e+03 angle pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " pdb=" OP2 DA 1 46 " ideal model delta sigma weight residual 108.00 172.28 -64.28 3.00e+00 1.11e-01 4.59e+02 angle pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " pdb=" O5' DA 1 46 " ideal model delta sigma weight residual 104.00 73.89 30.11 1.50e+00 4.44e-01 4.03e+02 angle pdb=" CA MET T 157 " pdb=" CB MET T 157 " pdb=" CG MET T 157 " ideal model delta sigma weight residual 114.10 152.37 -38.27 2.00e+00 2.50e-01 3.66e+02 angle pdb=" C PRO G 309 " pdb=" CA PRO G 309 " pdb=" CB PRO G 309 " ideal model delta sigma weight residual 111.56 87.93 23.63 1.27e+00 6.20e-01 3.46e+02 ... (remaining 64845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.44: 26229 32.44 - 64.87: 2174 64.87 - 97.31: 114 97.31 - 129.75: 1 129.75 - 162.18: 4 Dihedral angle restraints: 28522 sinusoidal: 13178 harmonic: 15344 Sorted by residual: dihedral pdb=" C MET T 157 " pdb=" N MET T 157 " pdb=" CA MET T 157 " pdb=" CB MET T 157 " ideal model delta harmonic sigma weight residual -122.60 -167.49 44.89 0 2.50e+00 1.60e-01 3.22e+02 dihedral pdb=" N MET T 157 " pdb=" C MET T 157 " pdb=" CA MET T 157 " pdb=" CB MET T 157 " ideal model delta harmonic sigma weight residual 122.80 166.92 -44.12 0 2.50e+00 1.60e-01 3.12e+02 dihedral pdb=" C PRO G 309 " pdb=" N PRO G 309 " pdb=" CA PRO G 309 " pdb=" CB PRO G 309 " ideal model delta harmonic sigma weight residual -120.70 -87.72 -32.98 0 2.50e+00 1.60e-01 1.74e+02 ... (remaining 28519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.514: 7418 0.514 - 1.027: 47 1.027 - 1.541: 0 1.541 - 2.054: 1 2.054 - 2.568: 1 Chirality restraints: 7467 Sorted by residual: chirality pdb=" C3' DG 1 13 " pdb=" C4' DG 1 13 " pdb=" O3' DG 1 13 " pdb=" C2' DG 1 13 " both_signs ideal model delta sigma weight residual False -2.66 -0.09 -2.57 2.00e-01 2.50e+01 1.65e+02 chirality pdb=" CA MET T 157 " pdb=" N MET T 157 " pdb=" C MET T 157 " pdb=" CB MET T 157 " both_signs ideal model delta sigma weight residual False 2.51 0.57 1.94 2.00e-01 2.50e+01 9.39e+01 chirality pdb=" CA ILE T 167 " pdb=" N ILE T 167 " pdb=" C ILE T 167 " pdb=" CB ILE T 167 " both_signs ideal model delta sigma weight residual False 2.43 1.42 1.01 2.00e-01 2.50e+01 2.56e+01 ... (remaining 7464 not shown) Planarity restraints: 7705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU S 84 " 0.086 2.00e-02 2.50e+03 1.70e-01 2.90e+02 pdb=" C LEU S 84 " -0.293 2.00e-02 2.50e+03 pdb=" O LEU S 84 " 0.125 2.00e-02 2.50e+03 pdb=" N ILE S 85 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU U 84 " -0.085 2.00e-02 2.50e+03 1.68e-01 2.82e+02 pdb=" C LEU U 84 " 0.290 2.00e-02 2.50e+03 pdb=" O LEU U 84 " -0.123 2.00e-02 2.50e+03 pdb=" N ILE U 85 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL T 195 " 0.066 2.00e-02 2.50e+03 1.32e-01 1.73e+02 pdb=" C VAL T 195 " -0.228 2.00e-02 2.50e+03 pdb=" O VAL T 195 " 0.083 2.00e-02 2.50e+03 pdb=" N PHE T 196 " 0.078 2.00e-02 2.50e+03 ... (remaining 7702 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.76: 52 1.76 - 2.54: 3930 2.54 - 3.33: 75632 3.33 - 4.11: 136149 4.11 - 4.90: 207172 Warning: very small nonbonded interaction distances. Nonbonded interactions: 422935 Sorted by model distance: nonbonded pdb=" CA PRO A 875 " pdb=" OH TYR A 960 " model vdw 0.972 3.470 nonbonded pdb=" O GLN T 193 " pdb=" CD1 LEU T 217 " model vdw 0.987 3.460 nonbonded pdb=" OE1 GLN U 5 " pdb=" CD GLN U 35 " model vdw 1.004 3.270 nonbonded pdb=" OH TYR V 180 " pdb=" CZ TYR V 191 " model vdw 1.155 3.260 nonbonded pdb=" CD GLN U 5 " pdb=" OE1 GLN U 35 " model vdw 1.183 3.270 ... (remaining 422930 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 'C' selection = chain 'D' } ncs_group { reference = (chain 'S' and (resid 1 through 262 or resid 272 through 303)) selection = chain 'T' selection = chain 'U' selection = (chain 'V' and (resid 1 through 262 or resid 272 through 303)) } ncs_group { reference = chain 'X' selection = chain 'Y' } 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=0.10 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.830 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: 0.040 Extract box with map and model: 0.680 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 49.220 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 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 : 0.031 1.342 47260 Z= 1.690 Angle : 2.811 78.487 64862 Z= 1.621 Chirality : 0.140 2.568 7467 Planarity : 0.022 0.436 7705 Dihedral : 20.268 162.182 18602 Min Nonbonded Distance : 0.972 Molprobity Statistics. All-atom Clashscore : 180.44 Ramachandran Plot: Outliers : 5.50 % Allowed : 33.81 % Favored : 60.69 % Rotamer: Outliers : 7.38 % Allowed : 10.65 % Favored : 81.97 % Cbeta Deviations : 1.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.02 % Twisted General : 5.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.34 (0.07), residues: 5289 helix: -4.66 (0.07), residues: 1395 sheet: -4.96 (0.22), residues: 263 loop : -5.39 (0.07), residues: 3631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.002 ARG A 607 TYR 0.186 0.008 TYR G 85 PHE 0.126 0.007 PHE G 301 TRP 0.092 0.008 TRP C 199 HIS 0.072 0.007 HIS A 991 Details of bonding type rmsd covalent geometry : bond 0.03015 (47240) covalent geometry : angle 2.79440 (64850) SS BOND : bond 0.38274 ( 6) SS BOND : angle 22.34491 ( 12) hydrogen bonds : bond 0.30159 ( 1181) hydrogen bonds : angle 13.92798 ( 3100) Misc. bond : bond 0.31712 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1219 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 337 poor density : 882 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.6619 (mt) cc_final: 0.6348 (mt) REVERT: A 344 GLU cc_start: 0.8033 (mt-10) cc_final: 0.6731 (tm-30) REVERT: A 431 CYS cc_start: 0.8167 (t) cc_final: 0.6454 (p) REVERT: A 541 MET cc_start: 0.7258 (mmp) cc_final: 0.6989 (mmp) REVERT: B 77 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8037 (tm-30) REVERT: B 151 GLN cc_start: 0.5853 (mm-40) cc_final: 0.5196 (pp30) REVERT: B 648 VAL cc_start: 0.5636 (OUTLIER) cc_final: 0.5357 (m) REVERT: B 1119 THR cc_start: 0.7161 (p) cc_final: 0.6847 (m) REVERT: B 1128 VAL cc_start: 0.8999 (t) cc_final: 0.8784 (p) REVERT: C 77 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: C 169 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7490 (pt) REVERT: D 36 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8627 (m) REVERT: D 51 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8108 (t) REVERT: D 72 ARG cc_start: 0.8628 (mtp180) cc_final: 0.8259 (ttp80) REVERT: E 273 ASN cc_start: 0.7780 (p0) cc_final: 0.7309 (p0) REVERT: E 420 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7307 (tm-30) REVERT: E 441 ILE cc_start: 0.8517 (mt) cc_final: 0.8298 (mt) REVERT: E 587 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7763 (tt) REVERT: E 602 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.4718 (mm) REVERT: G 113 LEU cc_start: 0.8368 (mt) cc_final: 0.7962 (tt) REVERT: G 156 ASP cc_start: 0.8681 (m-30) cc_final: 0.8479 (m-30) REVERT: G 165 LEU cc_start: 0.2480 (OUTLIER) cc_final: 0.1791 (pp) REVERT: G 173 TYR cc_start: 0.7044 (m-80) cc_final: 0.6718 (m-10) REVERT: G 184 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7589 (tt) REVERT: S 151 LEU cc_start: 0.0564 (OUTLIER) cc_final: -0.0083 (mp) REVERT: S 278 MET cc_start: -0.4996 (mmm) cc_final: -0.5237 (mtt) REVERT: S 287 ILE cc_start: 0.0363 (OUTLIER) cc_final: 0.0127 (pt) REVERT: T 99 SER cc_start: 0.2299 (OUTLIER) cc_final: 0.2015 (t) REVERT: T 167 ILE cc_start: -0.0513 (OUTLIER) cc_final: -0.0867 (tt) REVERT: T 208 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5737 (pt0) REVERT: T 278 MET cc_start: 0.0870 (ptm) cc_final: 0.0084 (ptm) REVERT: U 182 ARG cc_start: 0.8691 (mtp180) cc_final: 0.8330 (mtm-85) REVERT: V 18 PHE cc_start: -0.2528 (OUTLIER) cc_final: -0.2832 (m-10) REVERT: V 25 CYS cc_start: -0.2055 (OUTLIER) cc_final: -0.3378 (t) REVERT: V 157 MET cc_start: 0.3823 (mmm) cc_final: 0.3237 (tpt) REVERT: V 167 ILE cc_start: -0.1988 (OUTLIER) cc_final: -0.2209 (mt) REVERT: X 145 MET cc_start: 0.5034 (mtt) cc_final: 0.4831 (mpp) REVERT: Y 196 ASP cc_start: 0.6552 (OUTLIER) cc_final: 0.6230 (t0) outliers start: 337 outliers final: 91 residues processed: 1147 average time/residue: 0.3125 time to fit residues: 571.5421 Evaluate side-chains 590 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 481 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 chunk 523 optimal weight: 0.7980 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 50.0000 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 9.9990 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 255 GLN A 385 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 ASN ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN A 858 ASN ** A 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 GLN ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN B 761 GLN ** B 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 GLN B1112 HIS B1147 GLN ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN D 38 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 HIS D 102 ASN D 222 ASN E 81 HIS E 101 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 281 ASN E 371 HIS E 431 ASN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 553 HIS E 568 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 HIS G 251 GLN S 53 HIS S 89 GLN S 147 ASN ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 235 GLN S 282 GLN S 292 HIS T 98 HIS T 110 GLN T 218 GLN T 286 GLN U 53 HIS ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 148 ASN ** U 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 300 ASN ** V 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 174 ASN V 193 GLN ** V 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.175135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.142353 restraints weight = 146235.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.140629 restraints weight = 196112.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.141594 restraints weight = 153965.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.142646 restraints weight = 114409.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.142759 restraints weight = 96570.973| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 47260 Z= 0.341 Angle : 1.375 23.009 64862 Z= 0.707 Chirality : 0.068 0.598 7467 Planarity : 0.012 0.174 7705 Dihedral : 21.032 166.410 8207 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 43.67 Ramachandran Plot: Outliers : 1.40 % Allowed : 19.93 % Favored : 78.67 % Rotamer: Outliers : 2.10 % Allowed : 10.23 % Favored : 87.67 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 1.56 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.19 (0.08), residues: 5289 helix: -3.71 (0.09), residues: 1461 sheet: -4.40 (0.22), residues: 313 loop : -4.61 (0.08), residues: 3515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.002 ARG A 993 TYR 0.047 0.004 TYR V 200 PHE 0.044 0.005 PHE E 468 TRP 0.044 0.004 TRP B 98 HIS 0.023 0.004 HIS V 175 Details of bonding type rmsd covalent geometry : bond 0.00727 (47240) covalent geometry : angle 1.37266 (64850) SS BOND : bond 0.01574 ( 6) SS BOND : angle 6.60455 ( 12) hydrogen bonds : bond 0.09306 ( 1181) hydrogen bonds : angle 8.99550 ( 3100) Misc. bond : bond 0.00977 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 731 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7237 (m-10) cc_final: 0.7016 (m-80) REVERT: A 119 LEU cc_start: 0.5623 (pt) cc_final: 0.5381 (pt) REVERT: A 344 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6307 (tm-30) REVERT: A 378 PHE cc_start: 0.7393 (m-10) cc_final: 0.7134 (m-80) REVERT: A 413 GLU cc_start: 0.8592 (pm20) cc_final: 0.7789 (pt0) REVERT: A 545 LEU cc_start: 0.9201 (tp) cc_final: 0.8684 (tp) REVERT: A 573 LEU cc_start: 0.9072 (tt) cc_final: 0.8870 (tt) REVERT: A 581 GLN cc_start: 0.7870 (pm20) cc_final: 0.7519 (pp30) REVERT: A 646 ASN cc_start: 0.7882 (t0) cc_final: 0.7628 (t0) REVERT: A 679 GLU cc_start: 0.8035 (pm20) cc_final: 0.7746 (pm20) REVERT: A 694 GLU cc_start: 0.7618 (pm20) cc_final: 0.6909 (tt0) REVERT: A 702 ILE cc_start: 0.9495 (mm) cc_final: 0.9260 (mm) REVERT: A 876 ASP cc_start: 0.8861 (p0) cc_final: 0.8556 (t0) REVERT: A 893 MET cc_start: 0.7168 (mtt) cc_final: 0.6953 (mtt) REVERT: A 900 GLU cc_start: 0.9033 (pm20) cc_final: 0.8481 (pm20) REVERT: A 947 TRP cc_start: 0.8691 (p-90) cc_final: 0.8412 (p-90) REVERT: A 985 LEU cc_start: 0.8653 (tp) cc_final: 0.8213 (tp) REVERT: A 1076 GLU cc_start: 0.8567 (pt0) cc_final: 0.8169 (pt0) REVERT: B 55 ASP cc_start: 0.8306 (t0) cc_final: 0.8016 (t0) REVERT: B 125 MET cc_start: 0.8700 (mpp) cc_final: 0.8165 (mpp) REVERT: B 155 ILE cc_start: 0.6458 (tp) cc_final: 0.6232 (tt) REVERT: B 225 MET cc_start: 0.8534 (ttt) cc_final: 0.8042 (ttt) REVERT: B 232 LEU cc_start: 0.7903 (tt) cc_final: 0.7218 (tt) REVERT: B 538 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: B 667 GLN cc_start: 0.6572 (pm20) cc_final: 0.6366 (pm20) REVERT: B 693 MET cc_start: 0.7823 (mpp) cc_final: 0.7534 (mpp) REVERT: B 1114 LEU cc_start: 0.9155 (mt) cc_final: 0.8632 (mt) REVERT: B 1121 LEU cc_start: 0.9314 (mt) cc_final: 0.8836 (mt) REVERT: B 1131 SER cc_start: 0.9442 (m) cc_final: 0.9091 (p) REVERT: B 1202 LEU cc_start: 0.8301 (mp) cc_final: 0.7794 (mp) REVERT: B 1221 THR cc_start: 0.7827 (p) cc_final: 0.7611 (m) REVERT: C 42 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7455 (mtt90) REVERT: C 74 ASP cc_start: 0.7840 (t0) cc_final: 0.6998 (p0) REVERT: C 77 GLU cc_start: 0.8122 (pm20) cc_final: 0.6844 (mm-30) REVERT: C 86 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8925 (mm) REVERT: D 80 MET cc_start: 0.8041 (tpt) cc_final: 0.7800 (tpt) REVERT: D 82 MET cc_start: 0.6829 (mmp) cc_final: 0.6568 (mmm) REVERT: D 86 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8454 (tp) REVERT: D 183 VAL cc_start: 0.8414 (t) cc_final: 0.7074 (t) REVERT: D 193 ARG cc_start: 0.8405 (ttm110) cc_final: 0.7771 (ptp-110) REVERT: E 129 LEU cc_start: 0.8232 (mt) cc_final: 0.7115 (mt) REVERT: E 131 MET cc_start: 0.7119 (mmp) cc_final: 0.6779 (mmm) REVERT: E 146 VAL cc_start: 0.9166 (m) cc_final: 0.8868 (p) REVERT: E 240 LYS cc_start: 0.8419 (mttp) cc_final: 0.8007 (mtpt) REVERT: E 321 ARG cc_start: 0.8658 (ptt180) cc_final: 0.8313 (ptt180) REVERT: E 338 ILE cc_start: 0.7856 (pt) cc_final: 0.7197 (pt) REVERT: E 339 GLU cc_start: 0.7751 (mp0) cc_final: 0.7499 (mp0) REVERT: E 379 MET cc_start: 0.7968 (ptp) cc_final: 0.7659 (mtm) REVERT: E 442 GLN cc_start: 0.7898 (mt0) cc_final: 0.7550 (mt0) REVERT: E 468 PHE cc_start: 0.8791 (m-80) cc_final: 0.8485 (m-10) REVERT: E 482 GLU cc_start: 0.7064 (pm20) cc_final: 0.6615 (pm20) REVERT: E 513 MET cc_start: 0.8468 (mtt) cc_final: 0.8054 (mtt) REVERT: F 31 ILE cc_start: 0.8880 (mt) cc_final: 0.8635 (mm) REVERT: F 62 ILE cc_start: 0.9160 (mm) cc_final: 0.8779 (tt) REVERT: F 64 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: G 110 LEU cc_start: 0.9379 (pp) cc_final: 0.9162 (tt) REVERT: G 185 GLN cc_start: 0.8416 (mm110) cc_final: 0.8185 (tp40) REVERT: S 157 MET cc_start: 0.0542 (tpt) cc_final: 0.0303 (tpt) REVERT: V 157 MET cc_start: 0.2107 (mmm) cc_final: 0.1385 (mmm) REVERT: X 90 TYR cc_start: 0.6153 (m-80) cc_final: 0.5804 (m-80) REVERT: X 145 MET cc_start: 0.5808 (mtt) cc_final: 0.4821 (mpp) REVERT: X 187 ARG cc_start: 0.3571 (tpt170) cc_final: 0.3123 (tpt170) REVERT: Y 145 MET cc_start: 0.7017 (mpp) cc_final: 0.6568 (mmp) REVERT: Y 202 MET cc_start: 0.7406 (mmt) cc_final: 0.6963 (mmm) outliers start: 96 outliers final: 26 residues processed: 818 average time/residue: 0.2855 time to fit residues: 384.7341 Evaluate side-chains 502 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 472 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 453 optimal weight: 30.0000 chunk 318 optimal weight: 0.8980 chunk 484 optimal weight: 50.0000 chunk 79 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 510 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 55 optimal weight: 2.9990 chunk 535 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN A 333 GLN A 389 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 HIS ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 GLN ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN E 431 ASN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 HIS ** E 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN F 34 GLN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 110 GLN ** T 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 120 GLN ** U 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 282 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 148 ASN X 91 HIS X 132 GLN X 142 HIS X 176 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.172373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.141144 restraints weight = 147532.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.138364 restraints weight = 233758.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.139909 restraints weight = 197171.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.140737 restraints weight = 132061.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.140685 restraints weight = 127044.751| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4003 r_free = 0.4003 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4003 r_free = 0.4003 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 47260 Z= 0.274 Angle : 1.116 22.318 64862 Z= 0.575 Chirality : 0.057 0.422 7467 Planarity : 0.009 0.172 7705 Dihedral : 20.443 169.681 8207 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 35.35 Ramachandran Plot: Outliers : 0.96 % Allowed : 19.29 % Favored : 79.75 % Rotamer: Outliers : 0.68 % Allowed : 8.54 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.45 (0.09), residues: 5289 helix: -2.99 (0.11), residues: 1493 sheet: -3.93 (0.22), residues: 364 loop : -4.17 (0.09), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 993 TYR 0.039 0.003 TYR E 117 PHE 0.067 0.003 PHE U 229 TRP 0.039 0.004 TRP S 294 HIS 0.013 0.003 HIS E 553 Details of bonding type rmsd covalent geometry : bond 0.00607 (47240) covalent geometry : angle 1.11325 (64850) SS BOND : bond 0.01545 ( 6) SS BOND : angle 5.96069 ( 12) hydrogen bonds : bond 0.07329 ( 1181) hydrogen bonds : angle 7.97785 ( 3100) Misc. bond : bond 0.00732 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 643 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8227 (mtmt) cc_final: 0.8015 (pttt) REVERT: A 274 ARG cc_start: 0.7764 (ttp-170) cc_final: 0.7217 (ttp80) REVERT: A 344 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6443 (tm-30) REVERT: A 413 GLU cc_start: 0.8732 (pm20) cc_final: 0.8333 (pt0) REVERT: A 541 MET cc_start: 0.9004 (mmm) cc_final: 0.8514 (mmm) REVERT: A 646 ASN cc_start: 0.8064 (t0) cc_final: 0.7775 (t0) REVERT: A 679 GLU cc_start: 0.8078 (pm20) cc_final: 0.7319 (pm20) REVERT: A 694 GLU cc_start: 0.7591 (pm20) cc_final: 0.7166 (tt0) REVERT: A 702 ILE cc_start: 0.9410 (mm) cc_final: 0.9121 (mm) REVERT: A 748 LEU cc_start: 0.8999 (tt) cc_final: 0.8768 (pp) REVERT: A 864 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7899 (ttm170) REVERT: A 876 ASP cc_start: 0.8850 (p0) cc_final: 0.8298 (t0) REVERT: A 922 MET cc_start: 0.7027 (ttt) cc_final: 0.6798 (ttt) REVERT: A 1004 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7220 (mm110) REVERT: B 77 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7441 (tp30) REVERT: B 225 MET cc_start: 0.8327 (ttt) cc_final: 0.7937 (ttt) REVERT: B 1221 THR cc_start: 0.7468 (p) cc_final: 0.7147 (m) REVERT: C 74 ASP cc_start: 0.7675 (t0) cc_final: 0.6711 (p0) REVERT: C 77 GLU cc_start: 0.7954 (pm20) cc_final: 0.6909 (mt-10) REVERT: C 100 LEU cc_start: 0.8512 (mt) cc_final: 0.8308 (mt) REVERT: D 183 VAL cc_start: 0.8496 (t) cc_final: 0.7361 (m) REVERT: D 193 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7781 (ptp-110) REVERT: D 222 ASN cc_start: 0.5345 (t0) cc_final: 0.5004 (m110) REVERT: D 224 LEU cc_start: 0.8044 (tp) cc_final: 0.7610 (tt) REVERT: E 70 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6577 (tt0) REVERT: E 81 HIS cc_start: 0.7326 (t-90) cc_final: 0.7082 (t-90) REVERT: E 242 GLU cc_start: 0.8647 (pm20) cc_final: 0.8317 (pm20) REVERT: E 321 ARG cc_start: 0.8631 (ptt180) cc_final: 0.8066 (ptt90) REVERT: E 338 ILE cc_start: 0.8170 (pt) cc_final: 0.7590 (pt) REVERT: E 339 GLU cc_start: 0.7921 (mp0) cc_final: 0.7144 (pm20) REVERT: E 379 MET cc_start: 0.8054 (ptp) cc_final: 0.7811 (ptp) REVERT: E 468 PHE cc_start: 0.8683 (m-80) cc_final: 0.8381 (m-80) REVERT: E 481 LEU cc_start: 0.9285 (pp) cc_final: 0.8937 (mp) REVERT: E 513 MET cc_start: 0.8496 (mtt) cc_final: 0.8266 (mtt) REVERT: E 534 TYR cc_start: 0.6581 (p90) cc_final: 0.6350 (p90) REVERT: F 64 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: G 78 THR cc_start: 0.8057 (t) cc_final: 0.7693 (m) REVERT: G 300 ASP cc_start: 0.7140 (m-30) cc_final: 0.6833 (m-30) REVERT: S 278 MET cc_start: -0.1639 (ttt) cc_final: -0.5437 (mtt) REVERT: U 1 MET cc_start: 0.2282 (ttm) cc_final: 0.1388 (mtp) REVERT: U 202 MET cc_start: -0.1161 (ptp) cc_final: -0.2800 (ptp) REVERT: V 157 MET cc_start: 0.2211 (mmm) cc_final: 0.1584 (mmm) REVERT: X 145 MET cc_start: 0.5344 (mtt) cc_final: 0.4900 (mpp) outliers start: 31 outliers final: 11 residues processed: 668 average time/residue: 0.2802 time to fit residues: 311.5476 Evaluate side-chains 450 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 437 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 130 optimal weight: 0.8980 chunk 187 optimal weight: 0.0060 chunk 231 optimal weight: 0.0470 chunk 457 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 chunk 214 optimal weight: 40.0000 chunk 445 optimal weight: 8.9990 chunk 541 optimal weight: 0.6980 chunk 427 optimal weight: 9.9990 chunk 467 optimal weight: 40.0000 chunk 285 optimal weight: 30.0000 overall best weight: 0.7296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 GLN A 684 GLN ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 ASN A 937 GLN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 HIS C 38 ASN C 125 GLN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 101 HIS E 114 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN E 431 ASN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 HIS ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 549 GLN E 616 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.174509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.140394 restraints weight = 144429.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.138428 restraints weight = 191638.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.139846 restraints weight = 151598.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.139866 restraints weight = 105265.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.140289 restraints weight = 97123.912| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.7844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 47260 Z= 0.201 Angle : 1.014 21.656 64862 Z= 0.518 Chirality : 0.054 0.463 7467 Planarity : 0.008 0.194 7705 Dihedral : 20.150 169.068 8207 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 28.77 Ramachandran Plot: Outliers : 0.87 % Allowed : 17.30 % Favored : 81.83 % Rotamer: Outliers : 0.24 % Allowed : 6.79 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.03 (0.10), residues: 5289 helix: -2.64 (0.11), residues: 1523 sheet: -3.73 (0.23), residues: 322 loop : -3.90 (0.09), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 607 TYR 0.026 0.002 TYR S 104 PHE 0.032 0.003 PHE X 152 TRP 0.039 0.003 TRP E 416 HIS 0.038 0.002 HIS S 98 Details of bonding type rmsd covalent geometry : bond 0.00431 (47240) covalent geometry : angle 1.01095 (64850) SS BOND : bond 0.00825 ( 6) SS BOND : angle 6.18885 ( 12) hydrogen bonds : bond 0.06247 ( 1181) hydrogen bonds : angle 7.35449 ( 3100) Misc. bond : bond 0.00850 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 641 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8423 (pp) cc_final: 0.8115 (mp) REVERT: A 53 PHE cc_start: 0.6660 (m-80) cc_final: 0.5580 (m-80) REVERT: A 118 ASP cc_start: 0.5308 (m-30) cc_final: 0.4212 (p0) REVERT: A 128 PHE cc_start: 0.8271 (m-10) cc_final: 0.8060 (m-10) REVERT: A 184 TRP cc_start: 0.7653 (m100) cc_final: 0.6984 (m100) REVERT: A 187 ILE cc_start: 0.6508 (tt) cc_final: 0.6230 (tt) REVERT: A 265 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7730 (tttt) REVERT: A 344 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6266 (tm-30) REVERT: A 431 CYS cc_start: 0.8944 (t) cc_final: 0.8422 (p) REVERT: A 507 GLN cc_start: 0.7264 (tp-100) cc_final: 0.6816 (mp10) REVERT: A 573 LEU cc_start: 0.9160 (tt) cc_final: 0.8907 (tt) REVERT: A 646 ASN cc_start: 0.7694 (t0) cc_final: 0.7348 (t0) REVERT: A 667 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7660 (pp30) REVERT: A 685 ASN cc_start: 0.9196 (m-40) cc_final: 0.8791 (m-40) REVERT: A 694 GLU cc_start: 0.7649 (pm20) cc_final: 0.7230 (tt0) REVERT: A 748 LEU cc_start: 0.8958 (tt) cc_final: 0.8607 (pp) REVERT: A 846 ILE cc_start: 0.8990 (pt) cc_final: 0.8735 (pt) REVERT: A 947 TRP cc_start: 0.9003 (p-90) cc_final: 0.7404 (p-90) REVERT: A 957 ILE cc_start: 0.9009 (mm) cc_final: 0.8758 (mm) REVERT: A 1050 GLU cc_start: 0.8885 (tt0) cc_final: 0.8374 (tt0) REVERT: B 55 ASP cc_start: 0.8268 (t0) cc_final: 0.7837 (t0) REVERT: B 67 GLU cc_start: 0.9449 (OUTLIER) cc_final: 0.9190 (pp20) REVERT: B 120 ASN cc_start: 0.7611 (t0) cc_final: 0.7388 (m-40) REVERT: B 234 LYS cc_start: 0.6297 (tptt) cc_final: 0.5296 (mtpt) REVERT: B 353 MET cc_start: 0.4877 (tpt) cc_final: 0.4449 (mpp) REVERT: B 688 PRO cc_start: 0.7273 (OUTLIER) cc_final: 0.6998 (Cg_endo) REVERT: B 692 LEU cc_start: 0.8979 (mp) cc_final: 0.8697 (mp) REVERT: B 1221 THR cc_start: 0.7569 (p) cc_final: 0.7289 (m) REVERT: C 32 GLN cc_start: 0.6626 (tp40) cc_final: 0.6244 (tp40) REVERT: C 77 GLU cc_start: 0.7360 (pm20) cc_final: 0.6786 (mt-10) REVERT: C 80 MET cc_start: 0.7792 (mmp) cc_final: 0.7568 (mmp) REVERT: C 100 LEU cc_start: 0.8719 (mt) cc_final: 0.8352 (mt) REVERT: D 80 MET cc_start: 0.7860 (tpt) cc_final: 0.7626 (tpt) REVERT: D 183 VAL cc_start: 0.8504 (t) cc_final: 0.8289 (m) REVERT: D 222 ASN cc_start: 0.5630 (t0) cc_final: 0.5409 (m110) REVERT: D 224 LEU cc_start: 0.7586 (tp) cc_final: 0.7172 (tt) REVERT: E 81 HIS cc_start: 0.7178 (t-90) cc_final: 0.6874 (t-90) REVERT: E 103 MET cc_start: 0.7428 (mmm) cc_final: 0.6842 (mmp) REVERT: E 233 ASN cc_start: 0.8985 (m-40) cc_final: 0.7964 (m-40) REVERT: E 273 ASN cc_start: 0.8825 (p0) cc_final: 0.7991 (p0) REVERT: E 321 ARG cc_start: 0.8548 (ptt180) cc_final: 0.8209 (ptt180) REVERT: E 338 ILE cc_start: 0.8032 (pt) cc_final: 0.7618 (pt) REVERT: E 348 ASN cc_start: 0.7434 (m110) cc_final: 0.6920 (t0) REVERT: E 377 ARG cc_start: 0.8849 (ttm-80) cc_final: 0.7808 (mmm-85) REVERT: E 407 LEU cc_start: 0.8863 (pp) cc_final: 0.8349 (mt) REVERT: E 439 LEU cc_start: 0.8153 (tp) cc_final: 0.7837 (tp) REVERT: E 519 TYR cc_start: 0.8814 (t80) cc_final: 0.8538 (t80) REVERT: G 158 MET cc_start: 0.7708 (ppp) cc_final: 0.7290 (ppp) REVERT: G 300 ASP cc_start: 0.7352 (m-30) cc_final: 0.6917 (m-30) REVERT: S 278 MET cc_start: -0.1541 (ttt) cc_final: -0.4999 (mtt) REVERT: U 1 MET cc_start: 0.1973 (ttm) cc_final: 0.1419 (mtp) REVERT: U 278 MET cc_start: -0.3346 (mtt) cc_final: -0.5321 (mmt) REVERT: V 1 MET cc_start: -0.2587 (ptt) cc_final: -0.2899 (ptt) REVERT: V 157 MET cc_start: 0.2793 (mmm) cc_final: 0.2271 (mmm) REVERT: X 145 MET cc_start: 0.5152 (mtt) cc_final: 0.4878 (mpp) outliers start: 11 outliers final: 2 residues processed: 651 average time/residue: 0.2732 time to fit residues: 299.4615 Evaluate side-chains 467 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 462 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 477 optimal weight: 0.9990 chunk 512 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 376 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 502 optimal weight: 50.0000 chunk 133 optimal weight: 10.0000 chunk 402 optimal weight: 9.9990 chunk 243 optimal weight: 1.9990 chunk 474 optimal weight: 20.0000 chunk 489 optimal weight: 9.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN A 802 ASN A 991 HIS A1003 GLN ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 484 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 HIS X 177 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.172547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.141724 restraints weight = 144862.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.138758 restraints weight = 195779.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.140175 restraints weight = 193095.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.139704 restraints weight = 132344.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.140426 restraints weight = 118726.314| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4006 r_free = 0.4006 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4006 r_free = 0.4006 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.4006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.8552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 47260 Z= 0.205 Angle : 0.975 19.212 64862 Z= 0.498 Chirality : 0.052 0.395 7467 Planarity : 0.007 0.175 7705 Dihedral : 20.015 171.505 8207 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.87 % Allowed : 16.92 % Favored : 82.21 % Rotamer: Outliers : 0.11 % Allowed : 5.59 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.74 (0.10), residues: 5289 helix: -2.41 (0.11), residues: 1526 sheet: -3.43 (0.23), residues: 363 loop : -3.71 (0.09), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 282 TYR 0.029 0.002 TYR A 600 PHE 0.030 0.003 PHE X 152 TRP 0.044 0.003 TRP E 416 HIS 0.022 0.002 HIS E 553 Details of bonding type rmsd covalent geometry : bond 0.00447 (47240) covalent geometry : angle 0.97188 (64850) SS BOND : bond 0.01182 ( 6) SS BOND : angle 6.19296 ( 12) hydrogen bonds : bond 0.05822 ( 1181) hydrogen bonds : angle 6.99092 ( 3100) Misc. bond : bond 0.00747 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 600 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.6313 (m-80) cc_final: 0.5732 (m-80) REVERT: A 82 GLU cc_start: 0.8166 (pm20) cc_final: 0.7520 (pm20) REVERT: A 118 ASP cc_start: 0.5750 (m-30) cc_final: 0.3981 (p0) REVERT: A 265 LYS cc_start: 0.8349 (mtmt) cc_final: 0.7901 (tttt) REVERT: A 344 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6379 (tm-30) REVERT: A 431 CYS cc_start: 0.9182 (t) cc_final: 0.8264 (p) REVERT: A 507 GLN cc_start: 0.7408 (tp-100) cc_final: 0.7090 (mp10) REVERT: A 541 MET cc_start: 0.8969 (mmp) cc_final: 0.8502 (mmm) REVERT: A 646 ASN cc_start: 0.7899 (t0) cc_final: 0.7554 (t0) REVERT: A 694 GLU cc_start: 0.7375 (pm20) cc_final: 0.7130 (tt0) REVERT: A 748 LEU cc_start: 0.9058 (tt) cc_final: 0.8672 (pp) REVERT: A 864 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7709 (ttm170) REVERT: A 922 MET cc_start: 0.6792 (ttt) cc_final: 0.6420 (ttt) REVERT: A 940 ARG cc_start: 0.8643 (ptm-80) cc_final: 0.8403 (ptm160) REVERT: B 38 ASP cc_start: 0.7878 (m-30) cc_final: 0.7185 (t0) REVERT: B 55 ASP cc_start: 0.8278 (t0) cc_final: 0.7940 (t0) REVERT: B 216 THR cc_start: 0.8215 (m) cc_final: 0.7821 (p) REVERT: B 234 LYS cc_start: 0.6419 (tptt) cc_final: 0.5495 (tttt) REVERT: B 353 MET cc_start: 0.4730 (tpt) cc_final: 0.4523 (mpp) REVERT: B 1174 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7638 (tp30) REVERT: B 1221 THR cc_start: 0.7319 (p) cc_final: 0.7019 (m) REVERT: C 74 ASP cc_start: 0.7717 (p0) cc_final: 0.7199 (p0) REVERT: C 77 GLU cc_start: 0.7556 (pm20) cc_final: 0.7151 (mt-10) REVERT: C 80 MET cc_start: 0.7320 (mmp) cc_final: 0.6962 (tpp) REVERT: C 166 ILE cc_start: 0.7621 (tp) cc_final: 0.7319 (pt) REVERT: D 80 MET cc_start: 0.7988 (tpt) cc_final: 0.7589 (tpt) REVERT: D 224 LEU cc_start: 0.7386 (tp) cc_final: 0.7044 (tt) REVERT: E 81 HIS cc_start: 0.6855 (t-90) cc_final: 0.6593 (t-90) REVERT: E 105 TYR cc_start: 0.7204 (p90) cc_final: 0.6834 (p90) REVERT: E 129 LEU cc_start: 0.8576 (mt) cc_final: 0.7817 (mt) REVERT: E 233 ASN cc_start: 0.8785 (m-40) cc_final: 0.8067 (m110) REVERT: E 273 ASN cc_start: 0.8967 (p0) cc_final: 0.8290 (p0) REVERT: E 321 ARG cc_start: 0.8550 (ptt180) cc_final: 0.8144 (ptt180) REVERT: E 348 ASN cc_start: 0.7585 (m110) cc_final: 0.7184 (t0) REVERT: E 407 LEU cc_start: 0.9037 (pp) cc_final: 0.8491 (mt) REVERT: E 473 MET cc_start: 0.8310 (ptm) cc_final: 0.8046 (ptm) REVERT: E 481 LEU cc_start: 0.9157 (pp) cc_final: 0.8715 (pp) REVERT: F 62 ILE cc_start: 0.8791 (mt) cc_final: 0.8530 (mm) REVERT: G 158 MET cc_start: 0.7828 (ppp) cc_final: 0.7454 (ppp) REVERT: G 300 ASP cc_start: 0.7354 (m-30) cc_final: 0.6820 (m-30) REVERT: G 345 ASP cc_start: 0.6577 (m-30) cc_final: 0.6164 (p0) REVERT: S 278 MET cc_start: -0.1179 (ttt) cc_final: -0.4771 (mtt) REVERT: U 1 MET cc_start: 0.1783 (ttm) cc_final: 0.1313 (mtp) REVERT: U 202 MET cc_start: -0.2236 (ptp) cc_final: -0.2596 (ptp) REVERT: U 278 MET cc_start: -0.2949 (ttm) cc_final: -0.4666 (mmt) REVERT: V 157 MET cc_start: 0.2720 (mmm) cc_final: 0.2259 (mmm) REVERT: X 120 MET cc_start: 0.7748 (ppp) cc_final: 0.7418 (mtt) outliers start: 5 outliers final: 1 residues processed: 604 average time/residue: 0.2778 time to fit residues: 280.3074 Evaluate side-chains 444 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 442 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 329 optimal weight: 0.9980 chunk 193 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 417 optimal weight: 50.0000 chunk 361 optimal weight: 9.9990 chunk 409 optimal weight: 9.9990 chunk 245 optimal weight: 1.9990 chunk 398 optimal weight: 30.0000 chunk 183 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 430 optimal weight: 30.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 228 GLN A 389 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 372 GLN E 426 HIS ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 382 ASN S 52 ASN ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 147 ASN ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.164670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.129488 restraints weight = 136485.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.126895 restraints weight = 215160.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.127908 restraints weight = 200158.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.127517 restraints weight = 132557.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.128002 restraints weight = 120510.701| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.9270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 47260 Z= 0.337 Angle : 1.106 18.630 64862 Z= 0.566 Chirality : 0.056 0.511 7467 Planarity : 0.009 0.151 7705 Dihedral : 20.183 175.810 8207 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 30.61 Ramachandran Plot: Outliers : 0.83 % Allowed : 17.91 % Favored : 81.26 % Rotamer: Outliers : 0.11 % Allowed : 5.13 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.73 (0.10), residues: 5289 helix: -2.39 (0.11), residues: 1553 sheet: -3.42 (0.22), residues: 392 loop : -3.72 (0.09), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 86 TYR 0.044 0.004 TYR A 642 PHE 0.045 0.003 PHE U 229 TRP 0.068 0.004 TRP U 294 HIS 0.015 0.003 HIS A1087 Details of bonding type rmsd covalent geometry : bond 0.00737 (47240) covalent geometry : angle 1.10191 (64850) SS BOND : bond 0.02109 ( 6) SS BOND : angle 7.02905 ( 12) hydrogen bonds : bond 0.06533 ( 1181) hydrogen bonds : angle 7.16249 ( 3100) Misc. bond : bond 0.00646 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 519 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7893 (m-10) cc_final: 0.7485 (m-80) REVERT: A 128 PHE cc_start: 0.8911 (m-10) cc_final: 0.8677 (m-10) REVERT: A 188 ASP cc_start: 0.6983 (m-30) cc_final: 0.6638 (m-30) REVERT: A 265 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8004 (tttt) REVERT: A 344 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7035 (tm-30) REVERT: A 541 MET cc_start: 0.8851 (mmp) cc_final: 0.8140 (mmm) REVERT: A 646 ASN cc_start: 0.8203 (t0) cc_final: 0.7826 (t0) REVERT: A 706 GLU cc_start: 0.8202 (tt0) cc_final: 0.7940 (tt0) REVERT: A 876 ASP cc_start: 0.8900 (p0) cc_final: 0.8629 (p0) REVERT: A 885 ASN cc_start: 0.9090 (t0) cc_final: 0.8889 (t0) REVERT: A 922 MET cc_start: 0.7075 (ttt) cc_final: 0.6720 (ttt) REVERT: A 994 SER cc_start: 0.8388 (t) cc_final: 0.8143 (p) REVERT: B 38 ASP cc_start: 0.8098 (m-30) cc_final: 0.7295 (t0) REVERT: B 216 THR cc_start: 0.8755 (m) cc_final: 0.8315 (p) REVERT: B 353 MET cc_start: 0.4641 (tpt) cc_final: 0.4230 (mpp) REVERT: B 1197 ILE cc_start: 0.8520 (pt) cc_final: 0.8273 (mp) REVERT: B 1204 THR cc_start: 0.6342 (p) cc_final: 0.6140 (m) REVERT: B 1205 ASP cc_start: 0.5889 (p0) cc_final: 0.5682 (m-30) REVERT: C 77 GLU cc_start: 0.7858 (pm20) cc_final: 0.6985 (mt-10) REVERT: C 80 MET cc_start: 0.8174 (mmp) cc_final: 0.7919 (tpp) REVERT: C 93 GLN cc_start: 0.8749 (mt0) cc_final: 0.8517 (mt0) REVERT: D 80 MET cc_start: 0.8254 (tpt) cc_final: 0.7871 (tpt) REVERT: E 89 CYS cc_start: 0.8675 (t) cc_final: 0.7985 (p) REVERT: E 233 ASN cc_start: 0.9013 (m-40) cc_final: 0.8337 (m-40) REVERT: E 321 ARG cc_start: 0.8558 (ptt180) cc_final: 0.8131 (ptt180) REVERT: E 348 ASN cc_start: 0.7631 (m110) cc_final: 0.7381 (t0) REVERT: E 350 LEU cc_start: 0.8852 (tp) cc_final: 0.8550 (tt) REVERT: E 387 PHE cc_start: 0.8852 (m-80) cc_final: 0.8641 (m-10) REVERT: E 407 LEU cc_start: 0.9124 (pp) cc_final: 0.8843 (mt) REVERT: E 479 LEU cc_start: 0.9362 (tp) cc_final: 0.9083 (tp) REVERT: E 513 MET cc_start: 0.8403 (mtt) cc_final: 0.8169 (mtp) REVERT: E 524 ASN cc_start: 0.7113 (t0) cc_final: 0.6728 (t0) REVERT: F 62 ILE cc_start: 0.9113 (mt) cc_final: 0.8823 (mt) REVERT: G 158 MET cc_start: 0.8001 (ppp) cc_final: 0.7556 (ppp) REVERT: G 196 GLU cc_start: 0.7816 (pm20) cc_final: 0.7593 (mp0) REVERT: G 300 ASP cc_start: 0.7221 (m-30) cc_final: 0.6672 (m-30) REVERT: S 278 MET cc_start: -0.0553 (ttt) cc_final: -0.4161 (mtt) REVERT: U 157 MET cc_start: -0.3574 (ptp) cc_final: -0.3794 (ptt) REVERT: U 278 MET cc_start: -0.2457 (ttm) cc_final: -0.4588 (mmt) REVERT: V 157 MET cc_start: 0.3327 (mmm) cc_final: 0.2896 (mmm) REVERT: X 120 MET cc_start: 0.7762 (ppp) cc_final: 0.7427 (mtt) outliers start: 5 outliers final: 1 residues processed: 523 average time/residue: 0.2745 time to fit residues: 241.1167 Evaluate side-chains 390 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 389 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 322 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 chunk 455 optimal weight: 10.0000 chunk 472 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 373 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 389 optimal weight: 4.9990 chunk 456 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN A 389 GLN A 547 HIS A 781 GLN A 802 ASN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 GLN ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 GLN E 616 ASN F 13 GLN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 193 GLN V 295 GLN ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 206 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.169696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.133194 restraints weight = 136850.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.129828 restraints weight = 202663.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.131593 restraints weight = 172792.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.130800 restraints weight = 117197.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.131024 restraints weight = 124319.566| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.9661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 47260 Z= 0.186 Angle : 0.946 23.276 64862 Z= 0.481 Chirality : 0.051 0.518 7467 Planarity : 0.008 0.348 7705 Dihedral : 20.009 173.933 8207 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.78 % Allowed : 15.66 % Favored : 83.57 % Rotamer: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.46 (0.10), residues: 5289 helix: -2.14 (0.11), residues: 1592 sheet: -3.31 (0.23), residues: 380 loop : -3.55 (0.10), residues: 3317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.001 ARG E 346 TYR 0.070 0.002 TYR D 178 PHE 0.048 0.002 PHE B1097 TRP 0.052 0.003 TRP U 294 HIS 0.010 0.001 HIS V 292 Details of bonding type rmsd covalent geometry : bond 0.00405 (47240) covalent geometry : angle 0.94414 (64850) SS BOND : bond 0.00317 ( 6) SS BOND : angle 4.87326 ( 12) hydrogen bonds : bond 0.05486 ( 1181) hydrogen bonds : angle 6.65515 ( 3100) Misc. bond : bond 0.00743 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 564 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7538 (m-10) cc_final: 0.7307 (m-80) REVERT: A 162 SER cc_start: 0.7497 (m) cc_final: 0.7226 (m) REVERT: A 187 ILE cc_start: 0.8473 (pt) cc_final: 0.8044 (pt) REVERT: A 188 ASP cc_start: 0.6902 (m-30) cc_final: 0.6701 (m-30) REVERT: A 265 LYS cc_start: 0.8481 (mtmt) cc_final: 0.8163 (tttt) REVERT: A 344 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6864 (tm-30) REVERT: A 541 MET cc_start: 0.9289 (mmp) cc_final: 0.8596 (mmm) REVERT: A 646 ASN cc_start: 0.8043 (t0) cc_final: 0.7661 (t0) REVERT: A 684 GLN cc_start: 0.8578 (mp10) cc_final: 0.8311 (mp10) REVERT: A 685 ASN cc_start: 0.9170 (m-40) cc_final: 0.8855 (m-40) REVERT: A 702 ILE cc_start: 0.8883 (mm) cc_final: 0.8656 (mm) REVERT: A 704 ILE cc_start: 0.8763 (tp) cc_final: 0.8533 (tp) REVERT: A 706 GLU cc_start: 0.8089 (tt0) cc_final: 0.7715 (tt0) REVERT: A 749 ARG cc_start: 0.7516 (ptp-110) cc_final: 0.7311 (ptp-110) REVERT: A 850 ASP cc_start: 0.8718 (m-30) cc_final: 0.8214 (m-30) REVERT: A 922 MET cc_start: 0.6803 (ttt) cc_final: 0.6489 (ttt) REVERT: A 956 LYS cc_start: 0.8790 (mppt) cc_final: 0.8380 (mttm) REVERT: A 1045 MET cc_start: 0.6841 (mpp) cc_final: 0.6587 (mmt) REVERT: B 38 ASP cc_start: 0.7995 (m-30) cc_final: 0.7324 (t70) REVERT: B 56 LEU cc_start: 0.7834 (mt) cc_final: 0.7572 (mp) REVERT: B 143 MET cc_start: 0.2289 (tpt) cc_final: 0.1695 (tpt) REVERT: B 332 MET cc_start: 0.4333 (tpp) cc_final: 0.4114 (tpp) REVERT: B 353 MET cc_start: 0.4545 (tpt) cc_final: 0.4152 (mpp) REVERT: B 776 TYR cc_start: 0.5827 (t80) cc_final: 0.5583 (t80) REVERT: B 1244 LEU cc_start: 0.9064 (tt) cc_final: 0.8855 (tt) REVERT: C 74 ASP cc_start: 0.7548 (p0) cc_final: 0.7196 (p0) REVERT: C 77 GLU cc_start: 0.7346 (pm20) cc_final: 0.7123 (mt-10) REVERT: C 80 MET cc_start: 0.8271 (mmp) cc_final: 0.7950 (tpp) REVERT: C 93 GLN cc_start: 0.8695 (mt0) cc_final: 0.8412 (mt0) REVERT: C 166 ILE cc_start: 0.7796 (tp) cc_final: 0.7446 (pt) REVERT: D 80 MET cc_start: 0.8116 (tpt) cc_final: 0.7558 (tpt) REVERT: E 89 CYS cc_start: 0.8510 (t) cc_final: 0.7864 (p) REVERT: E 103 MET cc_start: 0.8007 (mmm) cc_final: 0.7729 (mmp) REVERT: E 258 PRO cc_start: 0.9188 (Cg_endo) cc_final: 0.8881 (Cg_exo) REVERT: E 273 ASN cc_start: 0.8998 (p0) cc_final: 0.8383 (p0) REVERT: E 321 ARG cc_start: 0.8526 (ptt180) cc_final: 0.8126 (ptt180) REVERT: E 407 LEU cc_start: 0.8927 (pp) cc_final: 0.8664 (mt) REVERT: E 439 LEU cc_start: 0.8663 (tp) cc_final: 0.8328 (tp) REVERT: E 482 GLU cc_start: 0.7881 (tp30) cc_final: 0.7584 (tp30) REVERT: E 524 ASN cc_start: 0.7011 (t0) cc_final: 0.6644 (t0) REVERT: E 552 LEU cc_start: 0.8533 (tt) cc_final: 0.8283 (tt) REVERT: F 19 GLU cc_start: 0.7849 (tp30) cc_final: 0.7257 (tp30) REVERT: F 45 GLU cc_start: 0.8646 (pm20) cc_final: 0.8414 (pm20) REVERT: G 156 ASP cc_start: 0.8180 (m-30) cc_final: 0.7703 (m-30) REVERT: G 196 GLU cc_start: 0.7669 (pm20) cc_final: 0.7402 (mp0) REVERT: G 300 ASP cc_start: 0.7571 (m-30) cc_final: 0.6586 (m-30) REVERT: S 278 MET cc_start: -0.0578 (ttt) cc_final: -0.4135 (mtt) REVERT: U 278 MET cc_start: -0.2845 (ttm) cc_final: -0.4870 (mmt) REVERT: V 157 MET cc_start: 0.3766 (mmm) cc_final: 0.3193 (mmm) REVERT: X 120 MET cc_start: 0.7836 (ppp) cc_final: 0.7498 (mtt) outliers start: 2 outliers final: 2 residues processed: 565 average time/residue: 0.2784 time to fit residues: 263.0344 Evaluate side-chains 402 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 400 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 246 optimal weight: 0.6980 chunk 271 optimal weight: 7.9990 chunk 317 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 457 optimal weight: 40.0000 chunk 497 optimal weight: 9.9990 chunk 323 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 471 optimal weight: 7.9990 chunk 109 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS B 92 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 HIS B 637 HIS ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN E 143 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 GLN ** E 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 147 ASN T 174 ASN ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.168909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.132290 restraints weight = 136119.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.128654 restraints weight = 219150.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.129987 restraints weight = 213636.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.130149 restraints weight = 150656.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.131128 restraints weight = 124452.567| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.9934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.244 47260 Z= 0.210 Angle : 0.978 21.341 64862 Z= 0.501 Chirality : 0.052 0.516 7467 Planarity : 0.007 0.177 7705 Dihedral : 19.961 173.634 8207 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 25.58 Ramachandran Plot: Outliers : 0.79 % Allowed : 16.47 % Favored : 82.74 % Rotamer: Outliers : 0.04 % Allowed : 2.37 % Favored : 97.59 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.37 (0.10), residues: 5289 helix: -2.06 (0.11), residues: 1589 sheet: -3.24 (0.23), residues: 382 loop : -3.50 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 346 TYR 0.045 0.002 TYR G 388 PHE 0.137 0.003 PHE A 516 TRP 0.068 0.003 TRP E 416 HIS 0.010 0.002 HIS V 175 Details of bonding type rmsd covalent geometry : bond 0.00473 (47240) covalent geometry : angle 0.97277 (64850) SS BOND : bond 0.01343 ( 6) SS BOND : angle 7.32755 ( 12) hydrogen bonds : bond 0.05453 ( 1181) hydrogen bonds : angle 6.63418 ( 3100) Misc. bond : bond 0.01020 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 528 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6756 (tm-30) REVERT: A 559 MET cc_start: 0.8966 (tpp) cc_final: 0.7910 (mmm) REVERT: A 684 GLN cc_start: 0.8575 (mp10) cc_final: 0.8343 (mp10) REVERT: A 685 ASN cc_start: 0.9228 (m-40) cc_final: 0.8965 (m110) REVERT: A 704 ILE cc_start: 0.8799 (tp) cc_final: 0.8571 (tp) REVERT: A 706 GLU cc_start: 0.8032 (tt0) cc_final: 0.7668 (tt0) REVERT: A 749 ARG cc_start: 0.7499 (ptp-110) cc_final: 0.7133 (ptp-110) REVERT: A 850 ASP cc_start: 0.8550 (m-30) cc_final: 0.8241 (m-30) REVERT: A 876 ASP cc_start: 0.8824 (p0) cc_final: 0.8566 (p0) REVERT: A 885 ASN cc_start: 0.8849 (t0) cc_final: 0.8639 (t0) REVERT: A 893 MET cc_start: 0.7747 (mmp) cc_final: 0.7456 (mmt) REVERT: A 922 MET cc_start: 0.6962 (ttt) cc_final: 0.6642 (ttt) REVERT: A 956 LYS cc_start: 0.9026 (mppt) cc_final: 0.8385 (mttm) REVERT: B 38 ASP cc_start: 0.8392 (m-30) cc_final: 0.7718 (t70) REVERT: B 353 MET cc_start: 0.4665 (tpt) cc_final: 0.4385 (mpp) REVERT: B 776 TYR cc_start: 0.5864 (t80) cc_final: 0.5457 (t80) REVERT: C 77 GLU cc_start: 0.7250 (pm20) cc_final: 0.7031 (mt-10) REVERT: C 80 MET cc_start: 0.8242 (mmp) cc_final: 0.7951 (tpp) REVERT: C 93 GLN cc_start: 0.8672 (mt0) cc_final: 0.8425 (mt0) REVERT: C 166 ILE cc_start: 0.7802 (tp) cc_final: 0.7551 (pt) REVERT: C 205 SER cc_start: 0.8878 (t) cc_final: 0.8070 (m) REVERT: D 80 MET cc_start: 0.8130 (tpt) cc_final: 0.7653 (tpt) REVERT: E 28 ARG cc_start: 0.7266 (mpt90) cc_final: 0.6850 (mpt180) REVERT: E 89 CYS cc_start: 0.8535 (t) cc_final: 0.7735 (p) REVERT: E 258 PRO cc_start: 0.8908 (Cg_endo) cc_final: 0.8610 (Cg_exo) REVERT: E 273 ASN cc_start: 0.9267 (p0) cc_final: 0.8685 (p0) REVERT: E 321 ARG cc_start: 0.8547 (ptt180) cc_final: 0.8127 (ptt180) REVERT: E 377 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.7783 (tpt170) REVERT: E 407 LEU cc_start: 0.8906 (pp) cc_final: 0.8687 (mt) REVERT: E 473 MET cc_start: 0.8540 (ptp) cc_final: 0.8244 (ptm) REVERT: E 475 VAL cc_start: 0.9431 (t) cc_final: 0.9216 (t) REVERT: E 482 GLU cc_start: 0.7941 (tp30) cc_final: 0.7711 (tp30) REVERT: E 524 ASN cc_start: 0.7251 (t0) cc_final: 0.6783 (t0) REVERT: E 551 ASP cc_start: 0.8323 (t0) cc_final: 0.8063 (t0) REVERT: F 19 GLU cc_start: 0.7759 (tp30) cc_final: 0.7241 (tp30) REVERT: F 62 ILE cc_start: 0.8846 (mt) cc_final: 0.8425 (mm) REVERT: G 156 ASP cc_start: 0.8160 (m-30) cc_final: 0.7638 (m-30) REVERT: G 196 GLU cc_start: 0.7628 (pm20) cc_final: 0.7416 (mp0) REVERT: S 278 MET cc_start: -0.0501 (ttt) cc_final: -0.4179 (mtt) REVERT: U 278 MET cc_start: -0.2742 (ttm) cc_final: -0.4789 (mmt) REVERT: V 157 MET cc_start: 0.3312 (mmm) cc_final: 0.2828 (mmm) REVERT: X 120 MET cc_start: 0.7751 (ppp) cc_final: 0.7479 (mtt) outliers start: 2 outliers final: 0 residues processed: 529 average time/residue: 0.2866 time to fit residues: 253.5933 Evaluate side-chains 393 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 521 optimal weight: 20.0000 chunk 220 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 241 optimal weight: 10.0000 chunk 314 optimal weight: 0.7980 chunk 233 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 318 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 86 optimal weight: 0.0980 chunk 295 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 ASN E 484 GLN E 616 ASN G 87 GLN S 52 ASN ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.170977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.136840 restraints weight = 136956.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.134027 restraints weight = 190381.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.135527 restraints weight = 176293.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.134930 restraints weight = 119982.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.135743 restraints weight = 107464.386| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3953 r_free = 0.3953 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3953 r_free = 0.3953 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 1.0282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 47260 Z= 0.175 Angle : 0.941 32.442 64862 Z= 0.477 Chirality : 0.050 0.447 7467 Planarity : 0.007 0.188 7705 Dihedral : 19.864 172.982 8207 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.78 % Allowed : 15.48 % Favored : 83.74 % Rotamer: Outliers : 0.04 % Allowed : 1.27 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.19 (0.10), residues: 5289 helix: -1.89 (0.12), residues: 1579 sheet: -3.13 (0.23), residues: 378 loop : -3.41 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG E 346 TYR 0.033 0.002 TYR A 698 PHE 0.070 0.003 PHE A 516 TRP 0.048 0.002 TRP E 416 HIS 0.010 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00384 (47240) covalent geometry : angle 0.93724 (64850) SS BOND : bond 0.01547 ( 6) SS BOND : angle 6.40483 ( 12) hydrogen bonds : bond 0.05153 ( 1181) hydrogen bonds : angle 6.51335 ( 3100) Misc. bond : bond 0.00698 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 544 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8591 (ptt-90) cc_final: 0.8329 (ptt-90) REVERT: A 118 ASP cc_start: 0.6344 (m-30) cc_final: 0.4398 (p0) REVERT: A 188 ASP cc_start: 0.7089 (m-30) cc_final: 0.6723 (m-30) REVERT: A 344 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6431 (tm-30) REVERT: A 541 MET cc_start: 0.9177 (mmp) cc_final: 0.8667 (mmm) REVERT: A 559 MET cc_start: 0.8560 (tpp) cc_final: 0.7549 (mmm) REVERT: A 684 GLN cc_start: 0.8633 (mp10) cc_final: 0.8396 (mp10) REVERT: A 685 ASN cc_start: 0.9126 (m-40) cc_final: 0.8906 (m-40) REVERT: A 706 GLU cc_start: 0.7935 (tt0) cc_final: 0.7582 (tt0) REVERT: A 749 ARG cc_start: 0.7486 (ptp-110) cc_final: 0.7223 (ptp-110) REVERT: A 758 ARG cc_start: 0.8402 (mtt90) cc_final: 0.8169 (mtt90) REVERT: A 850 ASP cc_start: 0.8785 (m-30) cc_final: 0.8458 (m-30) REVERT: A 922 MET cc_start: 0.6887 (ttt) cc_final: 0.6627 (ttt) REVERT: A 956 LYS cc_start: 0.8919 (mppt) cc_final: 0.8278 (mttt) REVERT: B 38 ASP cc_start: 0.7993 (m-30) cc_final: 0.7500 (t70) REVERT: B 776 TYR cc_start: 0.5904 (t80) cc_final: 0.5366 (t80) REVERT: C 80 MET cc_start: 0.8213 (mmp) cc_final: 0.7931 (tpp) REVERT: C 93 GLN cc_start: 0.8662 (mt0) cc_final: 0.8449 (mt0) REVERT: C 205 SER cc_start: 0.8802 (t) cc_final: 0.8104 (m) REVERT: D 80 MET cc_start: 0.8034 (tpt) cc_final: 0.7481 (tpt) REVERT: E 28 ARG cc_start: 0.7299 (mpt90) cc_final: 0.6764 (mpt180) REVERT: E 164 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7251 (mt-10) REVERT: E 261 GLN cc_start: 0.8353 (mm110) cc_final: 0.7633 (mm110) REVERT: E 272 LEU cc_start: 0.9502 (mt) cc_final: 0.9262 (mt) REVERT: E 273 ASN cc_start: 0.9146 (p0) cc_final: 0.8561 (p0) REVERT: E 321 ARG cc_start: 0.8465 (ptt180) cc_final: 0.8058 (ptt180) REVERT: E 382 GLU cc_start: 0.8519 (mp0) cc_final: 0.8152 (mp0) REVERT: E 459 LEU cc_start: 0.9374 (tp) cc_final: 0.9073 (tt) REVERT: E 482 GLU cc_start: 0.7871 (tp30) cc_final: 0.7634 (tp30) REVERT: E 524 ASN cc_start: 0.7226 (t0) cc_final: 0.6634 (t0) REVERT: E 551 ASP cc_start: 0.7978 (t0) cc_final: 0.7734 (t0) REVERT: F 19 GLU cc_start: 0.7663 (tp30) cc_final: 0.7190 (tp30) REVERT: F 37 ASN cc_start: 0.8631 (p0) cc_final: 0.8394 (m-40) REVERT: F 62 ILE cc_start: 0.8212 (mt) cc_final: 0.7807 (mm) REVERT: G 156 ASP cc_start: 0.8092 (m-30) cc_final: 0.7470 (m-30) REVERT: G 174 MET cc_start: 0.8330 (tmm) cc_final: 0.8076 (tmm) REVERT: G 188 SER cc_start: 0.9273 (m) cc_final: 0.8770 (t) REVERT: G 266 MET cc_start: 0.6044 (mtt) cc_final: 0.5750 (mmt) REVERT: G 301 PHE cc_start: 0.7465 (m-80) cc_final: 0.7233 (m-80) REVERT: S 157 MET cc_start: 0.2531 (mmp) cc_final: 0.2106 (mmm) REVERT: S 278 MET cc_start: -0.0440 (ttt) cc_final: -0.4190 (mtt) REVERT: U 278 MET cc_start: -0.2912 (ttm) cc_final: -0.4735 (mmt) REVERT: V 157 MET cc_start: 0.3057 (mmm) cc_final: 0.2774 (mmm) REVERT: X 120 MET cc_start: 0.7799 (ppp) cc_final: 0.7554 (mtt) outliers start: 2 outliers final: 1 residues processed: 544 average time/residue: 0.2244 time to fit residues: 207.0860 Evaluate side-chains 397 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 382 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 350 optimal weight: 0.5980 chunk 174 optimal weight: 0.0060 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 303 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 184 optimal weight: 9.9990 chunk 510 optimal weight: 8.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN A 802 ASN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS B 92 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN D 38 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 ASN ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 HIS ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.171879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.140553 restraints weight = 138834.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.137053 restraints weight = 216368.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.138708 restraints weight = 215707.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.138013 restraints weight = 145278.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.138684 restraints weight = 132837.475| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 1.0572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 47260 Z= 0.173 Angle : 0.932 41.924 64862 Z= 0.472 Chirality : 0.050 0.497 7467 Planarity : 0.008 0.401 7705 Dihedral : 19.747 172.965 8207 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.74 % Allowed : 15.30 % Favored : 83.97 % Rotamer: Outliers : 0.02 % Allowed : 0.66 % Favored : 99.32 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.03 (0.10), residues: 5289 helix: -1.77 (0.12), residues: 1572 sheet: -2.88 (0.25), residues: 345 loop : -3.31 (0.10), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.056 0.001 ARG E 346 TYR 0.033 0.002 TYR A 698 PHE 0.081 0.002 PHE E 345 TRP 0.040 0.003 TRP U 294 HIS 0.009 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00382 (47240) covalent geometry : angle 0.92846 (64850) SS BOND : bond 0.01602 ( 6) SS BOND : angle 5.83803 ( 12) hydrogen bonds : bond 0.05062 ( 1181) hydrogen bonds : angle 6.39831 ( 3100) Misc. bond : bond 0.01159 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 550 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.6175 (m-30) cc_final: 0.4371 (p0) REVERT: A 188 ASP cc_start: 0.7210 (m-30) cc_final: 0.6920 (m-30) REVERT: A 344 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6463 (tm-30) REVERT: A 559 MET cc_start: 0.8353 (tpp) cc_final: 0.7472 (mmm) REVERT: A 680 LEU cc_start: 0.8990 (mm) cc_final: 0.8718 (mm) REVERT: A 685 ASN cc_start: 0.9201 (m-40) cc_final: 0.8977 (m110) REVERT: A 706 GLU cc_start: 0.8010 (tt0) cc_final: 0.7648 (tt0) REVERT: A 712 ASP cc_start: 0.7829 (m-30) cc_final: 0.7628 (m-30) REVERT: A 749 ARG cc_start: 0.7358 (ptp-110) cc_final: 0.6869 (ptp-110) REVERT: A 956 LYS cc_start: 0.8733 (mppt) cc_final: 0.8223 (mttt) REVERT: A 984 HIS cc_start: 0.7247 (m170) cc_final: 0.6736 (t-170) REVERT: B 38 ASP cc_start: 0.7764 (m-30) cc_final: 0.7293 (t70) REVERT: B 308 MET cc_start: 0.8174 (mmm) cc_final: 0.7892 (mmm) REVERT: B 325 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8308 (tp30) REVERT: B 1213 PHE cc_start: 0.6383 (p90) cc_final: 0.6153 (p90) REVERT: C 205 SER cc_start: 0.8734 (t) cc_final: 0.8116 (m) REVERT: D 80 MET cc_start: 0.7865 (tpt) cc_final: 0.7351 (tpt) REVERT: E 28 ARG cc_start: 0.7510 (mpt90) cc_final: 0.6789 (mpt180) REVERT: E 164 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7397 (mt-10) REVERT: E 233 ASN cc_start: 0.9066 (m-40) cc_final: 0.8483 (m-40) REVERT: E 273 ASN cc_start: 0.9156 (p0) cc_final: 0.8610 (p0) REVERT: E 405 LYS cc_start: 0.8158 (pptt) cc_final: 0.7840 (pttt) REVERT: E 524 ASN cc_start: 0.7200 (t0) cc_final: 0.6968 (t0) REVERT: E 543 MET cc_start: 0.8071 (mpp) cc_final: 0.7767 (mpp) REVERT: F 19 GLU cc_start: 0.7389 (tp30) cc_final: 0.7169 (tp30) REVERT: F 37 ASN cc_start: 0.8650 (p0) cc_final: 0.8371 (m-40) REVERT: F 62 ILE cc_start: 0.8084 (mt) cc_final: 0.7773 (mm) REVERT: G 156 ASP cc_start: 0.8216 (m-30) cc_final: 0.7502 (m-30) REVERT: G 174 MET cc_start: 0.8378 (tmm) cc_final: 0.8141 (tmm) REVERT: G 188 SER cc_start: 0.9215 (m) cc_final: 0.8743 (t) REVERT: G 196 GLU cc_start: 0.7866 (mp0) cc_final: 0.7571 (mp0) REVERT: G 266 MET cc_start: 0.6135 (mtt) cc_final: 0.5914 (mmt) REVERT: G 343 LEU cc_start: 0.7137 (tp) cc_final: 0.6860 (tp) REVERT: S 157 MET cc_start: 0.2278 (mmp) cc_final: 0.1790 (mmm) REVERT: S 278 MET cc_start: -0.0360 (ttt) cc_final: -0.3960 (mtt) REVERT: T 146 MET cc_start: -0.3943 (mtm) cc_final: -0.4486 (mtt) REVERT: U 278 MET cc_start: -0.2750 (ttm) cc_final: -0.4854 (mmt) REVERT: V 157 MET cc_start: 0.2581 (mmm) cc_final: 0.1548 (mpp) outliers start: 1 outliers final: 0 residues processed: 550 average time/residue: 0.1995 time to fit residues: 187.6312 Evaluate side-chains 405 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 200 optimal weight: 50.0000 chunk 81 optimal weight: 5.9990 chunk 102 optimal weight: 0.0870 chunk 352 optimal weight: 0.6980 chunk 533 optimal weight: 5.9990 chunk 338 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 404 optimal weight: 50.0000 chunk 535 optimal weight: 0.8980 chunk 212 optimal weight: 7.9990 chunk 90 optimal weight: 0.3980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS B 92 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN D 207 GLN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 HIS ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 7 GLN ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 295 GLN ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.171741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.138624 restraints weight = 136445.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.134843 restraints weight = 203854.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.135959 restraints weight = 190902.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.136858 restraints weight = 125057.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.136667 restraints weight = 116867.030| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 1.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 47260 Z= 0.169 Angle : 0.889 14.833 64862 Z= 0.452 Chirality : 0.048 0.368 7467 Planarity : 0.007 0.147 7705 Dihedral : 19.646 173.417 8207 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.39 % Favored : 83.91 % Rotamer: Outliers : 0.04 % Allowed : 0.57 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.92 (0.10), residues: 5289 helix: -1.66 (0.12), residues: 1572 sheet: -2.84 (0.25), residues: 332 loop : -3.26 (0.10), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG E 346 TYR 0.033 0.002 TYR A 698 PHE 0.095 0.002 PHE A 516 TRP 0.031 0.002 TRP U 294 HIS 0.011 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00372 (47240) covalent geometry : angle 0.88543 (64850) SS BOND : bond 0.01426 ( 6) SS BOND : angle 5.51081 ( 12) hydrogen bonds : bond 0.04935 ( 1181) hydrogen bonds : angle 6.32400 ( 3100) Misc. bond : bond 0.01123 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7850.70 seconds wall clock time: 137 minutes 19.05 seconds (8239.05 seconds total)