Starting phenix.real_space_refine on Thu Dec 26 14:40:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3v_34475/12_2024/8h3v_34475_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3v_34475/12_2024/8h3v_34475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h3v_34475/12_2024/8h3v_34475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3v_34475/12_2024/8h3v_34475.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3v_34475/12_2024/8h3v_34475_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3v_34475/12_2024/8h3v_34475_neut.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 1.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 25.78, per 1000 atoms: 0.56 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: 15.20 Conformation dependent library (CDL) restraints added in 6.0 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: 18.37 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: 21.55 Time building geometry restraints manager: 16.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.38: 18033 1.38 - 1.78: 29001 1.78 - 2.17: 205 2.17 - 2.56: 0 2.56 - 2.95: 1 Bond restraints: 47240 Sorted by residual: bond pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " ideal model delta sigma weight residual 1.607 2.949 -1.342 1.50e-02 4.44e+03 8.00e+03 bond pdb=" C GLY U 154 " pdb=" N ARG U 155 " ideal model delta sigma weight residual 1.332 1.733 -0.401 1.40e-02 5.10e+03 8.19e+02 bond pdb=" CA GLN G 87 " pdb=" C GLN G 87 " ideal model delta sigma weight residual 1.524 1.132 0.393 1.48e-02 4.57e+03 7.03e+02 bond pdb=" N PRO E 150 " pdb=" CD PRO E 150 " ideal model delta sigma weight residual 1.473 1.148 0.325 1.40e-02 5.10e+03 5.39e+02 bond pdb=" N PRO U 176 " pdb=" CD PRO U 176 " ideal model delta sigma weight residual 1.473 1.148 0.325 1.40e-02 5.10e+03 5.37e+02 ... (remaining 47235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.70: 64662 15.70 - 31.39: 170 31.39 - 47.09: 14 47.09 - 62.79: 2 62.79 - 78.49: 2 Bond angle restraints: 64850 Sorted by residual: angle pdb=" C3' DC 1 45 " pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " ideal model delta sigma weight residual 120.20 41.71 78.49 1.50e+00 4.44e-01 2.74e+03 angle pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " pdb=" OP2 DA 1 46 " ideal model delta sigma weight residual 108.00 172.28 -64.28 3.00e+00 1.11e-01 4.59e+02 angle pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " pdb=" O5' DA 1 46 " ideal model delta sigma weight residual 104.00 73.89 30.11 1.50e+00 4.44e-01 4.03e+02 angle pdb=" CA MET T 157 " pdb=" CB MET T 157 " pdb=" CG MET T 157 " ideal model delta sigma weight residual 114.10 152.37 -38.27 2.00e+00 2.50e-01 3.66e+02 angle pdb=" C PRO G 309 " pdb=" CA PRO G 309 " pdb=" CB PRO G 309 " ideal model delta sigma weight residual 111.56 87.93 23.63 1.27e+00 6.20e-01 3.46e+02 ... (remaining 64845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.44: 26229 32.44 - 64.87: 2174 64.87 - 97.31: 114 97.31 - 129.75: 1 129.75 - 162.18: 4 Dihedral angle restraints: 28522 sinusoidal: 13178 harmonic: 15344 Sorted by residual: dihedral pdb=" C MET T 157 " pdb=" N MET T 157 " pdb=" CA MET T 157 " pdb=" CB MET T 157 " ideal model delta harmonic sigma weight residual -122.60 -167.49 44.89 0 2.50e+00 1.60e-01 3.22e+02 dihedral pdb=" N MET T 157 " pdb=" C MET T 157 " pdb=" CA MET T 157 " pdb=" CB MET T 157 " ideal model delta harmonic sigma weight residual 122.80 166.92 -44.12 0 2.50e+00 1.60e-01 3.12e+02 dihedral pdb=" C PRO G 309 " pdb=" N PRO G 309 " pdb=" CA PRO G 309 " pdb=" CB PRO G 309 " ideal model delta harmonic sigma weight residual -120.70 -87.72 -32.98 0 2.50e+00 1.60e-01 1.74e+02 ... (remaining 28519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.514: 7418 0.514 - 1.027: 47 1.027 - 1.541: 0 1.541 - 2.054: 1 2.054 - 2.568: 1 Chirality restraints: 7467 Sorted by residual: chirality pdb=" C3' DG 1 13 " pdb=" C4' DG 1 13 " pdb=" O3' DG 1 13 " pdb=" C2' DG 1 13 " both_signs ideal model delta sigma weight residual False -2.66 -0.09 -2.57 2.00e-01 2.50e+01 1.65e+02 chirality pdb=" CA MET T 157 " pdb=" N MET T 157 " pdb=" C MET T 157 " pdb=" CB MET T 157 " both_signs ideal model delta sigma weight residual False 2.51 0.57 1.94 2.00e-01 2.50e+01 9.39e+01 chirality pdb=" CA ILE T 167 " pdb=" N ILE T 167 " pdb=" C ILE T 167 " pdb=" CB ILE T 167 " both_signs ideal model delta sigma weight residual False 2.43 1.42 1.01 2.00e-01 2.50e+01 2.56e+01 ... (remaining 7464 not shown) Planarity restraints: 7705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU S 84 " 0.086 2.00e-02 2.50e+03 1.70e-01 2.90e+02 pdb=" C LEU S 84 " -0.293 2.00e-02 2.50e+03 pdb=" O LEU S 84 " 0.125 2.00e-02 2.50e+03 pdb=" N ILE S 85 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU U 84 " -0.085 2.00e-02 2.50e+03 1.68e-01 2.82e+02 pdb=" C LEU U 84 " 0.290 2.00e-02 2.50e+03 pdb=" O LEU U 84 " -0.123 2.00e-02 2.50e+03 pdb=" N ILE U 85 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL T 195 " 0.066 2.00e-02 2.50e+03 1.32e-01 1.73e+02 pdb=" C VAL T 195 " -0.228 2.00e-02 2.50e+03 pdb=" O VAL T 195 " 0.083 2.00e-02 2.50e+03 pdb=" N PHE T 196 " 0.078 2.00e-02 2.50e+03 ... (remaining 7702 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.76: 52 1.76 - 2.54: 3930 2.54 - 3.33: 75632 3.33 - 4.11: 136149 4.11 - 4.90: 207172 Warning: very small nonbonded interaction distances. Nonbonded interactions: 422935 Sorted by model distance: nonbonded pdb=" CA PRO A 875 " pdb=" OH TYR A 960 " model vdw 0.972 3.470 nonbonded pdb=" O GLN T 193 " pdb=" CD1 LEU T 217 " model vdw 0.987 3.460 nonbonded pdb=" OE1 GLN U 5 " pdb=" CD GLN U 35 " model vdw 1.004 3.270 nonbonded pdb=" OH TYR V 180 " pdb=" CZ TYR V 191 " model vdw 1.155 3.260 nonbonded pdb=" CD GLN U 5 " pdb=" OE1 GLN U 35 " model vdw 1.183 3.270 ... (remaining 422930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'S' and (resid 1 through 262 or resid 272 through 303)) selection = chain 'T' selection = chain 'U' selection = (chain 'V' and (resid 1 through 262 or resid 272 through 303)) } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.890 Check model and map are aligned: 0.340 Set scattering table: 0.460 Process input model: 117.600 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.270 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: 0.020 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.030 1.342 47240 Z= 1.958 Angle : 2.794 78.487 64850 Z= 1.615 Chirality : 0.140 2.568 7467 Planarity : 0.022 0.436 7705 Dihedral : 20.268 162.182 18602 Min Nonbonded Distance : 0.972 Molprobity Statistics. All-atom Clashscore : 180.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.092 0.008 TRP C 199 HIS 0.072 0.007 HIS A 991 PHE 0.126 0.007 PHE G 301 TYR 0.186 0.008 TYR G 85 ARG 0.097 0.002 ARG A 607 *********************** 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 : 4.370 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: A 344 GLU cc_start: 0.8033 (mt-10) cc_final: 0.6730 (tm-30) REVERT: A 431 CYS cc_start: 0.8167 (t) cc_final: 0.6461 (p) REVERT: A 541 MET cc_start: 0.7258 (mmp) cc_final: 0.6989 (mmp) REVERT: B 77 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8038 (tm-30) REVERT: B 151 GLN cc_start: 0.5853 (mm-40) cc_final: 0.5202 (pp30) REVERT: B 648 VAL cc_start: 0.5636 (OUTLIER) cc_final: 0.5352 (m) REVERT: B 1119 THR cc_start: 0.7161 (p) cc_final: 0.6842 (m) REVERT: B 1128 VAL cc_start: 0.8999 (t) cc_final: 0.8778 (p) REVERT: C 77 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.6796 (mm-30) REVERT: C 169 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7473 (pt) REVERT: D 36 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8624 (m) REVERT: D 51 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8109 (t) REVERT: D 72 ARG cc_start: 0.8628 (mtp180) cc_final: 0.8259 (ttp80) REVERT: D 183 VAL cc_start: 0.7818 (t) cc_final: 0.7596 (t) REVERT: E 273 ASN cc_start: 0.7780 (p0) cc_final: 0.7309 (p0) REVERT: E 420 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7302 (tm-30) REVERT: E 587 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7769 (tt) REVERT: E 602 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.4723 (mm) REVERT: G 113 LEU cc_start: 0.8368 (mt) cc_final: 0.7978 (tt) REVERT: G 165 LEU cc_start: 0.2480 (OUTLIER) cc_final: 0.1812 (pp) REVERT: G 173 TYR cc_start: 0.7044 (m-80) cc_final: 0.6726 (m-10) REVERT: G 184 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7594 (tt) REVERT: S 151 LEU cc_start: 0.0564 (OUTLIER) cc_final: -0.0087 (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: 0.0131 (pt) REVERT: T 99 SER cc_start: 0.2299 (OUTLIER) cc_final: 0.2021 (t) REVERT: T 167 ILE cc_start: -0.0513 (OUTLIER) cc_final: -0.0875 (tt) REVERT: T 208 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5742 (pt0) REVERT: T 278 MET cc_start: 0.0870 (ptm) cc_final: 0.0018 (ptm) REVERT: U 182 ARG cc_start: 0.8691 (mtp180) cc_final: 0.8328 (mtm-85) REVERT: V 18 PHE cc_start: -0.2528 (OUTLIER) cc_final: -0.2839 (m-10) REVERT: V 25 CYS cc_start: -0.2055 (OUTLIER) cc_final: -0.3381 (t) REVERT: V 157 MET cc_start: 0.3823 (mmm) cc_final: 0.3331 (tpt) REVERT: Y 196 ASP cc_start: 0.6552 (OUTLIER) cc_final: 0.6233 (t0) outliers start: 337 outliers final: 90 residues processed: 1147 average time/residue: 0.6456 time to fit residues: 1178.8359 Evaluate side-chains 583 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 476 time to evaluate : 5.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 460 optimal weight: 9.9990 chunk 413 optimal weight: 4.9990 chunk 229 optimal weight: 30.0000 chunk 141 optimal weight: 8.9990 chunk 278 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 427 optimal weight: 50.0000 chunk 165 optimal weight: 0.0040 chunk 259 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 chunk 494 optimal weight: 5.9990 overall best weight: 2.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 255 GLN A 385 GLN A 389 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN A 858 ASN ** A 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** 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 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 ASN ** 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 D 38 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 HIS D 102 ASN D 222 ASN E 81 HIS E 101 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 281 ASN E 371 HIS E 431 ASN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 553 HIS E 568 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 HIS G 251 GLN S 53 HIS S 89 GLN S 147 ASN ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 235 GLN S 282 GLN ** S 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS T 110 GLN ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 218 GLN T 286 GLN U 53 HIS ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 148 ASN ** U 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 300 ASN ** V 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 174 ASN V 193 GLN ** V 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 47240 Z= 0.512 Angle : 1.376 22.225 64850 Z= 0.708 Chirality : 0.067 0.596 7467 Planarity : 0.012 0.179 7705 Dihedral : 21.061 166.623 8207 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 45.49 Ramachandran Plot: Outliers : 1.44 % Allowed : 20.65 % Favored : 77.92 % Rotamer: Outliers : 1.82 % Allowed : 10.47 % Favored : 87.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 1.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.23 (0.08), residues: 5289 helix: -3.73 (0.09), residues: 1466 sheet: -4.30 (0.22), residues: 313 loop : -4.65 (0.08), residues: 3510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP B 98 HIS 0.021 0.004 HIS S 292 PHE 0.047 0.005 PHE Y 75 TYR 0.047 0.004 TYR U 200 ARG 0.066 0.002 ARG A 993 *********************** 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 799 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 716 time to evaluate : 5.390 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: A 119 LEU cc_start: 0.5672 (pt) cc_final: 0.5470 (pt) REVERT: A 344 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6336 (tm-30) REVERT: A 378 PHE cc_start: 0.7436 (m-10) cc_final: 0.7117 (m-80) REVERT: A 400 ARG cc_start: 0.8943 (ptm160) cc_final: 0.8551 (ptm-80) REVERT: A 413 GLU cc_start: 0.8158 (pm20) cc_final: 0.7317 (pt0) REVERT: A 581 GLN cc_start: 0.8050 (pm20) cc_final: 0.7518 (pp30) REVERT: A 646 ASN cc_start: 0.7763 (t0) cc_final: 0.7488 (t0) REVERT: A 679 GLU cc_start: 0.7955 (pm20) cc_final: 0.7729 (pm20) REVERT: A 694 GLU cc_start: 0.7568 (pm20) cc_final: 0.6936 (tt0) REVERT: A 876 ASP cc_start: 0.8519 (p0) cc_final: 0.7819 (t0) REVERT: A 893 MET cc_start: 0.6952 (mtt) cc_final: 0.6661 (mtt) REVERT: A 900 GLU cc_start: 0.8723 (pm20) cc_final: 0.8310 (pm20) REVERT: A 1076 GLU cc_start: 0.8538 (pt0) cc_final: 0.7986 (pt0) REVERT: B 38 ASP cc_start: 0.8327 (m-30) cc_final: 0.8109 (m-30) REVERT: B 55 ASP cc_start: 0.8658 (t0) cc_final: 0.8391 (t0) REVERT: B 125 MET cc_start: 0.8755 (mpp) cc_final: 0.8132 (mpp) REVERT: B 155 ILE cc_start: 0.6467 (tp) cc_final: 0.6243 (tt) REVERT: B 225 MET cc_start: 0.8306 (ttt) cc_final: 0.8028 (ttt) REVERT: B 232 LEU cc_start: 0.7873 (tt) cc_final: 0.7595 (tt) REVERT: B 353 MET cc_start: 0.4666 (tpt) cc_final: 0.4295 (mpp) REVERT: B 538 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: B 693 MET cc_start: 0.8469 (mpp) cc_final: 0.8166 (mpp) REVERT: B 1121 LEU cc_start: 0.9262 (mt) cc_final: 0.8702 (mt) REVERT: B 1202 LEU cc_start: 0.8355 (mp) cc_final: 0.7935 (mp) REVERT: B 1221 THR cc_start: 0.7450 (p) cc_final: 0.7246 (m) REVERT: C 74 ASP cc_start: 0.7587 (t0) cc_final: 0.7287 (p0) REVERT: C 77 GLU cc_start: 0.7907 (pm20) cc_final: 0.6618 (mm-30) REVERT: C 80 MET cc_start: 0.8879 (mmm) cc_final: 0.8549 (mmp) REVERT: D 82 MET cc_start: 0.7215 (mmp) cc_final: 0.6792 (mmm) REVERT: D 86 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8312 (tp) REVERT: D 183 VAL cc_start: 0.8438 (t) cc_final: 0.7624 (m) REVERT: E 76 TYR cc_start: 0.5860 (m-10) cc_final: 0.5571 (m-80) REVERT: E 240 LYS cc_start: 0.8367 (mttp) cc_final: 0.7896 (mtpt) REVERT: E 338 ILE cc_start: 0.7834 (pt) cc_final: 0.7196 (pt) REVERT: E 339 GLU cc_start: 0.7833 (mp0) cc_final: 0.7538 (mp0) REVERT: E 371 HIS cc_start: 0.5881 (m-70) cc_final: 0.5508 (m-70) REVERT: E 379 MET cc_start: 0.7825 (ptp) cc_final: 0.7392 (mtm) REVERT: E 400 ASN cc_start: 0.5292 (t0) cc_final: 0.4571 (t0) REVERT: E 468 PHE cc_start: 0.9061 (m-80) cc_final: 0.8803 (m-10) REVERT: E 482 GLU cc_start: 0.7179 (pm20) cc_final: 0.6871 (pm20) REVERT: E 494 SER cc_start: 0.6111 (t) cc_final: 0.5677 (p) REVERT: E 513 MET cc_start: 0.8348 (mtt) cc_final: 0.7961 (mtt) REVERT: F 62 ILE cc_start: 0.9081 (mm) cc_final: 0.8718 (tt) REVERT: G 118 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8489 (pp20) REVERT: G 226 SER cc_start: 0.8445 (p) cc_final: 0.8229 (t) REVERT: G 266 MET cc_start: 0.6454 (mtt) cc_final: 0.6186 (mtt) REVERT: S 157 MET cc_start: -0.0409 (tpt) cc_final: -0.0629 (tpt) REVERT: U 182 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7397 (mtm-85) REVERT: V 157 MET cc_start: 0.2905 (mmm) cc_final: 0.2429 (mmm) REVERT: X 90 TYR cc_start: 0.5844 (m-80) cc_final: 0.5437 (m-80) outliers start: 83 outliers final: 21 residues processed: 791 average time/residue: 0.6075 time to fit residues: 794.4884 Evaluate side-chains 484 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 460 time to evaluate : 5.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 275 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 411 optimal weight: 6.9990 chunk 337 optimal weight: 0.0870 chunk 136 optimal weight: 0.9980 chunk 495 optimal weight: 20.0000 chunk 535 optimal weight: 20.0000 chunk 441 optimal weight: 10.0000 chunk 491 optimal weight: 50.0000 chunk 169 optimal weight: 2.9990 chunk 397 optimal weight: 0.0670 overall best weight: 1.2300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN A 333 GLN A 389 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 HIS ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN A 897 GLN ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 ASN B 92 GLN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 347 GLN ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN B 761 GLN ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 GLN B 989 GLN B1132 GLN ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 549 GLN F 13 GLN F 34 GLN G 87 GLN T 110 GLN ** T 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 120 GLN ** U 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 148 ASN X 91 HIS X 132 GLN X 142 HIS X 176 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.7008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 47240 Z= 0.335 Angle : 1.086 22.575 64850 Z= 0.559 Chirality : 0.057 0.428 7467 Planarity : 0.009 0.165 7705 Dihedral : 20.359 168.531 8207 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 32.26 Ramachandran Plot: Outliers : 0.96 % Allowed : 18.72 % Favored : 80.32 % Rotamer: Outliers : 0.66 % Allowed : 8.87 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.36 (0.09), residues: 5289 helix: -2.89 (0.11), residues: 1500 sheet: -3.90 (0.23), residues: 332 loop : -4.12 (0.09), residues: 3457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP E 416 HIS 0.018 0.002 HIS E 553 PHE 0.062 0.003 PHE U 229 TYR 0.045 0.003 TYR E 117 ARG 0.027 0.001 ARG A 993 *********************** 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 707 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 677 time to evaluate : 5.383 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 31 ILE cc_start: 0.9038 (tp) cc_final: 0.8755 (tp) REVERT: A 187 ILE cc_start: 0.6493 (tt) cc_final: 0.6177 (tt) REVERT: A 192 LYS cc_start: 0.5034 (pttm) cc_final: 0.4711 (ptpt) REVERT: A 330 GLU cc_start: 0.8333 (mp0) cc_final: 0.8125 (mp0) REVERT: A 344 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6299 (tm-30) REVERT: A 413 GLU cc_start: 0.8206 (pm20) cc_final: 0.7776 (pt0) REVERT: A 542 ILE cc_start: 0.9193 (mt) cc_final: 0.8972 (mt) REVERT: A 555 MET cc_start: 0.7535 (ppp) cc_final: 0.7329 (ppp) REVERT: A 585 ASP cc_start: 0.7435 (m-30) cc_final: 0.7107 (m-30) REVERT: A 646 ASN cc_start: 0.7618 (t0) cc_final: 0.7342 (t0) REVERT: A 679 GLU cc_start: 0.8060 (pm20) cc_final: 0.7281 (pm20) REVERT: A 876 ASP cc_start: 0.8566 (p0) cc_final: 0.7768 (t0) REVERT: A 922 MET cc_start: 0.6843 (ttt) cc_final: 0.6572 (ttt) REVERT: A 991 HIS cc_start: 0.7594 (t-90) cc_final: 0.7011 (t-170) REVERT: A 1015 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8347 (mm-40) REVERT: A 1076 GLU cc_start: 0.8599 (pt0) cc_final: 0.8397 (pt0) REVERT: A 1079 SER cc_start: 0.8378 (p) cc_final: 0.8135 (t) REVERT: B 51 ILE cc_start: 0.8925 (pt) cc_final: 0.8697 (tp) REVERT: B 55 ASP cc_start: 0.8322 (t0) cc_final: 0.7391 (t0) REVERT: B 56 LEU cc_start: 0.7984 (mt) cc_final: 0.7654 (mt) REVERT: B 67 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.9074 (pp20) REVERT: B 77 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7859 (tp30) REVERT: B 120 ASN cc_start: 0.7641 (t0) cc_final: 0.6986 (m-40) REVERT: B 214 CYS cc_start: 0.6428 (OUTLIER) cc_final: 0.2252 (m) REVERT: B 216 THR cc_start: 0.7880 (m) cc_final: 0.6880 (m) REVERT: B 225 MET cc_start: 0.8166 (ttt) cc_final: 0.7715 (ttt) REVERT: B 353 MET cc_start: 0.4634 (tpt) cc_final: 0.4355 (mpp) REVERT: B 1114 LEU cc_start: 0.8948 (mt) cc_final: 0.8101 (tp) REVERT: B 1121 LEU cc_start: 0.9062 (mt) cc_final: 0.8489 (mt) REVERT: B 1127 MET cc_start: 0.8005 (tmm) cc_final: 0.7775 (tmm) REVERT: B 1174 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: C 42 ARG cc_start: 0.7463 (mmm-85) cc_final: 0.7164 (mtt90) REVERT: C 74 ASP cc_start: 0.7186 (t0) cc_final: 0.6924 (p0) REVERT: C 77 GLU cc_start: 0.7545 (pm20) cc_final: 0.6895 (mt-10) REVERT: C 100 LEU cc_start: 0.8590 (mt) cc_final: 0.8373 (mt) REVERT: C 137 GLU cc_start: 0.7645 (pm20) cc_final: 0.7405 (pm20) REVERT: D 136 LEU cc_start: 0.7112 (tp) cc_final: 0.6820 (mp) REVERT: D 183 VAL cc_start: 0.8267 (t) cc_final: 0.7841 (m) REVERT: D 222 ASN cc_start: 0.5644 (t0) cc_final: 0.5009 (m-40) REVERT: D 224 LEU cc_start: 0.8124 (tp) cc_final: 0.7877 (tt) REVERT: E 54 MET cc_start: 0.7057 (ttm) cc_final: 0.6580 (tpt) REVERT: E 81 HIS cc_start: 0.7398 (t-90) cc_final: 0.7101 (t-90) REVERT: E 240 LYS cc_start: 0.8280 (mttp) cc_final: 0.7993 (mtpt) REVERT: E 242 GLU cc_start: 0.8989 (pm20) cc_final: 0.8632 (pm20) REVERT: E 273 ASN cc_start: 0.8511 (p0) cc_final: 0.7649 (p0) REVERT: E 314 ILE cc_start: 0.9328 (mp) cc_final: 0.9075 (tp) REVERT: E 321 ARG cc_start: 0.8176 (ptt180) cc_final: 0.7842 (ptt90) REVERT: E 338 ILE cc_start: 0.8170 (pt) cc_final: 0.7848 (pt) REVERT: E 339 GLU cc_start: 0.7669 (mp0) cc_final: 0.6975 (pm20) REVERT: E 371 HIS cc_start: 0.5932 (m-70) cc_final: 0.5670 (m-70) REVERT: E 494 SER cc_start: 0.6857 (t) cc_final: 0.6652 (p) REVERT: E 596 ASP cc_start: 0.7656 (t0) cc_final: 0.7380 (t0) REVERT: G 78 THR cc_start: 0.8212 (t) cc_final: 0.7775 (m) REVERT: G 87 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6687 (tm-30) REVERT: G 98 ASP cc_start: 0.7324 (p0) cc_final: 0.7120 (p0) REVERT: G 158 MET cc_start: 0.7994 (ppp) cc_final: 0.7537 (ppp) REVERT: G 174 MET cc_start: 0.6893 (ppp) cc_final: 0.6481 (ppp) REVERT: G 185 GLN cc_start: 0.8424 (tp40) cc_final: 0.8205 (mm-40) REVERT: G 236 TYR cc_start: 0.6413 (t80) cc_final: 0.6059 (t80) REVERT: G 266 MET cc_start: 0.6529 (mtt) cc_final: 0.6297 (mtt) REVERT: G 300 ASP cc_start: 0.6894 (m-30) cc_final: 0.6589 (m-30) REVERT: U 1 MET cc_start: 0.1418 (ttm) cc_final: 0.0584 (mtp) REVERT: U 182 ARG cc_start: 0.7563 (mtp180) cc_final: 0.6855 (mtm-85) REVERT: U 202 MET cc_start: -0.2744 (ptp) cc_final: -0.3039 (ptp) REVERT: V 157 MET cc_start: 0.3392 (mmm) cc_final: 0.2913 (mmm) REVERT: Y 36 PHE cc_start: 0.8072 (t80) cc_final: 0.7855 (t80) outliers start: 30 outliers final: 10 residues processed: 702 average time/residue: 0.5812 time to fit residues: 684.2075 Evaluate side-chains 491 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 477 time to evaluate : 5.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 489 optimal weight: 50.0000 chunk 372 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 236 optimal weight: 4.9990 chunk 332 optimal weight: 0.8980 chunk 497 optimal weight: 20.0000 chunk 526 optimal weight: 20.0000 chunk 259 optimal weight: 7.9990 chunk 471 optimal weight: 40.0000 chunk 141 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 500 ASN ** 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 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 ASN ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 347 GLN ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 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 328 ASN E 476 HIS ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** 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** U 282 GLN ** V 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.7821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 47240 Z= 0.393 Angle : 1.067 24.036 64850 Z= 0.545 Chirality : 0.055 0.494 7467 Planarity : 0.009 0.236 7705 Dihedral : 20.220 170.154 8207 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 31.83 Ramachandran Plot: Outliers : 0.91 % Allowed : 18.11 % Favored : 80.98 % Rotamer: Outliers : 0.20 % Allowed : 6.81 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.10), residues: 5289 helix: -2.54 (0.11), residues: 1487 sheet: -3.74 (0.23), residues: 335 loop : -3.91 (0.09), residues: 3467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.004 TRP S 294 HIS 0.019 0.003 HIS S 98 PHE 0.030 0.003 PHE U 229 TYR 0.029 0.003 TYR A 600 ARG 0.034 0.001 ARG E 282 *********************** 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 617 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 608 time to evaluate : 5.235 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: A 53 PHE cc_start: 0.6746 (m-80) cc_final: 0.6493 (m-80) REVERT: A 265 LYS cc_start: 0.8234 (mtmt) cc_final: 0.8014 (tttt) REVERT: A 317 ILE cc_start: 0.8798 (mt) cc_final: 0.8560 (mt) REVERT: A 344 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6489 (tm-30) REVERT: A 413 GLU cc_start: 0.8211 (pm20) cc_final: 0.7910 (pt0) REVERT: A 526 TYR cc_start: 0.7507 (m-80) cc_final: 0.7303 (m-10) REVERT: A 535 VAL cc_start: 0.8938 (m) cc_final: 0.8713 (m) REVERT: A 541 MET cc_start: 0.9155 (mmm) cc_final: 0.8844 (mmm) REVERT: A 566 LEU cc_start: 0.9514 (mp) cc_final: 0.9303 (mp) REVERT: A 585 ASP cc_start: 0.8010 (m-30) cc_final: 0.7737 (m-30) REVERT: A 646 ASN cc_start: 0.7897 (t0) cc_final: 0.7635 (t0) REVERT: A 702 ILE cc_start: 0.8969 (mm) cc_final: 0.8671 (mm) REVERT: A 876 ASP cc_start: 0.8832 (p0) cc_final: 0.7819 (t70) REVERT: A 922 MET cc_start: 0.6874 (ttt) cc_final: 0.6605 (ttt) REVERT: A 1050 GLU cc_start: 0.8777 (tt0) cc_final: 0.8213 (tt0) REVERT: B 55 ASP cc_start: 0.8392 (t0) cc_final: 0.8046 (t0) REVERT: B 120 ASN cc_start: 0.7578 (t0) cc_final: 0.7038 (m-40) REVERT: B 301 TRP cc_start: 0.7704 (m-10) cc_final: 0.7498 (m-10) REVERT: B 692 LEU cc_start: 0.9104 (mp) cc_final: 0.8822 (mp) REVERT: B 776 TYR cc_start: 0.5913 (t80) cc_final: 0.5630 (t80) REVERT: B 1127 MET cc_start: 0.7924 (tmm) cc_final: 0.7618 (tmm) REVERT: C 32 GLN cc_start: 0.6847 (tp40) cc_final: 0.6442 (tp40) REVERT: C 74 ASP cc_start: 0.7663 (t0) cc_final: 0.7016 (p0) REVERT: C 77 GLU cc_start: 0.7874 (pm20) cc_final: 0.6997 (mt-10) REVERT: D 80 MET cc_start: 0.7982 (tpt) cc_final: 0.7604 (tpt) REVERT: D 183 VAL cc_start: 0.8559 (t) cc_final: 0.7277 (m) REVERT: D 193 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7836 (ptp-110) REVERT: D 222 ASN cc_start: 0.6382 (t0) cc_final: 0.5746 (m110) REVERT: D 224 LEU cc_start: 0.8316 (tp) cc_final: 0.7773 (tt) REVERT: E 70 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6416 (tt0) REVERT: E 81 HIS cc_start: 0.7281 (t-90) cc_final: 0.6854 (t-90) REVERT: E 114 HIS cc_start: 0.8670 (t70) cc_final: 0.8390 (t70) REVERT: E 129 LEU cc_start: 0.8562 (mt) cc_final: 0.8291 (mt) REVERT: E 233 ASN cc_start: 0.8942 (m-40) cc_final: 0.8375 (m-40) REVERT: E 240 LYS cc_start: 0.8485 (mttp) cc_final: 0.8235 (mtpt) REVERT: E 273 ASN cc_start: 0.8821 (p0) cc_final: 0.8112 (p0) REVERT: E 338 ILE cc_start: 0.8485 (pt) cc_final: 0.7894 (pt) REVERT: E 339 GLU cc_start: 0.8113 (mp0) cc_final: 0.7516 (pm20) REVERT: E 348 ASN cc_start: 0.7241 (m110) cc_final: 0.6946 (t0) REVERT: E 407 LEU cc_start: 0.8615 (pp) cc_final: 0.8141 (mt) REVERT: E 423 ILE cc_start: 0.8738 (pt) cc_final: 0.8528 (pt) REVERT: E 596 ASP cc_start: 0.8074 (t0) cc_final: 0.7822 (t0) REVERT: G 78 THR cc_start: 0.8084 (t) cc_final: 0.7836 (m) REVERT: G 158 MET cc_start: 0.7917 (ppp) cc_final: 0.7632 (ppp) REVERT: G 196 GLU cc_start: 0.7666 (pm20) cc_final: 0.7350 (mp0) REVERT: G 236 TYR cc_start: 0.6227 (t80) cc_final: 0.5924 (t80) REVERT: G 266 MET cc_start: 0.6676 (mtt) cc_final: 0.6460 (mtt) REVERT: G 300 ASP cc_start: 0.6873 (m-30) cc_final: 0.6544 (m-30) REVERT: S 278 MET cc_start: -0.5892 (OUTLIER) cc_final: -0.6233 (mmm) REVERT: U 1 MET cc_start: 0.1315 (ttm) cc_final: 0.0746 (mtp) REVERT: U 182 ARG cc_start: 0.7458 (mtp180) cc_final: 0.6719 (mpp-170) REVERT: U 278 MET cc_start: 0.2638 (mtp) cc_final: 0.1146 (mmt) REVERT: V 157 MET cc_start: 0.3450 (mmm) cc_final: 0.3125 (mmm) outliers start: 9 outliers final: 3 residues processed: 616 average time/residue: 0.6007 time to fit residues: 618.3164 Evaluate side-chains 442 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 438 time to evaluate : 5.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 438 optimal weight: 5.9990 chunk 299 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 392 optimal weight: 50.0000 chunk 217 optimal weight: 30.0000 chunk 449 optimal weight: 8.9990 chunk 364 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 268 optimal weight: 4.9990 chunk 472 optimal weight: 0.9980 chunk 132 optimal weight: 0.0470 overall best weight: 3.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** 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 ** 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 647 GLN A 652 ASN ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** 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** B1203 ASN ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** 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 372 GLN E 426 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 ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 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 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.8627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 47240 Z= 0.396 Angle : 1.056 21.198 64850 Z= 0.539 Chirality : 0.054 0.454 7467 Planarity : 0.008 0.192 7705 Dihedral : 20.231 173.876 8207 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 29.92 Ramachandran Plot: Outliers : 0.93 % Allowed : 18.23 % Favored : 80.85 % Rotamer: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.10), residues: 5289 helix: -2.42 (0.11), residues: 1511 sheet: -3.61 (0.23), residues: 358 loop : -3.86 (0.09), residues: 3420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP E 416 HIS 0.013 0.002 HIS E 553 PHE 0.031 0.003 PHE C 163 TYR 0.044 0.003 TYR A 600 ARG 0.024 0.001 ARG A 607 *********************** 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 558 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 554 time to evaluate : 5.490 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 265 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8318 (tttt) REVERT: A 344 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6743 (tm-30) REVERT: A 541 MET cc_start: 0.9109 (mmm) cc_final: 0.8502 (mmm) REVERT: A 566 LEU cc_start: 0.9518 (mp) cc_final: 0.9304 (mp) REVERT: A 646 ASN cc_start: 0.8070 (t0) cc_final: 0.7703 (t0) REVERT: A 702 ILE cc_start: 0.9142 (mm) cc_final: 0.8757 (mm) REVERT: A 704 ILE cc_start: 0.9058 (tp) cc_final: 0.8819 (tp) REVERT: A 706 GLU cc_start: 0.7528 (pt0) cc_final: 0.7177 (tt0) REVERT: A 922 MET cc_start: 0.6755 (ttt) cc_final: 0.6493 (ttt) REVERT: A 1050 GLU cc_start: 0.8625 (tt0) cc_final: 0.8413 (tt0) REVERT: B 120 ASN cc_start: 0.7920 (t0) cc_final: 0.7616 (t0) REVERT: B 216 THR cc_start: 0.8592 (m) cc_final: 0.8213 (p) REVERT: B 1127 MET cc_start: 0.7869 (tmm) cc_final: 0.7567 (tmm) REVERT: B 1197 ILE cc_start: 0.8191 (pt) cc_final: 0.7851 (mp) REVERT: C 32 GLN cc_start: 0.6825 (tp40) cc_final: 0.6602 (tp40) REVERT: C 100 LEU cc_start: 0.8698 (mt) cc_final: 0.8376 (mt) REVERT: D 30 ARG cc_start: 0.7208 (ttp80) cc_final: 0.6832 (tpt170) REVERT: D 80 MET cc_start: 0.7914 (tpt) cc_final: 0.7433 (tpt) REVERT: D 183 VAL cc_start: 0.8783 (t) cc_final: 0.7666 (m) REVERT: D 193 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7878 (ptp-110) REVERT: D 222 ASN cc_start: 0.6984 (t0) cc_final: 0.6573 (m110) REVERT: E 81 HIS cc_start: 0.7109 (t-90) cc_final: 0.6836 (t-90) REVERT: E 233 ASN cc_start: 0.9001 (m-40) cc_final: 0.8565 (m-40) REVERT: E 240 LYS cc_start: 0.8767 (mttp) cc_final: 0.8242 (mtpt) REVERT: E 339 GLU cc_start: 0.8099 (mp0) cc_final: 0.6528 (pt0) REVERT: E 492 LEU cc_start: 0.8255 (tp) cc_final: 0.7953 (tp) REVERT: E 513 MET cc_start: 0.8246 (mtt) cc_final: 0.8046 (mtp) REVERT: G 158 MET cc_start: 0.8149 (ppp) cc_final: 0.7746 (ppp) REVERT: G 266 MET cc_start: 0.6583 (mtt) cc_final: 0.6310 (mtt) REVERT: G 345 ASP cc_start: 0.6926 (m-30) cc_final: 0.6465 (p0) REVERT: U 1 MET cc_start: 0.1163 (ttm) cc_final: 0.0691 (mtp) REVERT: U 182 ARG cc_start: 0.7410 (mtp180) cc_final: 0.6683 (mpp-170) REVERT: U 278 MET cc_start: 0.2324 (mtp) cc_final: 0.1462 (ttt) REVERT: V 157 MET cc_start: 0.4159 (mmm) cc_final: 0.3820 (mmm) REVERT: Y 36 PHE cc_start: 0.8310 (t80) cc_final: 0.8098 (t80) outliers start: 4 outliers final: 2 residues processed: 558 average time/residue: 0.5908 time to fit residues: 557.2236 Evaluate side-chains 406 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 404 time to evaluate : 5.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 177 optimal weight: 0.0970 chunk 474 optimal weight: 0.1980 chunk 104 optimal weight: 0.4980 chunk 309 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 527 optimal weight: 4.9990 chunk 437 optimal weight: 20.0000 chunk 244 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 174 optimal weight: 30.0000 chunk 276 optimal weight: 3.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 333 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN A 667 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** 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 19 HIS C 125 GLN ** 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 371 HIS E 484 GLN E 511 GLN E 568 GLN E 616 ASN ** F 13 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 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 147 ASN ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 177 GLN X 206 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.9166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 47240 Z= 0.253 Angle : 0.983 25.773 64850 Z= 0.495 Chirality : 0.053 0.566 7467 Planarity : 0.007 0.147 7705 Dihedral : 20.013 172.635 8207 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.81 % Allowed : 15.94 % Favored : 83.25 % Rotamer: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.10), residues: 5289 helix: -2.30 (0.11), residues: 1554 sheet: -3.63 (0.23), residues: 359 loop : -3.57 (0.10), residues: 3376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP U 294 HIS 0.013 0.001 HIS C 63 PHE 0.043 0.002 PHE U 229 TYR 0.038 0.002 TYR V 191 ARG 0.022 0.001 ARG B 366 *********************** 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 623 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 618 time to evaluate : 5.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7025 (m-10) cc_final: 0.6639 (m-80) REVERT: A 127 THR cc_start: 0.6307 (t) cc_final: 0.5675 (t) REVERT: A 137 ILE cc_start: 0.8465 (mt) cc_final: 0.8252 (mm) REVERT: A 188 ASP cc_start: 0.6921 (m-30) cc_final: 0.6441 (m-30) REVERT: A 344 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6368 (tm-30) REVERT: A 534 ILE cc_start: 0.8959 (mp) cc_final: 0.8662 (mp) REVERT: A 541 MET cc_start: 0.9014 (mmm) cc_final: 0.8618 (mmm) REVERT: A 605 GLU cc_start: 0.7127 (tt0) cc_final: 0.6723 (mt-10) REVERT: A 646 ASN cc_start: 0.7761 (t0) cc_final: 0.7423 (t0) REVERT: A 667 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7952 (pp30) REVERT: A 706 GLU cc_start: 0.7419 (pt0) cc_final: 0.6904 (tt0) REVERT: A 850 ASP cc_start: 0.8240 (m-30) cc_final: 0.7964 (m-30) REVERT: A 947 TRP cc_start: 0.8814 (p-90) cc_final: 0.7949 (p-90) REVERT: A 956 LYS cc_start: 0.8874 (mppt) cc_final: 0.8663 (mttm) REVERT: A 984 HIS cc_start: 0.7751 (m170) cc_final: 0.6714 (t-170) REVERT: A 1022 VAL cc_start: 0.9061 (p) cc_final: 0.8853 (p) REVERT: A 1050 GLU cc_start: 0.8383 (tt0) cc_final: 0.7977 (tt0) REVERT: A 1059 LYS cc_start: 0.6247 (mmtt) cc_final: 0.6007 (mptt) REVERT: B 38 ASP cc_start: 0.7969 (m-30) cc_final: 0.7067 (t0) REVERT: B 77 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7497 (tm-30) REVERT: B 120 ASN cc_start: 0.7569 (t0) cc_final: 0.7249 (m-40) REVERT: B 216 THR cc_start: 0.8399 (m) cc_final: 0.7953 (p) REVERT: B 310 ASP cc_start: 0.7683 (m-30) cc_final: 0.7351 (m-30) REVERT: B 776 TYR cc_start: 0.5396 (t80) cc_final: 0.4992 (t80) REVERT: B 1127 MET cc_start: 0.7887 (tmm) cc_final: 0.7504 (tmm) REVERT: B 1197 ILE cc_start: 0.7941 (pt) cc_final: 0.7660 (mp) REVERT: B 1213 PHE cc_start: 0.5604 (p90) cc_final: 0.5343 (p90) REVERT: B 1244 LEU cc_start: 0.8897 (tt) cc_final: 0.8553 (tt) REVERT: C 74 ASP cc_start: 0.7610 (t0) cc_final: 0.6537 (t0) REVERT: C 77 GLU cc_start: 0.7453 (pm20) cc_final: 0.6402 (mt-10) REVERT: C 93 GLN cc_start: 0.8534 (mt0) cc_final: 0.8168 (mt0) REVERT: D 80 MET cc_start: 0.7663 (tpt) cc_final: 0.7317 (tpt) REVERT: E 103 MET cc_start: 0.7567 (mmm) cc_final: 0.7144 (mmp) REVERT: E 164 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6421 (mt-10) REVERT: E 233 ASN cc_start: 0.8651 (m-40) cc_final: 0.8228 (m-40) REVERT: E 240 LYS cc_start: 0.8565 (mttp) cc_final: 0.8227 (mtpp) REVERT: E 273 ASN cc_start: 0.8889 (p0) cc_final: 0.8236 (p0) REVERT: E 377 ARG cc_start: 0.8591 (ttm-80) cc_final: 0.8373 (tpp80) REVERT: E 407 LEU cc_start: 0.8462 (pp) cc_final: 0.8059 (mt) REVERT: F 62 ILE cc_start: 0.8800 (mm) cc_final: 0.8587 (mt) REVERT: G 156 ASP cc_start: 0.8249 (m-30) cc_final: 0.7734 (m-30) REVERT: G 266 MET cc_start: 0.6176 (mtt) cc_final: 0.5971 (mtt) REVERT: G 287 GLU cc_start: 0.8346 (tp30) cc_final: 0.7721 (tp30) REVERT: G 301 PHE cc_start: 0.7259 (m-80) cc_final: 0.6859 (m-80) REVERT: S 157 MET cc_start: 0.0823 (mmp) cc_final: 0.0609 (mmm) REVERT: U 182 ARG cc_start: 0.7223 (mtp180) cc_final: 0.6519 (mpp-170) REVERT: U 278 MET cc_start: 0.2719 (mtp) cc_final: 0.2416 (mtp) REVERT: V 157 MET cc_start: 0.4680 (mmm) cc_final: 0.4262 (mmm) REVERT: X 135 MET cc_start: 0.4436 (ttt) cc_final: 0.4223 (ttp) REVERT: Y 36 PHE cc_start: 0.8253 (t80) cc_final: 0.8046 (t80) outliers start: 5 outliers final: 2 residues processed: 622 average time/residue: 0.5876 time to fit residues: 611.1762 Evaluate side-chains 437 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 434 time to evaluate : 4.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 508 optimal weight: 0.0010 chunk 59 optimal weight: 1.9990 chunk 300 optimal weight: 5.9990 chunk 385 optimal weight: 5.9990 chunk 298 optimal weight: 8.9990 chunk 443 optimal weight: 0.9990 chunk 294 optimal weight: 0.8980 chunk 525 optimal weight: 3.9990 chunk 328 optimal weight: 2.9990 chunk 320 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN ** A 728 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 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 HIS ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 175 HIS ** V 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 206 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.9493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 47240 Z= 0.268 Angle : 0.952 24.223 64850 Z= 0.483 Chirality : 0.052 0.547 7467 Planarity : 0.008 0.372 7705 Dihedral : 19.956 171.996 8207 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.79 % Allowed : 16.07 % Favored : 83.13 % Rotamer: Outliers : 0.07 % Allowed : 2.85 % Favored : 97.09 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.10), residues: 5289 helix: -2.12 (0.12), residues: 1558 sheet: -3.37 (0.24), residues: 353 loop : -3.46 (0.10), residues: 3378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP E 416 HIS 0.013 0.001 HIS C 63 PHE 0.070 0.002 PHE A 516 TYR 0.043 0.002 TYR A 698 ARG 0.071 0.001 ARG E 346 *********************** 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 561 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 558 time to evaluate : 5.417 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: A 79 TYR cc_start: 0.7121 (m-10) cc_final: 0.6891 (m-80) REVERT: A 184 TRP cc_start: 0.7275 (m100) cc_final: 0.6016 (m-90) REVERT: A 188 ASP cc_start: 0.6997 (m-30) cc_final: 0.6569 (m-30) REVERT: A 330 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7392 (mm-30) REVERT: A 344 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6337 (tm-30) REVERT: A 541 MET cc_start: 0.9032 (mmm) cc_final: 0.8598 (mmm) REVERT: A 605 GLU cc_start: 0.6972 (tt0) cc_final: 0.6593 (mt-10) REVERT: A 646 ASN cc_start: 0.7810 (t0) cc_final: 0.7459 (t0) REVERT: A 702 ILE cc_start: 0.8899 (mm) cc_final: 0.8698 (mm) REVERT: A 757 ILE cc_start: 0.8201 (tp) cc_final: 0.7965 (tp) REVERT: A 947 TRP cc_start: 0.8980 (p-90) cc_final: 0.8139 (p-90) REVERT: A 956 LYS cc_start: 0.9000 (mppt) cc_final: 0.8514 (mttm) REVERT: A 984 HIS cc_start: 0.7666 (m170) cc_final: 0.6810 (t-170) REVERT: A 1050 GLU cc_start: 0.8350 (tt0) cc_final: 0.8063 (tt0) REVERT: B 38 ASP cc_start: 0.7966 (m-30) cc_final: 0.7328 (t70) REVERT: B 77 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7526 (tm-30) REVERT: B 234 LYS cc_start: 0.5709 (tptt) cc_final: 0.4664 (tttt) REVERT: B 310 ASP cc_start: 0.7543 (m-30) cc_final: 0.7310 (m-30) REVERT: B 776 TYR cc_start: 0.5276 (t80) cc_final: 0.4884 (t80) REVERT: B 1127 MET cc_start: 0.7817 (tmm) cc_final: 0.7486 (tmm) REVERT: B 1130 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7566 (mm-40) REVERT: B 1213 PHE cc_start: 0.5594 (p90) cc_final: 0.5183 (p90) REVERT: C 74 ASP cc_start: 0.7764 (t0) cc_final: 0.6793 (t0) REVERT: C 77 GLU cc_start: 0.7491 (pm20) cc_final: 0.6500 (mt-10) REVERT: C 93 GLN cc_start: 0.8478 (mt0) cc_final: 0.8134 (mt0) REVERT: D 80 MET cc_start: 0.8010 (tpt) cc_final: 0.7453 (tpt) REVERT: D 193 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.6877 (ttp-110) REVERT: E 103 MET cc_start: 0.7433 (mmm) cc_final: 0.7095 (mmp) REVERT: E 240 LYS cc_start: 0.8642 (mttp) cc_final: 0.8169 (mtpt) REVERT: E 258 PRO cc_start: 0.8954 (Cg_endo) cc_final: 0.8524 (Cg_exo) REVERT: E 273 ASN cc_start: 0.8992 (p0) cc_final: 0.8340 (p0) REVERT: E 407 LEU cc_start: 0.8456 (pp) cc_final: 0.8235 (mp) REVERT: E 524 ASN cc_start: 0.6704 (t0) cc_final: 0.6419 (t0) REVERT: E 542 ILE cc_start: 0.8741 (mm) cc_final: 0.8378 (mm) REVERT: E 543 MET cc_start: 0.7815 (mmm) cc_final: 0.7533 (mpp) REVERT: G 156 ASP cc_start: 0.8182 (m-30) cc_final: 0.7628 (m-30) REVERT: G 266 MET cc_start: 0.6049 (mtt) cc_final: 0.5814 (mtt) REVERT: G 287 GLU cc_start: 0.8212 (tp30) cc_final: 0.8011 (tp30) REVERT: G 301 PHE cc_start: 0.7270 (m-80) cc_final: 0.6980 (m-80) REVERT: S 278 MET cc_start: -0.4655 (mtt) cc_final: -0.5279 (mmt) REVERT: U 182 ARG cc_start: 0.7167 (mtp180) cc_final: 0.6457 (mpp-170) REVERT: U 278 MET cc_start: 0.2175 (mtp) cc_final: 0.1697 (mtp) REVERT: V 157 MET cc_start: 0.4922 (mmm) cc_final: 0.4574 (mmm) REVERT: Y 36 PHE cc_start: 0.8206 (t80) cc_final: 0.7998 (t80) outliers start: 3 outliers final: 0 residues processed: 559 average time/residue: 0.5674 time to fit residues: 540.2358 Evaluate side-chains 418 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 5.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 324 optimal weight: 1.9990 chunk 209 optimal weight: 30.0000 chunk 313 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 333 optimal weight: 0.5980 chunk 357 optimal weight: 0.7980 chunk 259 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 412 optimal weight: 40.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN E 101 HIS ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 281 ASN E 372 GLN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 484 GLN E 616 ASN ** G 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 147 ASN ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 132 GLN X 206 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.9827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 47240 Z= 0.252 Angle : 0.919 22.806 64850 Z= 0.466 Chirality : 0.050 0.480 7467 Planarity : 0.008 0.403 7705 Dihedral : 19.900 172.442 8207 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.79 % Allowed : 15.56 % Favored : 83.65 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.10), residues: 5289 helix: -1.92 (0.12), residues: 1557 sheet: -3.35 (0.23), residues: 366 loop : -3.39 (0.10), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 199 HIS 0.011 0.001 HIS C 63 PHE 0.053 0.002 PHE A 516 TYR 0.035 0.002 TYR G 388 ARG 0.033 0.001 ARG E 346 *********************** 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 555 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 555 time to evaluate : 5.201 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: A 50 LEU cc_start: 0.8455 (pp) cc_final: 0.8218 (tp) REVERT: A 79 TYR cc_start: 0.7079 (m-10) cc_final: 0.6765 (m-80) REVERT: A 184 TRP cc_start: 0.7140 (m100) cc_final: 0.5656 (m-90) REVERT: A 188 ASP cc_start: 0.7020 (m-30) cc_final: 0.6486 (m-30) REVERT: A 344 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6302 (tm-30) REVERT: A 646 ASN cc_start: 0.7650 (t0) cc_final: 0.7362 (t0) REVERT: A 702 ILE cc_start: 0.8963 (mm) cc_final: 0.8722 (mm) REVERT: A 706 GLU cc_start: 0.7263 (tt0) cc_final: 0.7017 (tt0) REVERT: A 757 ILE cc_start: 0.8202 (tp) cc_final: 0.7967 (tp) REVERT: A 876 ASP cc_start: 0.8811 (p0) cc_final: 0.8363 (p0) REVERT: A 956 LYS cc_start: 0.8974 (mppt) cc_final: 0.8404 (mttm) REVERT: A 984 HIS cc_start: 0.7630 (m170) cc_final: 0.6753 (t-170) REVERT: A 1050 GLU cc_start: 0.8393 (tt0) cc_final: 0.8122 (tt0) REVERT: B 38 ASP cc_start: 0.7978 (m-30) cc_final: 0.7451 (t70) REVERT: B 77 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7659 (tm-30) REVERT: B 234 LYS cc_start: 0.5242 (tptt) cc_final: 0.4352 (tttt) REVERT: B 310 ASP cc_start: 0.7479 (m-30) cc_final: 0.7033 (m-30) REVERT: B 776 TYR cc_start: 0.5487 (t80) cc_final: 0.5046 (t80) REVERT: B 1107 TYR cc_start: 0.4803 (t80) cc_final: 0.4576 (t80) REVERT: B 1127 MET cc_start: 0.7788 (tmm) cc_final: 0.7391 (tmm) REVERT: B 1213 PHE cc_start: 0.5315 (p90) cc_final: 0.5012 (p90) REVERT: C 74 ASP cc_start: 0.7500 (t0) cc_final: 0.7252 (p0) REVERT: C 77 GLU cc_start: 0.7394 (pm20) cc_final: 0.6817 (mt-10) REVERT: C 82 MET cc_start: 0.8014 (mmt) cc_final: 0.7422 (mmm) REVERT: C 93 GLN cc_start: 0.8513 (mt0) cc_final: 0.8224 (mt0) REVERT: C 150 THR cc_start: 0.7314 (t) cc_final: 0.7068 (m) REVERT: D 80 MET cc_start: 0.8035 (tpt) cc_final: 0.7526 (tpt) REVERT: E 103 MET cc_start: 0.7601 (mmm) cc_final: 0.7392 (mmp) REVERT: E 240 LYS cc_start: 0.8653 (mttp) cc_final: 0.8366 (mtpt) REVERT: E 258 PRO cc_start: 0.8812 (Cg_endo) cc_final: 0.8462 (Cg_exo) REVERT: E 273 ASN cc_start: 0.8983 (p0) cc_final: 0.8328 (p0) REVERT: E 524 ASN cc_start: 0.6742 (t0) cc_final: 0.6510 (t0) REVERT: E 551 ASP cc_start: 0.7787 (t0) cc_final: 0.7580 (t0) REVERT: F 62 ILE cc_start: 0.8442 (mt) cc_final: 0.8058 (mm) REVERT: G 156 ASP cc_start: 0.8214 (m-30) cc_final: 0.7653 (m-30) REVERT: G 287 GLU cc_start: 0.8114 (tp30) cc_final: 0.7822 (tp30) REVERT: G 301 PHE cc_start: 0.7409 (m-80) cc_final: 0.7020 (m-80) REVERT: S 278 MET cc_start: -0.4480 (mtt) cc_final: -0.5521 (mmt) REVERT: U 182 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6369 (mpp-170) REVERT: U 202 MET cc_start: -0.3892 (ptp) cc_final: -0.4479 (ptp) REVERT: U 278 MET cc_start: 0.0752 (mtp) cc_final: -0.2474 (mmt) REVERT: V 157 MET cc_start: 0.4709 (mmm) cc_final: 0.4362 (mmm) REVERT: V 278 MET cc_start: 0.6763 (ptm) cc_final: 0.6499 (ptm) outliers start: 0 outliers final: 0 residues processed: 555 average time/residue: 0.5673 time to fit residues: 533.4688 Evaluate side-chains 425 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 5.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 477 optimal weight: 30.0000 chunk 503 optimal weight: 8.9990 chunk 459 optimal weight: 30.0000 chunk 489 optimal weight: 50.0000 chunk 294 optimal weight: 0.8980 chunk 213 optimal weight: 30.0000 chunk 384 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 442 optimal weight: 4.9990 chunk 462 optimal weight: 1.9990 chunk 487 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN A 842 GLN ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** 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 850 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 372 GLN E 426 HIS ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 HIS ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 ASN ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 35 GLN ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 193 GLN X 213 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 1.0198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 47240 Z= 0.411 Angle : 1.032 22.727 64850 Z= 0.524 Chirality : 0.053 0.402 7467 Planarity : 0.008 0.157 7705 Dihedral : 19.978 176.404 8207 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 27.95 Ramachandran Plot: Outliers : 0.78 % Allowed : 17.17 % Favored : 82.06 % Rotamer: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.10), residues: 5289 helix: -1.93 (0.12), residues: 1547 sheet: -3.04 (0.25), residues: 354 loop : -3.47 (0.10), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP E 416 HIS 0.013 0.002 HIS C 63 PHE 0.046 0.003 PHE D 221 TYR 0.042 0.003 TYR A 698 ARG 0.023 0.001 ARG E 282 *********************** 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 517 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 515 time to evaluate : 5.497 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: A 50 LEU cc_start: 0.8683 (pp) cc_final: 0.8359 (tt) REVERT: A 188 ASP cc_start: 0.7361 (m-30) cc_final: 0.6909 (m-30) REVERT: A 331 LEU cc_start: 0.9299 (mm) cc_final: 0.9049 (mm) REVERT: A 344 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6769 (tm-30) REVERT: A 541 MET cc_start: 0.8845 (mmp) cc_final: 0.8306 (mmm) REVERT: A 646 ASN cc_start: 0.8031 (t0) cc_final: 0.7656 (t0) REVERT: A 702 ILE cc_start: 0.9113 (mm) cc_final: 0.8859 (mm) REVERT: A 842 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8615 (pm20) REVERT: A 956 LYS cc_start: 0.9193 (mppt) cc_final: 0.8741 (mttm) REVERT: A 985 LEU cc_start: 0.9158 (mm) cc_final: 0.8949 (mm) REVERT: A 988 ASP cc_start: 0.7921 (m-30) cc_final: 0.7680 (t0) REVERT: B 38 ASP cc_start: 0.8071 (m-30) cc_final: 0.7604 (t70) REVERT: B 77 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7633 (tm-30) REVERT: B 301 TRP cc_start: 0.8678 (m-10) cc_final: 0.8288 (m-10) REVERT: B 305 HIS cc_start: 0.7519 (t70) cc_final: 0.7262 (t70) REVERT: B 776 TYR cc_start: 0.5583 (t80) cc_final: 0.5111 (t80) REVERT: B 1127 MET cc_start: 0.7835 (tmm) cc_final: 0.7484 (tmm) REVERT: C 93 GLN cc_start: 0.8595 (mt0) cc_final: 0.8384 (mt0) REVERT: D 80 MET cc_start: 0.8248 (tpt) cc_final: 0.7836 (tpt) REVERT: D 136 LEU cc_start: 0.7158 (tt) cc_final: 0.6933 (tt) REVERT: E 51 LYS cc_start: 0.8750 (ptpp) cc_final: 0.8328 (mttt) REVERT: E 233 ASN cc_start: 0.8851 (m-40) cc_final: 0.8466 (m110) REVERT: E 240 LYS cc_start: 0.9131 (mttp) cc_final: 0.8556 (mtpt) REVERT: E 258 PRO cc_start: 0.9084 (Cg_endo) cc_final: 0.8849 (Cg_exo) REVERT: E 261 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6878 (mm110) REVERT: E 405 LYS cc_start: 0.7865 (pptt) cc_final: 0.7594 (pttt) REVERT: E 524 ASN cc_start: 0.7379 (t0) cc_final: 0.7120 (t0) REVERT: E 566 SER cc_start: 0.9318 (m) cc_final: 0.8870 (p) REVERT: E 570 ASP cc_start: 0.7610 (m-30) cc_final: 0.7202 (p0) REVERT: F 58 VAL cc_start: 0.8360 (p) cc_final: 0.8079 (p) REVERT: F 62 ILE cc_start: 0.8802 (mt) cc_final: 0.8526 (mt) REVERT: G 156 ASP cc_start: 0.8466 (m-30) cc_final: 0.7980 (m-30) REVERT: G 301 PHE cc_start: 0.7775 (m-80) cc_final: 0.7381 (m-80) REVERT: S 278 MET cc_start: -0.3366 (mtt) cc_final: -0.4565 (mmt) REVERT: U 182 ARG cc_start: 0.7036 (mtp180) cc_final: 0.6313 (mpp-170) REVERT: U 202 MET cc_start: -0.3915 (ptp) cc_final: -0.4427 (ptp) REVERT: U 278 MET cc_start: 0.0295 (mtp) cc_final: -0.2532 (mmt) REVERT: V 157 MET cc_start: 0.4776 (mmm) cc_final: 0.4052 (mpp) outliers start: 2 outliers final: 0 residues processed: 516 average time/residue: 0.5564 time to fit residues: 486.4772 Evaluate side-chains 399 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 397 time to evaluate : 5.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 321 optimal weight: 0.0050 chunk 517 optimal weight: 20.0000 chunk 315 optimal weight: 0.0870 chunk 245 optimal weight: 0.5980 chunk 359 optimal weight: 3.9990 chunk 542 optimal weight: 8.9990 chunk 499 optimal weight: 20.0000 chunk 432 optimal weight: 50.0000 chunk 44 optimal weight: 0.9990 chunk 333 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 overall best weight: 0.9376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 547 HIS A 624 ASN ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1004 GLN ** A1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN E 81 HIS ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN E 426 HIS E 553 HIS ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 213 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 1.0482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.195 47240 Z= 0.256 Angle : 0.932 22.423 64850 Z= 0.472 Chirality : 0.050 0.425 7467 Planarity : 0.007 0.158 7705 Dihedral : 19.848 173.834 8207 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.76 % Allowed : 15.30 % Favored : 83.95 % Rotamer: Outliers : 0.02 % Allowed : 0.74 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.10), residues: 5289 helix: -1.80 (0.12), residues: 1566 sheet: -3.04 (0.24), residues: 352 loop : -3.34 (0.10), residues: 3371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 416 HIS 0.010 0.001 HIS C 63 PHE 0.084 0.003 PHE A 516 TYR 0.036 0.002 TYR A 148 ARG 0.034 0.001 ARG E 346 ********************** 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 545 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 544 time to evaluate : 5.015 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: A 50 LEU cc_start: 0.8606 (pp) cc_final: 0.8176 (tt) REVERT: A 79 TYR cc_start: 0.7142 (m-10) cc_final: 0.6889 (m-80) REVERT: A 188 ASP cc_start: 0.7050 (m-30) cc_final: 0.6643 (m-30) REVERT: A 344 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6616 (tm-30) REVERT: A 541 MET cc_start: 0.9020 (mmp) cc_final: 0.8414 (mmm) REVERT: A 702 ILE cc_start: 0.9021 (mm) cc_final: 0.8726 (mm) REVERT: A 704 ILE cc_start: 0.8938 (tp) cc_final: 0.8641 (tp) REVERT: A 893 MET cc_start: 0.6901 (mmp) cc_final: 0.6559 (mmt) REVERT: A 956 LYS cc_start: 0.9055 (mppt) cc_final: 0.8573 (mttm) REVERT: A 984 HIS cc_start: 0.7608 (m170) cc_final: 0.6596 (t-170) REVERT: B 38 ASP cc_start: 0.7779 (m-30) cc_final: 0.7405 (t70) REVERT: B 77 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7606 (tt0) REVERT: B 301 TRP cc_start: 0.8482 (m-10) cc_final: 0.8078 (m-10) REVERT: B 310 ASP cc_start: 0.7386 (m-30) cc_final: 0.6843 (m-30) REVERT: B 619 LEU cc_start: 0.8973 (pp) cc_final: 0.8770 (pt) REVERT: B 776 TYR cc_start: 0.5585 (t80) cc_final: 0.5139 (t80) REVERT: B 1127 MET cc_start: 0.7802 (tmm) cc_final: 0.7506 (tmm) REVERT: B 1213 PHE cc_start: 0.5666 (p90) cc_final: 0.5132 (p90) REVERT: C 73 GLU cc_start: 0.7727 (mp0) cc_final: 0.7284 (mp0) REVERT: C 93 GLN cc_start: 0.8524 (mt0) cc_final: 0.8207 (mt0) REVERT: C 100 LEU cc_start: 0.8709 (mm) cc_final: 0.8466 (mt) REVERT: C 137 GLU cc_start: 0.7668 (pt0) cc_final: 0.7433 (pm20) REVERT: C 184 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7779 (mmm160) REVERT: D 80 MET cc_start: 0.7794 (tpt) cc_final: 0.7265 (tpt) REVERT: E 164 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6443 (pm20) REVERT: E 240 LYS cc_start: 0.8643 (mttp) cc_final: 0.8206 (mtpt) REVERT: E 258 PRO cc_start: 0.8808 (Cg_endo) cc_final: 0.8449 (Cg_exo) REVERT: E 273 ASN cc_start: 0.9066 (p0) cc_final: 0.8321 (p0) REVERT: E 405 LYS cc_start: 0.7928 (pptt) cc_final: 0.7726 (pttt) REVERT: E 438 ARG cc_start: 0.8509 (ttp-170) cc_final: 0.8264 (ttp-170) REVERT: E 524 ASN cc_start: 0.7597 (t0) cc_final: 0.7260 (t0) REVERT: E 566 SER cc_start: 0.9266 (m) cc_final: 0.8928 (p) REVERT: F 62 ILE cc_start: 0.8369 (mt) cc_final: 0.8137 (mt) REVERT: G 156 ASP cc_start: 0.8230 (m-30) cc_final: 0.7648 (m-30) REVERT: G 188 SER cc_start: 0.9506 (m) cc_final: 0.8908 (t) REVERT: S 278 MET cc_start: -0.3529 (mtp) cc_final: -0.4246 (mmt) REVERT: U 182 ARG cc_start: 0.6986 (mtp180) cc_final: 0.6290 (mpp-170) REVERT: U 278 MET cc_start: 0.0214 (mtp) cc_final: -0.2677 (mmt) REVERT: V 157 MET cc_start: 0.4730 (mmm) cc_final: 0.3924 (mpp) outliers start: 1 outliers final: 0 residues processed: 544 average time/residue: 0.5835 time to fit residues: 536.6220 Evaluate side-chains 405 residues out of total 4565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 5.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 343 optimal weight: 2.9990 chunk 460 optimal weight: 20.0000 chunk 132 optimal weight: 0.7980 chunk 398 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 433 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 444 optimal weight: 50.0000 chunk 54 optimal weight: 0.0010 chunk 79 optimal weight: 10.0000 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN C 47 ASN E 81 HIS ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 ASN E 372 GLN E 426 HIS ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 35 GLN ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 235 GLN ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.168190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.132030 restraints weight = 135585.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.128875 restraints weight = 200131.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.130267 restraints weight = 180597.329| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3870 r_free = 0.3870 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 1.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 47240 Z= 0.274 Angle : 0.924 22.334 64850 Z= 0.468 Chirality : 0.049 0.342 7467 Planarity : 0.007 0.160 7705 Dihedral : 19.784 175.074 8207 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.76 % Allowed : 15.98 % Favored : 83.27 % Rotamer: Outliers : 0.02 % Allowed : 0.61 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.10), residues: 5289 helix: -1.75 (0.12), residues: 1580 sheet: -2.87 (0.25), residues: 347 loop : -3.31 (0.10), residues: 3362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 199 HIS 0.022 0.001 HIS C 63 PHE 0.078 0.003 PHE A 516 TYR 0.035 0.002 TYR A 698 ARG 0.035 0.001 ARG E 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11140.90 seconds wall clock time: 203 minutes 20.38 seconds (12200.38 seconds total)