Starting phenix.real_space_refine on Mon Aug 10 09:22:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3v_34475/08_2026/8h3v_34475_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3v_34475/08_2026/8h3v_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 { model { file = "/net/cci-nas-00/data/ceres_data/8h3v_34475/08_2026/8h3v_34475_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3v_34475/08_2026/8h3v_34475_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h3v_34475/08_2026/8h3v_34475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3v_34475/08_2026/8h3v_34475.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.88, per 1000 atoms: 0.17 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: 4.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 5.72 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: 9.94 Time building geometry restraints manager: 5.53 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 1.20e-02 6.94e+03 1.25e+04 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 - 15.60: 64658 15.60 - 31.19: 174 31.19 - 46.79: 14 46.79 - 62.39: 2 62.39 - 77.99: 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 119.70 41.71 77.99 1.20e+00 6.94e-01 4.22e+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=" 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 angle pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " pdb=" OP1 DA 1 46 " ideal model delta sigma weight residual 108.00 53.54 54.46 3.00e+00 1.11e-01 3.29e+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 - 0.528: 7423 0.528 - 1.055: 42 1.055 - 1.583: 0 1.583 - 2.111: 1 2.111 - 2.638: 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 -2.73 -0.09 -2.64 2.00e-01 2.50e+01 1.74e+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: 3.670 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: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 42.840 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 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= 1.739 Angle : 2.816 77.987 64862 Z= 1.652 Chirality : 0.140 2.638 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 are 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/Z covalent geometry : bond 0.03022 / 1.64 (47240) covalent geometry : angle 2.79996 / 1.65 (64850) SS BOND : bond 0.38274 / 21.20 ( 6) SS BOND : angle 22.34491 / 30.16 ( 12) hydrogen bonds : bond 0.30159 / 33.78 ( 1181) hydrogen bonds : angle 13.92798 / 18.56 ( 3100) Misc. bond : bond 0.31712 / 29.79 ( 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 : 1.398 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: 0.6990 (mmp) REVERT: B 77 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8038 (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: 0.6848 (m) REVERT: B 1128 VAL cc_start: 0.8999 (t) cc_final: 0.8783 (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: 0.7491 (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: 0.8107 (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: 0.7308 (p0) REVERT: E 420 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7308 (tm-30) REVERT: E 441 ILE cc_start: 0.8517 (mt) cc_final: 0.8297 (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: 0.7960 (tt) REVERT: G 156 ASP cc_start: 0.8681 (m-30) cc_final: 0.8477 (m-30) REVERT: G 165 LEU cc_start: 0.2480 (OUTLIER) cc_final: 0.1802 (pp) REVERT: G 173 TYR cc_start: 0.7044 (m-80) cc_final: 0.6719 (m-10) REVERT: G 184 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7587 (tt) REVERT: S 151 LEU cc_start: 0.0564 (OUTLIER) cc_final: -0.0082 (mp) REVERT: S 278 MET cc_start: -0.4996 (mmm) cc_final: -0.5235 (mtt) REVERT: S 287 ILE cc_start: 0.0363 (OUTLIER) cc_final: 0.0130 (pt) REVERT: T 99 SER cc_start: 0.2299 (OUTLIER) cc_final: 0.2019 (t) REVERT: T 167 ILE cc_start: -0.0513 (OUTLIER) cc_final: -0.0870 (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: 0.0068 (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: -0.2821 (m-10) REVERT: V 25 CYS cc_start: -0.2055 (OUTLIER) cc_final: -0.3354 (t) REVERT: V 157 MET cc_start: 0.3823 (mmm) cc_final: 0.3233 (tpt) REVERT: V 167 ILE cc_start: -0.1988 (OUTLIER) cc_final: -0.2210 (mt) REVERT: X 145 MET cc_start: 0.5034 (mtt) cc_final: 0.4830 (mpp) REVERT: X 187 ARG cc_start: 0.4018 (tpm-80) cc_final: 0.3816 (tpt170) 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: 0.2736 time to fit residues: 505.5784 Evaluate side-chains 591 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 482 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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: 6.9990 chunk 430 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 chunk 523 optimal weight: 6.9990 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: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 385 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 933 HIS ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 HIS ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 HIS D 102 ASN E 81 HIS E 101 HIS ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN E 261 GLN E 281 ASN E 328 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 ** G 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 53 HIS S 89 GLN S 147 ASN ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 235 GLN S 282 GLN T 98 HIS T 110 GLN ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 218 GLN ** T 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 174 ASN ** V 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 193 GLN V 295 GLN ** 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: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.173774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.141648 restraints weight = 146474.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.139787 restraints weight = 203676.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.140860 restraints weight = 161895.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.141729 restraints weight = 116293.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.141700 restraints weight = 104088.486| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4032 r_free = 0.4032 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.181 47260 Z= 0.426 Angle : 1.544 24.072 64862 Z= 0.796 Chirality : 0.077 0.755 7467 Planarity : 0.013 0.218 7705 Dihedral : 21.451 169.037 8207 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 48.11 Ramachandran Plot: Outliers : 1.53 % Allowed : 21.10 % Favored : 77.37 % Rotamer: Outliers : 3.13 % Allowed : 11.52 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 2.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.31 (0.08), residues: 5289 helix: -3.83 (0.09), residues: 1481 sheet: -4.65 (0.21), residues: 295 loop : -4.66 (0.08), residues: 3513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.002 ARG A 993 TYR 0.055 0.005 TYR V 200 PHE 0.058 0.005 PHE Y 75 TRP 0.044 0.005 TRP B 98 HIS 0.034 0.005 HIS V 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00923 / 0.42 (47240) covalent geometry : angle 1.54126 / 0.79 (64850) SS BOND : bond 0.03982 / 3.07 ( 6) SS BOND : angle 6.94409 / 11.59 ( 12) hydrogen bonds : bond 0.10667 / 11.68 ( 1181) hydrogen bonds : angle 9.39985 / 12.91 ( 3100) Misc. bond : bond 0.02704 / 2.08 ( 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 835 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 692 time to evaluate : 1.299 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 48 GLU cc_start: 0.8057 (mp0) cc_final: 0.7583 (tm-30) REVERT: A 258 ASP cc_start: 0.8945 (p0) cc_final: 0.8357 (p0) REVERT: A 301 VAL cc_start: 0.8646 (t) cc_final: 0.8365 (p) REVERT: A 344 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6377 (tm-30) REVERT: A 378 PHE cc_start: 0.7721 (m-10) cc_final: 0.7441 (m-80) REVERT: A 545 LEU cc_start: 0.9313 (tp) cc_final: 0.8854 (tp) REVERT: A 573 LEU cc_start: 0.9109 (tt) cc_final: 0.8908 (tt) REVERT: A 578 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8571 (tt) REVERT: A 581 GLN cc_start: 0.8051 (pm20) cc_final: 0.7184 (pp30) REVERT: A 584 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7675 (ttm110) REVERT: A 646 ASN cc_start: 0.7819 (t0) cc_final: 0.7449 (t0) REVERT: A 679 GLU cc_start: 0.7748 (pm20) cc_final: 0.7543 (pm20) REVERT: A 694 GLU cc_start: 0.7558 (pm20) cc_final: 0.7023 (tt0) REVERT: A 728 GLN cc_start: 0.6893 (mp-120) cc_final: 0.6312 (pp30) REVERT: A 876 ASP cc_start: 0.8490 (p0) cc_final: 0.8000 (t0) REVERT: A 887 LEU cc_start: 0.9101 (mt) cc_final: 0.8814 (mt) REVERT: A 893 MET cc_start: 0.7380 (mtt) cc_final: 0.6895 (mtt) REVERT: A 900 GLU cc_start: 0.9167 (pm20) cc_final: 0.8573 (pm20) REVERT: A 1016 ARG cc_start: 0.8156 (tpt-90) cc_final: 0.7929 (ttt-90) REVERT: A 1038 LEU cc_start: 0.9081 (mm) cc_final: 0.8785 (mt) REVERT: A 1050 GLU cc_start: 0.8804 (tt0) cc_final: 0.8326 (tt0) REVERT: A 1074 MET cc_start: 0.8014 (tmm) cc_final: 0.7792 (tmm) REVERT: A 1076 GLU cc_start: 0.8331 (pt0) cc_final: 0.7875 (pt0) REVERT: B 55 ASP cc_start: 0.8107 (t0) cc_final: 0.7876 (t0) REVERT: B 125 MET cc_start: 0.8740 (mpp) cc_final: 0.8039 (mpp) REVERT: B 225 MET cc_start: 0.8523 (ttt) cc_final: 0.8238 (ttt) REVERT: B 232 LEU cc_start: 0.7808 (tt) cc_final: 0.7435 (tt) REVERT: B 693 MET cc_start: 0.7921 (mpp) cc_final: 0.7504 (mpp) REVERT: B 1121 LEU cc_start: 0.9461 (mt) cc_final: 0.9227 (mp) REVERT: B 1221 THR cc_start: 0.7865 (p) cc_final: 0.7658 (m) REVERT: C 170 PHE cc_start: 0.6831 (m-80) cc_final: 0.6346 (m-80) REVERT: D 9 VAL cc_start: 0.7310 (m) cc_final: 0.7067 (t) REVERT: D 61 VAL cc_start: 0.4039 (t) cc_final: 0.3816 (t) REVERT: D 82 MET cc_start: 0.7058 (mmp) cc_final: 0.6695 (mmm) REVERT: D 86 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8480 (tp) REVERT: D 183 VAL cc_start: 0.8514 (t) cc_final: 0.7892 (m) REVERT: E 76 TYR cc_start: 0.5867 (m-10) cc_final: 0.5599 (m-80) REVERT: E 251 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9081 (t) REVERT: E 338 ILE cc_start: 0.8013 (pt) cc_final: 0.7139 (pt) REVERT: E 339 GLU cc_start: 0.8065 (mp0) cc_final: 0.7389 (mp0) REVERT: E 346 ARG cc_start: 0.5090 (ttm-80) cc_final: 0.4467 (ttm-80) REVERT: E 368 LEU cc_start: 0.9194 (pp) cc_final: 0.8937 (pp) REVERT: E 379 MET cc_start: 0.8128 (ptp) cc_final: 0.7578 (mtm) REVERT: E 407 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8365 (mt) REVERT: E 429 MET cc_start: 0.7000 (ptp) cc_final: 0.6527 (mtt) REVERT: E 468 PHE cc_start: 0.9031 (m-80) cc_final: 0.8713 (m-80) REVERT: E 513 MET cc_start: 0.8533 (mtt) cc_final: 0.8162 (mtt) REVERT: G 112 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: G 185 GLN cc_start: 0.8304 (mm110) cc_final: 0.8073 (tp40) REVERT: G 230 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7687 (mtm-85) REVERT: V 157 MET cc_start: 0.2737 (mmm) cc_final: 0.2087 (mmm) REVERT: X 90 TYR cc_start: 0.6177 (m-80) cc_final: 0.5770 (m-80) REVERT: X 145 MET cc_start: 0.5681 (mtt) cc_final: 0.4722 (mpp) REVERT: Y 132 GLN cc_start: 0.6726 (mp10) cc_final: 0.6524 (mt0) outliers start: 143 outliers final: 34 residues processed: 818 average time/residue: 0.2494 time to fit residues: 340.4387 Evaluate side-chains 515 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 474 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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: 9.9990 chunk 318 optimal weight: 2.9990 chunk 484 optimal weight: 40.0000 chunk 79 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 510 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 295 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 55 optimal weight: 0.9980 chunk 535 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN A 389 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** 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 652 ASN ** 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 847 GLN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 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 B 760 GLN B 761 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 GLN B 989 GLN C 19 HIS C 95 GLN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 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 233 ASN ** 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 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** ** G 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 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** U 53 HIS U 120 GLN ** U 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 282 GLN ** V 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 91 HIS X 142 HIS ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.173116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.139846 restraints weight = 145825.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.137469 restraints weight = 163890.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.138970 restraints weight = 157970.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.138032 restraints weight = 111955.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.138304 restraints weight = 119983.147| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3974 r_free = 0.3974 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3974 r_free = 0.3974 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.6369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 47260 Z= 0.292 Angle : 1.179 21.296 64862 Z= 0.611 Chirality : 0.062 0.432 7467 Planarity : 0.009 0.178 7705 Dihedral : 20.810 167.612 8207 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 39.18 Ramachandran Plot: Outliers : 1.10 % Allowed : 20.33 % Favored : 78.58 % Rotamer: Outliers : 0.55 % Allowed : 7.97 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 1.01 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.61 (0.09), residues: 5289 helix: -3.14 (0.10), residues: 1475 sheet: -4.42 (0.21), residues: 331 loop : -4.22 (0.09), residues: 3483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 993 TYR 0.053 0.004 TYR S 104 PHE 0.035 0.004 PHE C 163 TRP 0.037 0.004 TRP E 416 HIS 0.019 0.002 HIS E 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.29 (47240) covalent geometry : angle 1.17702 / 0.61 (64850) SS BOND : bond 0.01254 / 0.84 ( 6) SS BOND : angle 5.62713 / 9.28 ( 12) hydrogen bonds : bond 0.08297 / 9.29 ( 1181) hydrogen bonds : angle 8.43467 / 11.67 ( 3100) Misc. bond : bond 0.02885 / 2.75 ( 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 665 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 640 time to evaluate : 1.105 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: A 102 LEU cc_start: 0.7757 (mt) cc_final: 0.7498 (mt) REVERT: A 128 PHE cc_start: 0.8367 (m-10) cc_final: 0.8044 (m-10) REVERT: A 192 LYS cc_start: 0.5067 (pttm) cc_final: 0.4669 (ptpt) REVERT: A 344 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6367 (tm-30) REVERT: A 378 PHE cc_start: 0.7236 (m-10) cc_final: 0.6907 (m-10) REVERT: A 395 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7522 (mm-30) REVERT: A 535 VAL cc_start: 0.9059 (m) cc_final: 0.8829 (m) REVERT: A 542 ILE cc_start: 0.9197 (mt) cc_final: 0.8947 (mt) REVERT: A 545 LEU cc_start: 0.9239 (tp) cc_final: 0.8992 (tp) REVERT: A 646 ASN cc_start: 0.7878 (t0) cc_final: 0.7665 (t0) REVERT: A 694 GLU cc_start: 0.7706 (pm20) cc_final: 0.7313 (tt0) REVERT: A 735 GLU cc_start: 0.7875 (tt0) cc_final: 0.7674 (tt0) REVERT: A 748 LEU cc_start: 0.8942 (pp) cc_final: 0.8722 (tp) REVERT: A 881 ASP cc_start: 0.9137 (p0) cc_final: 0.8757 (p0) REVERT: A 900 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8376 (pm20) REVERT: B 51 ILE cc_start: 0.8835 (pt) cc_final: 0.8427 (tp) REVERT: B 55 ASP cc_start: 0.8340 (t0) cc_final: 0.7471 (t0) REVERT: B 56 LEU cc_start: 0.8371 (mt) cc_final: 0.8021 (mt) REVERT: B 67 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.9120 (pp20) REVERT: B 143 MET cc_start: 0.4794 (tmm) cc_final: 0.4272 (tmm) REVERT: B 261 ASN cc_start: 0.7675 (m110) cc_final: 0.6548 (t0) REVERT: B 353 MET cc_start: 0.4758 (tpt) cc_final: 0.4204 (mpp) REVERT: B 1121 LEU cc_start: 0.9319 (mt) cc_final: 0.8781 (mt) REVERT: B 1127 MET cc_start: 0.8224 (tmm) cc_final: 0.7886 (tmm) REVERT: C 74 ASP cc_start: 0.8064 (t0) cc_final: 0.7122 (p0) REVERT: C 77 GLU cc_start: 0.7661 (pm20) cc_final: 0.6590 (mt-10) REVERT: C 199 TRP cc_start: 0.7921 (m100) cc_final: 0.7431 (m100) REVERT: D 166 ILE cc_start: 0.8760 (tt) cc_final: 0.8531 (tt) REVERT: D 183 VAL cc_start: 0.8309 (t) cc_final: 0.7492 (m) REVERT: D 193 ARG cc_start: 0.8493 (ttm110) cc_final: 0.8017 (ptp-110) REVERT: E 81 HIS cc_start: 0.7410 (t-90) cc_final: 0.7203 (t-90) REVERT: E 244 MET cc_start: 0.7597 (mtt) cc_final: 0.7302 (mtt) REVERT: E 321 ARG cc_start: 0.8534 (ptt180) cc_final: 0.8136 (ptt90) REVERT: E 339 GLU cc_start: 0.8096 (mp0) cc_final: 0.7793 (mp0) REVERT: E 407 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8574 (mp) REVERT: E 596 ASP cc_start: 0.7374 (t0) cc_final: 0.7144 (t0) REVERT: G 78 THR cc_start: 0.8107 (t) cc_final: 0.7863 (m) REVERT: G 174 MET cc_start: 0.7112 (ppp) cc_final: 0.6714 (ppp) REVERT: S 278 MET cc_start: -0.1987 (ttt) cc_final: -0.5003 (mtp) REVERT: T 278 MET cc_start: -0.2055 (ptt) cc_final: -0.2521 (ptt) REVERT: V 157 MET cc_start: 0.2514 (mmm) cc_final: 0.1977 (mmm) REVERT: X 145 MET cc_start: 0.5258 (mtt) cc_final: 0.4611 (mpp) outliers start: 25 outliers final: 8 residues processed: 661 average time/residue: 0.2398 time to fit residues: 267.2589 Evaluate side-chains 461 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 450 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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: 0.0980 chunk 187 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 457 optimal weight: 10.0000 chunk 287 optimal weight: 0.8980 chunk 214 optimal weight: 40.0000 chunk 445 optimal weight: 20.0000 chunk 541 optimal weight: 0.0010 chunk 427 optimal weight: 0.0570 chunk 467 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN A 215 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 ASN ** 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 ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN A 802 ASN ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 92 GLN B 99 ASN B 133 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** 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 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 HIS E 484 GLN ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 549 GLN E 616 ASN F 13 GLN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 382 ASN ** 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 132 GLN X 176 HIS ** Y 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.174122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.138651 restraints weight = 140229.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.137163 restraints weight = 174884.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.138406 restraints weight = 152430.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.137999 restraints weight = 120084.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.138523 restraints weight = 107309.157| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3986 r_free = 0.3986 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 = 0.3986 r_free = 0.3986 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 47260 Z= 0.227 Angle : 1.092 20.425 64862 Z= 0.559 Chirality : 0.059 0.628 7467 Planarity : 0.009 0.319 7705 Dihedral : 20.539 168.673 8207 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 32.91 Ramachandran Plot: Outliers : 0.98 % Allowed : 17.66 % Favored : 81.36 % Rotamer: Outliers : 0.42 % Allowed : 7.45 % Favored : 92.14 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.20 (0.10), residues: 5289 helix: -2.80 (0.11), residues: 1506 sheet: -4.09 (0.21), residues: 317 loop : -3.97 (0.09), residues: 3466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG A 159 TYR 0.039 0.003 TYR E 105 PHE 0.044 0.003 PHE X 152 TRP 0.036 0.003 TRP E 416 HIS 0.010 0.002 HIS S 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.23 (47240) covalent geometry : angle 1.08812 / 0.56 (64850) SS BOND : bond 0.02060 / 2.04 ( 6) SS BOND : angle 6.52754 / 10.90 ( 12) hydrogen bonds : bond 0.07259 / 7.99 ( 1181) hydrogen bonds : angle 7.83287 / 10.82 ( 3100) Misc. bond : bond 0.01452 / 1.44 ( 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: 19 poor density : 633 time to evaluate : 1.537 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: A 31 ILE cc_start: 0.9134 (tp) cc_final: 0.8752 (tp) REVERT: A 53 PHE cc_start: 0.6685 (m-80) cc_final: 0.6380 (m-80) REVERT: A 102 LEU cc_start: 0.7672 (mt) cc_final: 0.7370 (mt) REVERT: A 184 TRP cc_start: 0.7459 (m100) cc_final: 0.7067 (m100) REVERT: A 192 LYS cc_start: 0.4950 (pttm) cc_final: 0.4711 (ptpt) REVERT: A 210 PHE cc_start: 0.7102 (m-80) cc_final: 0.6723 (t80) REVERT: A 344 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6022 (tm-30) REVERT: A 535 VAL cc_start: 0.9197 (m) cc_final: 0.8932 (m) REVERT: A 585 ASP cc_start: 0.7727 (m-30) cc_final: 0.7411 (m-30) REVERT: A 646 ASN cc_start: 0.7763 (t0) cc_final: 0.7448 (t0) REVERT: A 667 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7648 (pp30) REVERT: A 694 GLU cc_start: 0.7391 (pm20) cc_final: 0.7094 (tt0) REVERT: A 702 ILE cc_start: 0.9378 (mm) cc_final: 0.9149 (mm) REVERT: A 871 MET cc_start: 0.7844 (ttm) cc_final: 0.7616 (ttm) REVERT: A 876 ASP cc_start: 0.8386 (p0) cc_final: 0.7618 (t0) REVERT: B 55 ASP cc_start: 0.8044 (t0) cc_final: 0.7744 (t0) REVERT: B 143 MET cc_start: 0.5216 (tmm) cc_final: 0.4911 (tmm) REVERT: B 261 ASN cc_start: 0.7622 (m110) cc_final: 0.6948 (p0) REVERT: B 273 GLU cc_start: 0.6876 (tp30) cc_final: 0.6655 (tp30) REVERT: B 353 MET cc_start: 0.4605 (tpt) cc_final: 0.4188 (mpp) REVERT: B 1114 LEU cc_start: 0.9212 (mt) cc_final: 0.8956 (tt) REVERT: C 42 ARG cc_start: 0.8457 (mtp180) cc_final: 0.7486 (mtt90) REVERT: C 74 ASP cc_start: 0.7993 (t0) cc_final: 0.6992 (p0) REVERT: C 77 GLU cc_start: 0.7674 (pm20) cc_final: 0.6739 (mm-30) REVERT: C 137 GLU cc_start: 0.7750 (pm20) cc_final: 0.7547 (pm20) REVERT: C 166 ILE cc_start: 0.7967 (tp) cc_final: 0.7281 (pt) REVERT: C 167 ASP cc_start: 0.5673 (p0) cc_final: 0.5173 (p0) REVERT: C 199 TRP cc_start: 0.7770 (m100) cc_final: 0.7405 (m100) REVERT: D 183 VAL cc_start: 0.8262 (t) cc_final: 0.7550 (m) REVERT: D 193 ARG cc_start: 0.8378 (ttm110) cc_final: 0.8001 (ptm160) REVERT: E 70 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6459 (tt0) REVERT: E 81 HIS cc_start: 0.7306 (t-90) cc_final: 0.6933 (t-90) REVERT: E 129 LEU cc_start: 0.8675 (mt) cc_final: 0.8169 (mt) REVERT: E 273 ASN cc_start: 0.8554 (p0) cc_final: 0.7961 (p0) REVERT: E 338 ILE cc_start: 0.8030 (pt) cc_final: 0.7107 (pt) REVERT: E 339 GLU cc_start: 0.8026 (mp0) cc_final: 0.7211 (pm20) REVERT: E 379 MET cc_start: 0.8286 (ptp) cc_final: 0.8033 (ptp) REVERT: E 407 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8608 (mt) REVERT: E 475 VAL cc_start: 0.9329 (t) cc_final: 0.9096 (t) REVERT: E 519 TYR cc_start: 0.8902 (t80) cc_final: 0.8622 (t80) REVERT: E 596 ASP cc_start: 0.7356 (t0) cc_final: 0.7124 (t0) REVERT: G 266 MET cc_start: 0.7218 (mtt) cc_final: 0.6917 (mtt) REVERT: S 278 MET cc_start: -0.1552 (ttt) cc_final: -0.5228 (mtt) REVERT: T 278 MET cc_start: -0.2451 (ptt) cc_final: -0.2670 (ptt) REVERT: U 202 MET cc_start: -0.1596 (ptp) cc_final: -0.3211 (ptt) REVERT: V 157 MET cc_start: 0.2184 (mmm) cc_final: 0.1864 (mmm) REVERT: X 145 MET cc_start: 0.5534 (mtt) cc_final: 0.4878 (mpp) outliers start: 19 outliers final: 8 residues processed: 650 average time/residue: 0.2413 time to fit residues: 266.1125 Evaluate side-chains 464 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 454 time to evaluate : 1.665 ------------------------------------------------------------------------------- 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: 20.0000 chunk 512 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 376 optimal weight: 0.0060 chunk 143 optimal weight: 0.0570 chunk 502 optimal weight: 50.0000 chunk 133 optimal weight: 10.0000 chunk 402 optimal weight: 10.0000 chunk 243 optimal weight: 0.0010 chunk 474 optimal weight: 50.0000 chunk 489 optimal weight: 20.0000 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A 228 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 423 HIS ** 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 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN A 858 ASN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 347 GLN B 554 GLN ** B1112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 HIS ** 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 132 GLN X 176 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.170336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.136809 restraints weight = 144281.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.134034 restraints weight = 210161.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.135441 restraints weight = 190654.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.135243 restraints weight = 129569.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.135631 restraints weight = 119152.446| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3930 r_free = 0.3930 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3930 r_free = 0.3930 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.7701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 47260 Z= 0.276 Angle : 1.076 20.130 64862 Z= 0.556 Chirality : 0.057 0.507 7467 Planarity : 0.009 0.241 7705 Dihedral : 20.409 170.130 8207 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 32.52 Ramachandran Plot: Outliers : 0.87 % Allowed : 18.89 % Favored : 80.24 % Rotamer: Outliers : 0.15 % Allowed : 5.59 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.05 (0.10), residues: 5289 helix: -2.65 (0.11), residues: 1535 sheet: -3.84 (0.21), residues: 362 loop : -3.90 (0.09), residues: 3392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG A 993 TYR 0.042 0.003 TYR E 105 PHE 0.042 0.003 PHE Y 75 TRP 0.046 0.003 TRP E 416 HIS 0.012 0.002 HIS E 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.27 (47240) covalent geometry : angle 1.07244 / 0.55 (64850) SS BOND : bond 0.04252 / 3.50 ( 6) SS BOND : angle 6.49591 / 10.69 ( 12) hydrogen bonds : bond 0.06974 / 7.76 ( 1181) hydrogen bonds : angle 7.65260 / 10.65 ( 3100) Misc. bond : bond 0.01093 / 1.07 ( 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 598 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 591 time to evaluate : 1.679 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: A 53 PHE cc_start: 0.7060 (m-80) cc_final: 0.6669 (m-80) REVERT: A 265 LYS cc_start: 0.8391 (mtmt) cc_final: 0.8031 (tttt) REVERT: A 344 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6410 (tm-30) REVERT: A 597 ASP cc_start: 0.7532 (t70) cc_final: 0.7008 (p0) REVERT: A 646 ASN cc_start: 0.8160 (t0) cc_final: 0.7733 (t0) REVERT: A 749 ARG cc_start: 0.6857 (ptp-110) cc_final: 0.6607 (ptp-110) REVERT: A 846 ILE cc_start: 0.9097 (pt) cc_final: 0.8867 (pt) REVERT: A 876 ASP cc_start: 0.8841 (p0) cc_final: 0.8056 (t0) REVERT: A 1045 MET cc_start: 0.7479 (mpp) cc_final: 0.6587 (mpp) REVERT: A 1050 GLU cc_start: 0.8903 (tt0) cc_final: 0.8617 (tt0) REVERT: B 55 ASP cc_start: 0.8350 (t0) cc_final: 0.7933 (t0) REVERT: B 147 MET cc_start: 0.3791 (ptp) cc_final: 0.2960 (mmt) REVERT: B 317 ILE cc_start: 0.9462 (pt) cc_final: 0.9252 (mp) REVERT: B 353 MET cc_start: 0.4663 (tpt) cc_final: 0.4392 (mpp) REVERT: B 688 PRO cc_start: 0.7142 (OUTLIER) cc_final: 0.6875 (Cg_endo) REVERT: B 1237 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8060 (mp0) REVERT: C 32 GLN cc_start: 0.6738 (tp40) cc_final: 0.6166 (tp40) REVERT: C 76 LEU cc_start: 0.8685 (tp) cc_final: 0.8427 (tp) REVERT: C 93 GLN cc_start: 0.8606 (mt0) cc_final: 0.8299 (mt0) REVERT: C 100 LEU cc_start: 0.8751 (mt) cc_final: 0.8442 (mt) REVERT: C 166 ILE cc_start: 0.7598 (tp) cc_final: 0.7305 (pt) REVERT: C 199 TRP cc_start: 0.8058 (m100) cc_final: 0.7764 (m100) REVERT: D 80 MET cc_start: 0.7855 (tpt) cc_final: 0.7456 (tpt) REVERT: D 183 VAL cc_start: 0.8731 (t) cc_final: 0.7664 (m) REVERT: D 193 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8024 (ptp-110) REVERT: E 70 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6594 (tt0) REVERT: E 81 HIS cc_start: 0.7193 (t-90) cc_final: 0.6889 (t-90) REVERT: E 89 CYS cc_start: 0.8530 (t) cc_final: 0.7783 (p) REVERT: E 240 LYS cc_start: 0.8740 (mttm) cc_final: 0.8346 (mtpp) REVERT: E 242 GLU cc_start: 0.8775 (pm20) cc_final: 0.8514 (pm20) REVERT: E 273 ASN cc_start: 0.8907 (p0) cc_final: 0.8365 (p0) REVERT: E 338 ILE cc_start: 0.8091 (pt) cc_final: 0.7817 (pt) REVERT: E 346 ARG cc_start: 0.6090 (ttm-80) cc_final: 0.5027 (ttm-80) REVERT: E 407 LEU cc_start: 0.9181 (pp) cc_final: 0.8644 (mt) REVERT: E 473 MET cc_start: 0.8959 (ptm) cc_final: 0.8669 (ptm) REVERT: E 534 TYR cc_start: 0.7263 (p90) cc_final: 0.6926 (p90) REVERT: E 555 TYR cc_start: 0.6830 (m-80) cc_final: 0.6551 (m-80) REVERT: G 158 MET cc_start: 0.8076 (ppp) cc_final: 0.7592 (ppp) REVERT: G 266 MET cc_start: 0.7427 (mtt) cc_final: 0.7196 (mtt) REVERT: S 278 MET cc_start: -0.1140 (ttt) cc_final: -0.4883 (mtt) REVERT: T 278 MET cc_start: -0.3053 (ptt) cc_final: -0.3513 (ptt) REVERT: U 278 MET cc_start: -0.2185 (mtp) cc_final: -0.3965 (mmt) REVERT: V 157 MET cc_start: 0.2750 (mmm) cc_final: 0.2201 (mmm) REVERT: X 145 MET cc_start: 0.5268 (mtt) cc_final: 0.4855 (mpp) outliers start: 7 outliers final: 1 residues processed: 598 average time/residue: 0.2331 time to fit residues: 237.7038 Evaluate side-chains 428 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 426 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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: 1.9990 chunk 193 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 417 optimal weight: 0.9980 chunk 361 optimal weight: 1.9990 chunk 409 optimal weight: 10.0000 chunk 245 optimal weight: 0.8980 chunk 398 optimal weight: 50.0000 chunk 183 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 430 optimal weight: 50.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN A 856 HIS A 885 ASN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 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 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN B 422 GLN ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 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** E 114 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 ASN ** 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** ** G 162 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** ** V 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 132 GLN X 176 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.170416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.137522 restraints weight = 143600.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.134832 restraints weight = 216902.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.136468 restraints weight = 195226.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.135827 restraints weight = 143563.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.136831 restraints weight = 127904.333| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 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 = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.8220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 47260 Z= 0.235 Angle : 1.039 19.289 64862 Z= 0.531 Chirality : 0.056 0.619 7467 Planarity : 0.008 0.193 7705 Dihedral : 20.281 171.180 8207 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 30.29 Ramachandran Plot: Outliers : 0.78 % Allowed : 18.57 % Favored : 80.66 % Rotamer: Outliers : 0.18 % Allowed : 4.75 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.88 (0.10), residues: 5289 helix: -2.52 (0.11), residues: 1529 sheet: -3.65 (0.22), residues: 341 loop : -3.80 (0.09), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG E 282 TYR 0.042 0.003 TYR A 642 PHE 0.030 0.003 PHE X 35 TRP 0.047 0.003 TRP G 133 HIS 0.012 0.002 HIS A 856 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 (47240) covalent geometry : angle 1.03403 / 0.53 (64850) SS BOND : bond 0.03987 / 2.63 ( 6) SS BOND : angle 7.15687 / 11.86 ( 12) hydrogen bonds : bond 0.06468 / 7.13 ( 1181) hydrogen bonds : angle 7.31415 / 10.14 ( 3100) Misc. bond : bond 0.00737 / 0.75 ( 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 589 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 581 time to evaluate : 1.717 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: A 265 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8168 (tttt) REVERT: A 344 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6350 (tm-30) REVERT: A 387 MET cc_start: 0.8594 (tmm) cc_final: 0.8350 (tmm) REVERT: A 446 SER cc_start: 0.8086 (m) cc_final: 0.6556 (m) REVERT: A 646 ASN cc_start: 0.8047 (t0) cc_final: 0.7774 (t0) REVERT: A 706 GLU cc_start: 0.8013 (pt0) cc_final: 0.7413 (tt0) REVERT: A 876 ASP cc_start: 0.8856 (p0) cc_final: 0.8067 (t0) REVERT: A 984 HIS cc_start: 0.7628 (m170) cc_final: 0.7427 (m170) REVERT: A 1041 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8094 (tppp) REVERT: A 1045 MET cc_start: 0.7404 (mpp) cc_final: 0.6681 (mpp) REVERT: A 1050 GLU cc_start: 0.8784 (tt0) cc_final: 0.8386 (tt0) REVERT: B 55 ASP cc_start: 0.8211 (t0) cc_final: 0.7844 (t0) REVERT: B 120 ASN cc_start: 0.7957 (t0) cc_final: 0.7581 (m-40) REVERT: B 353 MET cc_start: 0.4852 (tpt) cc_final: 0.4547 (mpp) REVERT: B 1174 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7637 (tp30) REVERT: B 1237 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7934 (mp0) REVERT: C 32 GLN cc_start: 0.6566 (tp40) cc_final: 0.6363 (tp40) REVERT: C 80 MET cc_start: 0.8008 (mmp) cc_final: 0.7790 (tpp) REVERT: C 93 GLN cc_start: 0.8658 (mt0) cc_final: 0.8357 (mt0) REVERT: C 100 LEU cc_start: 0.8715 (mt) cc_final: 0.8445 (mt) REVERT: C 166 ILE cc_start: 0.7627 (tp) cc_final: 0.7347 (pt) REVERT: D 80 MET cc_start: 0.7667 (tpt) cc_final: 0.7258 (tpt) REVERT: D 183 VAL cc_start: 0.8694 (t) cc_final: 0.7743 (m) REVERT: D 193 ARG cc_start: 0.8313 (ttm110) cc_final: 0.7936 (ptp-110) REVERT: E 89 CYS cc_start: 0.8554 (t) cc_final: 0.7809 (p) REVERT: E 105 TYR cc_start: 0.7045 (p90) cc_final: 0.6827 (p90) REVERT: E 233 ASN cc_start: 0.9052 (m-40) cc_final: 0.8527 (m110) REVERT: E 242 GLU cc_start: 0.8615 (pm20) cc_final: 0.8389 (pm20) REVERT: E 273 ASN cc_start: 0.9181 (p0) cc_final: 0.8529 (p0) REVERT: E 346 ARG cc_start: 0.5837 (ttm-80) cc_final: 0.4498 (ttm-80) REVERT: E 377 ARG cc_start: 0.8750 (ttm-80) cc_final: 0.8505 (tpp80) REVERT: E 407 LEU cc_start: 0.9181 (pp) cc_final: 0.8711 (mt) REVERT: E 473 MET cc_start: 0.8944 (ptm) cc_final: 0.8623 (ptm) REVERT: E 513 MET cc_start: 0.8452 (mtt) cc_final: 0.8240 (mtp) REVERT: E 534 TYR cc_start: 0.7168 (p90) cc_final: 0.6666 (p90) REVERT: G 158 MET cc_start: 0.7878 (ppp) cc_final: 0.7516 (ppp) REVERT: G 266 MET cc_start: 0.7436 (mtt) cc_final: 0.7171 (mtt) REVERT: G 287 GLU cc_start: 0.8357 (tp30) cc_final: 0.8023 (tp30) REVERT: G 301 PHE cc_start: 0.7570 (m-80) cc_final: 0.7306 (m-80) REVERT: S 278 MET cc_start: -0.1056 (ttt) cc_final: -0.4839 (mtt) REVERT: T 278 MET cc_start: -0.2700 (ptt) cc_final: -0.3116 (ptt) REVERT: U 278 MET cc_start: -0.2390 (mtp) cc_final: -0.4079 (mmt) REVERT: V 157 MET cc_start: 0.3215 (mmm) cc_final: 0.2623 (mmm) REVERT: X 145 MET cc_start: 0.5216 (mtt) cc_final: 0.4840 (mpp) REVERT: Y 145 MET cc_start: 0.7384 (mpp) cc_final: 0.5890 (mmp) outliers start: 8 outliers final: 1 residues processed: 588 average time/residue: 0.2428 time to fit residues: 242.2212 Evaluate side-chains 428 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 426 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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: 0.9990 chunk 90 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 358 optimal weight: 0.9980 chunk 455 optimal weight: 9.9990 chunk 472 optimal weight: 9.9990 chunk 139 optimal weight: 0.7980 chunk 373 optimal weight: 0.0770 chunk 64 optimal weight: 7.9990 chunk 389 optimal weight: 30.0000 chunk 456 optimal weight: 50.0000 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 228 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 423 HIS ** 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 A 652 ASN A 684 GLN A 802 ASN A 885 ASN ** A1004 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 305 HIS ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN B 368 HIS ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 114 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN E 219 GLN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 263 ASN ** 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** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 132 GLN X 176 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.172001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.138118 restraints weight = 138173.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.134250 restraints weight = 219239.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.135448 restraints weight = 202799.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.135905 restraints weight = 148808.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.136764 restraints weight = 120391.247| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3958 r_free = 0.3958 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 = 0.3958 r_free = 0.3958 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.8569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 47260 Z= 0.193 Angle : 0.992 21.130 64862 Z= 0.505 Chirality : 0.055 0.620 7467 Planarity : 0.008 0.173 7705 Dihedral : 20.144 172.391 8207 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 28.15 Ramachandran Plot: Outliers : 0.74 % Allowed : 18.02 % Favored : 81.24 % Rotamer: Outliers : 0.13 % Allowed : 3.04 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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 are not related in a simple way. whole: -4.72 (0.10), residues: 5289 helix: -2.40 (0.11), residues: 1540 sheet: -3.59 (0.23), residues: 342 loop : -3.68 (0.09), residues: 3407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG E 282 TYR 0.037 0.002 TYR V 200 PHE 0.026 0.002 PHE V 229 TRP 0.056 0.003 TRP C 199 HIS 0.011 0.002 HIS C 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (47240) covalent geometry : angle 0.98820 / 0.50 (64850) SS BOND : bond 0.01439 / 0.86 ( 6) SS BOND : angle 6.19926 / 10.18 ( 12) hydrogen bonds : bond 0.06172 / 6.83 ( 1181) hydrogen bonds : angle 7.11450 / 9.90 ( 3100) Misc. bond : bond 0.00901 / 0.86 ( 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 583 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 577 time to evaluate : 1.462 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: A 210 PHE cc_start: 0.7208 (m-80) cc_final: 0.6684 (t80) REVERT: A 258 ASP cc_start: 0.8387 (p0) cc_final: 0.8144 (p0) REVERT: A 265 LYS cc_start: 0.8411 (mtmt) cc_final: 0.8135 (tttt) REVERT: A 330 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7731 (mp0) REVERT: A 344 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6375 (tm-30) REVERT: A 646 ASN cc_start: 0.7960 (t0) cc_final: 0.7653 (t0) REVERT: A 684 GLN cc_start: 0.8618 (mp10) cc_final: 0.8339 (mp10) REVERT: A 702 ILE cc_start: 0.8917 (mm) cc_final: 0.8697 (mm) REVERT: A 706 GLU cc_start: 0.8122 (pt0) cc_final: 0.7548 (tt0) REVERT: A 815 VAL cc_start: 0.8949 (p) cc_final: 0.8544 (p) REVERT: A 876 ASP cc_start: 0.8746 (p0) cc_final: 0.8002 (t70) REVERT: A 984 HIS cc_start: 0.7638 (m170) cc_final: 0.7291 (m170) REVERT: A 1045 MET cc_start: 0.7247 (mpp) cc_final: 0.6595 (mpp) REVERT: A 1050 GLU cc_start: 0.8650 (tt0) cc_final: 0.8367 (tt0) REVERT: B 55 ASP cc_start: 0.7978 (t0) cc_final: 0.7542 (t0) REVERT: B 120 ASN cc_start: 0.7767 (t0) cc_final: 0.7439 (m-40) REVERT: B 216 THR cc_start: 0.8294 (m) cc_final: 0.7951 (p) REVERT: B 321 GLN cc_start: 0.9406 (pt0) cc_final: 0.9184 (tt0) REVERT: B 353 MET cc_start: 0.4657 (tpt) cc_final: 0.4289 (mpp) REVERT: C 32 GLN cc_start: 0.6395 (tp40) cc_final: 0.6168 (tp40) REVERT: C 74 ASP cc_start: 0.7826 (t0) cc_final: 0.7026 (p0) REVERT: C 77 GLU cc_start: 0.7954 (pm20) cc_final: 0.6897 (mm-30) REVERT: C 93 GLN cc_start: 0.8644 (mt0) cc_final: 0.8318 (mt0) REVERT: C 100 LEU cc_start: 0.8680 (mt) cc_final: 0.8465 (mt) REVERT: C 166 ILE cc_start: 0.7475 (tp) cc_final: 0.7107 (pt) REVERT: C 199 TRP cc_start: 0.8529 (m100) cc_final: 0.7494 (m100) REVERT: D 183 VAL cc_start: 0.8664 (t) cc_final: 0.8185 (m) REVERT: D 193 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7587 (ttp-110) REVERT: E 89 CYS cc_start: 0.8499 (t) cc_final: 0.7820 (p) REVERT: E 117 TYR cc_start: 0.8625 (m-80) cc_final: 0.8264 (m-80) REVERT: E 233 ASN cc_start: 0.8981 (m-40) cc_final: 0.8386 (m-40) REVERT: E 273 ASN cc_start: 0.8927 (p0) cc_final: 0.8260 (p0) REVERT: E 407 LEU cc_start: 0.9023 (pp) cc_final: 0.8742 (mt) REVERT: E 513 MET cc_start: 0.8323 (mtt) cc_final: 0.8118 (mtt) REVERT: F 62 ILE cc_start: 0.9040 (mt) cc_final: 0.8571 (mt) REVERT: G 266 MET cc_start: 0.7312 (mtt) cc_final: 0.7105 (mtt) REVERT: G 301 PHE cc_start: 0.7463 (m-80) cc_final: 0.7252 (m-80) REVERT: S 278 MET cc_start: -0.1608 (ttt) cc_final: -0.5646 (mtt) REVERT: T 278 MET cc_start: -0.2945 (ptt) cc_final: -0.3256 (ptt) REVERT: V 157 MET cc_start: 0.3469 (mmm) cc_final: 0.2746 (mmm) REVERT: X 145 MET cc_start: 0.5186 (mtt) cc_final: 0.4934 (mpp) REVERT: Y 145 MET cc_start: 0.7295 (mpp) cc_final: 0.6416 (mmp) outliers start: 6 outliers final: 1 residues processed: 582 average time/residue: 0.2380 time to fit residues: 236.1570 Evaluate side-chains 419 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 418 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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: 0.0570 chunk 271 optimal weight: 8.9990 chunk 317 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 457 optimal weight: 50.0000 chunk 497 optimal weight: 10.0000 chunk 323 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 471 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 66 optimal weight: 0.1980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 228 GLN A 335 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1004 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 347 GLN ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN ** B1112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** 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 261 GLN ** E 348 ASN ** 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 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 263 ASN ** 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** U 5 GLN V 19 GLN ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 132 GLN X 176 HIS X 206 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.173331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.140311 restraints weight = 144439.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.136831 restraints weight = 197276.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.137958 restraints weight = 179945.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.139639 restraints weight = 118924.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.139174 restraints weight = 105659.119| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.8933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 47260 Z= 0.182 Angle : 0.994 23.364 64862 Z= 0.501 Chirality : 0.054 0.730 7467 Planarity : 0.008 0.241 7705 Dihedral : 20.066 172.223 8207 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 26.06 Ramachandran Plot: Outliers : 0.68 % Allowed : 16.77 % Favored : 82.55 % Rotamer: Outliers : 0.04 % Allowed : 2.32 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.57 % 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 are not related in a simple way. whole: -4.55 (0.10), residues: 5289 helix: -2.29 (0.11), residues: 1534 sheet: -3.51 (0.22), residues: 374 loop : -3.54 (0.09), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG E 282 TYR 0.031 0.002 TYR E 519 PHE 0.025 0.002 PHE S 9 TRP 0.045 0.003 TRP C 199 HIS 0.011 0.001 HIS C 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (47240) covalent geometry : angle 0.98873 / 0.50 (64850) SS BOND : bond 0.01672 / 1.43 ( 6) SS BOND : angle 7.61657 / 12.61 ( 12) hydrogen bonds : bond 0.05891 / 6.49 ( 1181) hydrogen bonds : angle 6.88389 / 9.59 ( 3100) Misc. bond : bond 0.00658 / 0.66 ( 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 583 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 581 time to evaluate : 1.621 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: A 67 PHE cc_start: 0.6621 (m-80) cc_final: 0.6356 (m-80) REVERT: A 127 THR cc_start: 0.7704 (t) cc_final: 0.6936 (t) REVERT: A 187 ILE cc_start: 0.8066 (pt) cc_final: 0.7614 (pt) REVERT: A 258 ASP cc_start: 0.8368 (p0) cc_final: 0.8118 (p0) REVERT: A 265 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8168 (tttt) REVERT: A 283 LEU cc_start: 0.8003 (pp) cc_final: 0.7772 (pp) REVERT: A 330 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7872 (mp0) REVERT: A 344 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6192 (tm-30) REVERT: A 646 ASN cc_start: 0.7994 (t0) cc_final: 0.7623 (t0) REVERT: A 706 GLU cc_start: 0.8122 (pt0) cc_final: 0.7105 (tt0) REVERT: A 757 ILE cc_start: 0.8395 (tt) cc_final: 0.8125 (tp) REVERT: A 850 ASP cc_start: 0.8462 (m-30) cc_final: 0.8062 (m-30) REVERT: A 871 MET cc_start: 0.8119 (ttm) cc_final: 0.7677 (ttm) REVERT: A 984 HIS cc_start: 0.7574 (m170) cc_final: 0.7289 (m170) REVERT: A 1045 MET cc_start: 0.7227 (mpp) cc_final: 0.6743 (mpp) REVERT: A 1050 GLU cc_start: 0.8783 (tt0) cc_final: 0.8326 (tt0) REVERT: B 38 ASP cc_start: 0.7891 (m-30) cc_final: 0.7095 (t0) REVERT: B 55 ASP cc_start: 0.7935 (t0) cc_final: 0.7598 (t0) REVERT: B 120 ASN cc_start: 0.7740 (t0) cc_final: 0.7386 (m-40) REVERT: B 155 ILE cc_start: 0.5414 (mt) cc_final: 0.5123 (mt) REVERT: B 216 THR cc_start: 0.8384 (m) cc_final: 0.7895 (p) REVERT: B 776 TYR cc_start: 0.5719 (t80) cc_final: 0.5214 (t80) REVERT: B 1011 LEU cc_start: 0.9297 (mt) cc_final: 0.8982 (mt) REVERT: C 32 GLN cc_start: 0.6428 (tp40) cc_final: 0.6227 (tp40) REVERT: C 77 GLU cc_start: 0.7490 (pm20) cc_final: 0.6578 (mt-10) REVERT: C 93 GLN cc_start: 0.8740 (mt0) cc_final: 0.8396 (mt0) REVERT: C 100 LEU cc_start: 0.8616 (mt) cc_final: 0.8364 (mt) REVERT: C 199 TRP cc_start: 0.8429 (m100) cc_final: 0.7345 (m100) REVERT: C 216 ILE cc_start: 0.8440 (mt) cc_final: 0.8165 (mm) REVERT: E 89 CYS cc_start: 0.8507 (t) cc_final: 0.7732 (p) REVERT: E 233 ASN cc_start: 0.8950 (m-40) cc_final: 0.8492 (m110) REVERT: E 240 LYS cc_start: 0.8601 (mttm) cc_final: 0.8118 (mtpp) REVERT: E 273 ASN cc_start: 0.8893 (p0) cc_final: 0.8226 (p0) REVERT: E 407 LEU cc_start: 0.9057 (pp) cc_final: 0.8802 (mt) REVERT: F 62 ILE cc_start: 0.8819 (mt) cc_final: 0.8383 (mt) REVERT: G 301 PHE cc_start: 0.7547 (m-80) cc_final: 0.7276 (m-80) REVERT: S 278 MET cc_start: -0.1010 (ttt) cc_final: -0.5233 (mtt) REVERT: U 278 MET cc_start: -0.3176 (mtt) cc_final: -0.3599 (mtt) REVERT: V 157 MET cc_start: 0.3680 (mmm) cc_final: 0.3047 (mmm) REVERT: Y 36 PHE cc_start: 0.8072 (t80) cc_final: 0.7863 (t80) REVERT: Y 72 ASN cc_start: 0.6934 (m-40) cc_final: 0.6572 (m-40) outliers start: 2 outliers final: 0 residues processed: 582 average time/residue: 0.2259 time to fit residues: 224.6354 Evaluate side-chains 423 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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: 8.9990 chunk 220 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 chunk 314 optimal weight: 0.7980 chunk 233 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 318 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 86 optimal weight: 0.0670 chunk 295 optimal weight: 0.6980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 228 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 GLN ** 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 347 GLN ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 GLN B 850 GLN B1112 HIS B1175 GLN C 47 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN ** E 114 HIS ** 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 204 GLN ** E 348 ASN ** 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 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 263 ASN ** 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** ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.172904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.140002 restraints weight = 143580.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.138222 restraints weight = 186298.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.139473 restraints weight = 173173.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.138764 restraints weight = 117624.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.138965 restraints weight = 129305.300| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.9178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 47260 Z= 0.182 Angle : 0.987 30.465 64862 Z= 0.498 Chirality : 0.054 0.589 7467 Planarity : 0.008 0.200 7705 Dihedral : 19.935 172.446 8207 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.70 % Allowed : 16.41 % Favored : 82.89 % Rotamer: Outliers : 0.09 % Allowed : 1.38 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.57 % 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 are not related in a simple way. whole: -4.48 (0.10), residues: 5289 helix: -2.24 (0.11), residues: 1554 sheet: -3.50 (0.23), residues: 350 loop : -3.50 (0.09), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.001 ARG E 346 TYR 0.035 0.002 TYR E 519 PHE 0.040 0.002 PHE A1028 TRP 0.035 0.003 TRP C 199 HIS 0.014 0.002 HIS V 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (47240) covalent geometry : angle 0.98288 / 0.50 (64850) SS BOND : bond 0.00651 / 0.71 ( 6) SS BOND : angle 6.87740 / 11.37 ( 12) hydrogen bonds : bond 0.05802 / 6.38 ( 1181) hydrogen bonds : angle 6.81987 / 9.50 ( 3100) Misc. bond : bond 0.01014 / 0.95 ( 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 557 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 553 time to evaluate : 1.115 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 188 ASP cc_start: 0.6453 (m-30) cc_final: 0.6019 (m-30) REVERT: A 258 ASP cc_start: 0.8394 (p0) cc_final: 0.8156 (p0) REVERT: A 265 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8129 (tttt) REVERT: A 330 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7991 (mp0) REVERT: A 344 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6310 (tm-30) REVERT: A 520 THR cc_start: 0.7151 (p) cc_final: 0.6878 (p) REVERT: A 646 ASN cc_start: 0.7886 (t0) cc_final: 0.7461 (t0) REVERT: A 757 ILE cc_start: 0.8384 (tt) cc_final: 0.8124 (tp) REVERT: A 958 MET cc_start: 0.8815 (tpp) cc_final: 0.8580 (tpt) REVERT: A 984 HIS cc_start: 0.7543 (m170) cc_final: 0.7278 (m170) REVERT: A 1045 MET cc_start: 0.7207 (mpp) cc_final: 0.6744 (mpp) REVERT: A 1050 GLU cc_start: 0.8748 (tt0) cc_final: 0.8331 (tt0) REVERT: A 1076 GLU cc_start: 0.8490 (pt0) cc_final: 0.8101 (pt0) REVERT: B 38 ASP cc_start: 0.7907 (m-30) cc_final: 0.7188 (t0) REVERT: B 55 ASP cc_start: 0.7608 (t0) cc_final: 0.7377 (t0) REVERT: B 120 ASN cc_start: 0.7690 (t0) cc_final: 0.7417 (m-40) REVERT: B 216 THR cc_start: 0.8400 (m) cc_final: 0.7962 (p) REVERT: B 321 GLN cc_start: 0.9477 (pt0) cc_final: 0.9144 (tt0) REVERT: B 776 TYR cc_start: 0.5594 (t80) cc_final: 0.5118 (t80) REVERT: B 1127 MET cc_start: 0.8096 (tmm) cc_final: 0.7850 (tmm) REVERT: C 77 GLU cc_start: 0.7480 (pm20) cc_final: 0.7095 (mt-10) REVERT: C 93 GLN cc_start: 0.8714 (mt0) cc_final: 0.8397 (mt0) REVERT: C 199 TRP cc_start: 0.8438 (m100) cc_final: 0.7295 (m100) REVERT: C 216 ILE cc_start: 0.8460 (mt) cc_final: 0.8213 (mm) REVERT: D 30 ARG cc_start: 0.7132 (ttp80) cc_final: 0.6882 (tpt170) REVERT: E 89 CYS cc_start: 0.8591 (t) cc_final: 0.7773 (p) REVERT: E 114 HIS cc_start: 0.8111 (t70) cc_final: 0.7851 (t70) REVERT: E 233 ASN cc_start: 0.9061 (m-40) cc_final: 0.8604 (m110) REVERT: E 240 LYS cc_start: 0.8766 (mttm) cc_final: 0.8235 (mtpt) REVERT: E 273 ASN cc_start: 0.9005 (p0) cc_final: 0.8378 (p0) REVERT: F 62 ILE cc_start: 0.8773 (mt) cc_final: 0.8387 (mt) REVERT: G 266 MET cc_start: 0.6540 (mtt) cc_final: 0.6074 (mmt) REVERT: S 278 MET cc_start: -0.1175 (ttt) cc_final: -0.4964 (mtt) REVERT: U 202 MET cc_start: -0.2669 (ptt) cc_final: -0.2968 (ptt) REVERT: U 278 MET cc_start: -0.2595 (mtt) cc_final: -0.2998 (mtt) REVERT: V 157 MET cc_start: 0.3244 (mmm) cc_final: 0.2679 (mmm) outliers start: 4 outliers final: 0 residues processed: 556 average time/residue: 0.2006 time to fit residues: 192.0620 Evaluate side-chains 406 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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: 5.9990 chunk 287 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 350 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 510 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 389 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1003 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 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN B1112 HIS ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN D 207 GLN E 114 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN E 476 HIS ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 263 ASN ** 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 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.170947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.135131 restraints weight = 143168.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.132510 restraints weight = 193627.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.134313 restraints weight = 158064.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.133502 restraints weight = 123151.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.134011 restraints weight = 111406.302| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.9437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 47260 Z= 0.202 Angle : 0.985 26.550 64862 Z= 0.498 Chirality : 0.054 0.738 7467 Planarity : 0.008 0.168 7705 Dihedral : 19.914 173.249 8207 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.74 % Allowed : 16.49 % Favored : 82.78 % Rotamer: Outliers : 0.07 % Allowed : 0.74 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.57 % 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 are not related in a simple way. whole: -4.35 (0.10), residues: 5289 helix: -2.15 (0.12), residues: 1526 sheet: -3.28 (0.24), residues: 353 loop : -3.42 (0.10), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG E 282 TYR 0.045 0.003 TYR D 178 PHE 0.027 0.002 PHE A1028 TRP 0.034 0.003 TRP C 199 HIS 0.012 0.002 HIS S 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (47240) covalent geometry : angle 0.97999 / 0.50 (64850) SS BOND : bond 0.01034 / 1.00 ( 6) SS BOND : angle 7.20950 / 11.74 ( 12) hydrogen bonds : bond 0.05826 / 6.36 ( 1181) hydrogen bonds : angle 6.76356 / 9.45 ( 3100) Misc. bond : bond 0.01490 / 1.38 ( 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 539 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 536 time to evaluate : 1.337 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: A 79 TYR cc_start: 0.7512 (m-10) cc_final: 0.6931 (m-80) REVERT: A 118 ASP cc_start: 0.5851 (m-30) cc_final: 0.4180 (p0) REVERT: A 188 ASP cc_start: 0.6552 (m-30) cc_final: 0.6230 (m-30) REVERT: A 258 ASP cc_start: 0.8484 (p0) cc_final: 0.8221 (p0) REVERT: A 265 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8169 (tttt) REVERT: A 283 LEU cc_start: 0.7963 (pp) cc_final: 0.7756 (pp) REVERT: A 330 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8003 (mp0) REVERT: A 344 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6453 (tm-30) REVERT: A 533 GLN cc_start: 0.8262 (mp10) cc_final: 0.8052 (mp10) REVERT: A 646 ASN cc_start: 0.7819 (t0) cc_final: 0.7457 (t0) REVERT: A 706 GLU cc_start: 0.7946 (tt0) cc_final: 0.7721 (tt0) REVERT: A 757 ILE cc_start: 0.8421 (tt) cc_final: 0.8123 (tp) REVERT: A 984 HIS cc_start: 0.7565 (m170) cc_final: 0.7301 (m170) REVERT: A 1045 MET cc_start: 0.7156 (mpp) cc_final: 0.6702 (mpp) REVERT: A 1050 GLU cc_start: 0.8606 (tt0) cc_final: 0.8394 (tt0) REVERT: A 1059 LYS cc_start: 0.6045 (mmtt) cc_final: 0.5749 (mptt) REVERT: B 38 ASP cc_start: 0.8031 (m-30) cc_final: 0.7304 (t0) REVERT: B 55 ASP cc_start: 0.7845 (t0) cc_final: 0.7574 (t0) REVERT: B 120 ASN cc_start: 0.7836 (t0) cc_final: 0.7555 (m-40) REVERT: B 353 MET cc_start: 0.4761 (tpt) cc_final: 0.4111 (ptp) REVERT: B 776 TYR cc_start: 0.5512 (t80) cc_final: 0.4960 (t80) REVERT: C 77 GLU cc_start: 0.7586 (pm20) cc_final: 0.7254 (mt-10) REVERT: C 93 GLN cc_start: 0.8686 (mt0) cc_final: 0.8377 (mt0) REVERT: C 199 TRP cc_start: 0.8376 (m100) cc_final: 0.7295 (m100) REVERT: C 216 ILE cc_start: 0.8585 (mt) cc_final: 0.8340 (mm) REVERT: D 30 ARG cc_start: 0.7337 (ttp80) cc_final: 0.6851 (tpt170) REVERT: E 89 CYS cc_start: 0.8558 (t) cc_final: 0.7760 (p) REVERT: E 114 HIS cc_start: 0.8691 (t-90) cc_final: 0.7973 (t-90) REVERT: E 233 ASN cc_start: 0.9009 (m-40) cc_final: 0.8506 (m-40) REVERT: E 273 ASN cc_start: 0.9089 (p0) cc_final: 0.8564 (p0) REVERT: E 452 ARG cc_start: 0.8128 (mmt180) cc_final: 0.7775 (mmm160) REVERT: E 486 GLU cc_start: 0.8234 (tp30) cc_final: 0.7550 (tp30) REVERT: E 491 MET cc_start: 0.7341 (mmt) cc_final: 0.7109 (mmp) REVERT: F 62 ILE cc_start: 0.8850 (mt) cc_final: 0.8422 (mt) REVERT: G 266 MET cc_start: 0.6416 (mtt) cc_final: 0.6065 (mmt) REVERT: G 343 LEU cc_start: 0.7583 (tp) cc_final: 0.7362 (tp) REVERT: S 278 MET cc_start: -0.0984 (ttt) cc_final: -0.4802 (mtt) REVERT: U 278 MET cc_start: -0.2658 (mtt) cc_final: -0.3323 (mtt) REVERT: V 157 MET cc_start: 0.2951 (mmm) cc_final: 0.2518 (mmm) REVERT: V 202 MET cc_start: -0.4062 (mmm) cc_final: -0.4379 (mmt) REVERT: Y 36 PHE cc_start: 0.8057 (t80) cc_final: 0.7855 (t80) outliers start: 3 outliers final: 0 residues processed: 538 average time/residue: 0.2023 time to fit residues: 187.8028 Evaluate side-chains 408 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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: 6.9990 chunk 81 optimal weight: 3.9990 chunk 102 optimal weight: 0.0000 chunk 352 optimal weight: 0.1980 chunk 533 optimal weight: 10.0000 chunk 338 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 404 optimal weight: 40.0000 chunk 535 optimal weight: 3.9990 chunk 212 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 389 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1003 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 850 GLN B1203 ASN ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN D 38 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** 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 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 193 GLN ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.173207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.138916 restraints weight = 137292.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.136839 restraints weight = 171512.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.138053 restraints weight = 159147.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.137179 restraints weight = 108636.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.137411 restraints weight = 121339.487| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3982 r_free = 0.3982 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3982 r_free = 0.3982 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.9679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 47260 Z= 0.173 Angle : 0.959 23.210 64862 Z= 0.483 Chirality : 0.052 0.613 7467 Planarity : 0.008 0.188 7705 Dihedral : 19.838 173.103 8207 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 24.04 Ramachandran Plot: Outliers : 0.76 % Allowed : 15.56 % Favored : 83.68 % Rotamer: Outliers : 0.07 % Allowed : 0.57 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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 are not related in a simple way. whole: -4.29 (0.10), residues: 5289 helix: -2.10 (0.12), residues: 1552 sheet: -3.18 (0.25), residues: 328 loop : -3.40 (0.10), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG E 346 TYR 0.043 0.002 TYR E 557 PHE 0.040 0.002 PHE Y 152 TRP 0.032 0.002 TRP C 199 HIS 0.011 0.001 HIS C 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (47240) covalent geometry : angle 0.95496 / 0.48 (64850) SS BOND : bond 0.00765 / 0.75 ( 6) SS BOND : angle 6.53553 / 10.67 ( 12) hydrogen bonds : bond 0.05562 / 6.04 ( 1181) hydrogen bonds : angle 6.63257 / 9.29 ( 3100) Misc. bond : bond 0.01008 / 0.95 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7031.81 seconds wall clock time: 122 minutes 58.10 seconds (7378.10 seconds total)