Starting phenix.real_space_refine on Fri Sep 27 03:58:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ylv_33918/09_2024/7ylv_33918.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ylv_33918/09_2024/7ylv_33918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ylv_33918/09_2024/7ylv_33918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ylv_33918/09_2024/7ylv_33918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ylv_33918/09_2024/7ylv_33918.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ylv_33918/09_2024/7ylv_33918.cif" } resolution = 3.91 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= 0.060 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: 4 Type Number sf(0) Gaussians S 325 5.16 5 C 41076 2.51 5 N 11345 2.21 5 O 12749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 65495 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4103 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 11, 'TRANS': 531} Chain: "a" Number of atoms: 4103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4103 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 11, 'TRANS': 531} Chain: "B" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3930 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 10, 'TRANS': 506} Chain: "b" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3930 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 10, 'TRANS': 506} Chain: "G" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3982 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 19, 'TRANS': 498} Chain: "g" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3982 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 19, 'TRANS': 498} Chain: "D" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3985 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "d" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3985 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "E" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4068 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "e" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4068 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "Z" Number of atoms: 4110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4110 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Chain: "z" Number of atoms: 4110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4110 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Chain: "H" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3969 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 12, 'TRANS': 506} Chain: "h" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3969 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 12, 'TRANS': 506} Chain: "Q" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4125 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 19, 'TRANS': 523} Chain: "q" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4125 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 19, 'TRANS': 523} Chain: "P" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 951 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Time building chain proxies: 30.13, per 1000 atoms: 0.46 Number of scatterers: 65495 At special positions: 0 Unit cell: (196.382, 218.788, 183.202, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 325 16.00 O 12749 8.00 N 11345 7.00 C 41076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.92 Conformation dependent library (CDL) restraints added in 6.4 seconds 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15946 Finding SS restraints... Secondary structure from input PDB file: 344 helices and 96 sheets defined 55.4% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.55 Creating SS restraints... Processing helix chain 'A' and resid 22 through 41 removed outlier: 3.781A pdb=" N VAL A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 77 through 94 removed outlier: 4.216A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 118 Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.608A pdb=" N GLU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.922A pdb=" N ILE A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.614A pdb=" N ALA A 171 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 removed outlier: 5.459A pdb=" N ASN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 266 through 291 removed outlier: 3.517A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 Processing helix chain 'A' and resid 322 through 334 removed outlier: 4.089A pdb=" N ARG A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 removed outlier: 4.075A pdb=" N SER A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 438 removed outlier: 3.844A pdb=" N THR A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 456 removed outlier: 4.139A pdb=" N ALA A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 456 " --> pdb=" O ALA A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 469 through 487 Processing helix chain 'A' and resid 512 through 516 Processing helix chain 'A' and resid 521 through 540 Processing helix chain 'a' and resid 22 through 42 removed outlier: 3.770A pdb=" N VAL a 39 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL a 40 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER a 42 " --> pdb=" O ASN a 38 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 72 Processing helix chain 'a' and resid 77 through 94 removed outlier: 4.224A pdb=" N LEU a 83 " --> pdb=" O ALA a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 118 Processing helix chain 'a' and resid 121 through 142 removed outlier: 3.532A pdb=" N GLU a 142 " --> pdb=" O ARG a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 155 through 164 removed outlier: 3.566A pdb=" N ILE a 159 " --> pdb=" O THR a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 171 Processing helix chain 'a' and resid 172 through 186 removed outlier: 4.970A pdb=" N ASN a 178 " --> pdb=" O ASP a 174 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA a 186 " --> pdb=" O ASP a 182 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 216 Processing helix chain 'a' and resid 266 through 291 removed outlier: 4.567A pdb=" N VAL a 281 " --> pdb=" O GLU a 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG a 284 " --> pdb=" O ILE a 280 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 313 Processing helix chain 'a' and resid 322 through 333 Processing helix chain 'a' and resid 391 through 415 removed outlier: 3.506A pdb=" N GLU a 397 " --> pdb=" O TYR a 393 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER a 415 " --> pdb=" O ARG a 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 423 through 438 removed outlier: 3.874A pdb=" N THR a 438 " --> pdb=" O ASP a 434 " (cutoff:3.500A) Processing helix chain 'a' and resid 443 through 455 removed outlier: 3.558A pdb=" N ALA a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU a 455 " --> pdb=" O PHE a 451 " (cutoff:3.500A) Processing helix chain 'a' and resid 456 through 466 Processing helix chain 'a' and resid 469 through 488 removed outlier: 3.849A pdb=" N ALA a 475 " --> pdb=" O SER a 471 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER a 484 " --> pdb=" O TYR a 480 " (cutoff:3.500A) Processing helix chain 'a' and resid 489 through 491 No H-bonds generated for 'chain 'a' and resid 489 through 491' Processing helix chain 'a' and resid 512 through 516 Processing helix chain 'a' and resid 521 through 540 Processing helix chain 'B' and resid 14 through 34 removed outlier: 5.187A pdb=" N LEU B 20 " --> pdb=" O GLU B 16 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 71 through 88 removed outlier: 3.881A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 112 Processing helix chain 'B' and resid 116 through 138 Processing helix chain 'B' and resid 145 through 162 Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.089A pdb=" N GLN B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 183 removed outlier: 4.595A pdb=" N GLU B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 254 through 278 Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.734A pdb=" N LEU B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 Processing helix chain 'B' and resid 373 through 397 removed outlier: 3.537A pdb=" N LYS B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 419 Processing helix chain 'B' and resid 423 through 438 Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 451 through 465 Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 491 through 510 Processing helix chain 'b' and resid 14 through 34 removed outlier: 3.693A pdb=" N LEU b 32 " --> pdb=" O ALA b 28 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 37 No H-bonds generated for 'chain 'b' and resid 35 through 37' Processing helix chain 'b' and resid 59 through 67 Processing helix chain 'b' and resid 71 through 88 removed outlier: 3.685A pdb=" N VAL b 76 " --> pdb=" O PRO b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 112 removed outlier: 3.562A pdb=" N LYS b 108 " --> pdb=" O ARG b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 139 Processing helix chain 'b' and resid 145 through 161 Processing helix chain 'b' and resid 164 through 168 Processing helix chain 'b' and resid 169 through 183 removed outlier: 4.206A pdb=" N GLU b 175 " --> pdb=" O ASP b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 191 No H-bonds generated for 'chain 'b' and resid 189 through 191' Processing helix chain 'b' and resid 202 through 206 Processing helix chain 'b' and resid 254 through 278 removed outlier: 4.073A pdb=" N ALA b 264 " --> pdb=" O GLN b 260 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU b 265 " --> pdb=" O LEU b 261 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 301 Processing helix chain 'b' and resid 310 through 319 Processing helix chain 'b' and resid 373 through 395 removed outlier: 3.653A pdb=" N THR b 395 " --> pdb=" O LEU b 391 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 419 Processing helix chain 'b' and resid 423 through 438 removed outlier: 4.367A pdb=" N LEU b 428 " --> pdb=" O GLY b 424 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA b 429 " --> pdb=" O LYS b 425 " (cutoff:3.500A) Processing helix chain 'b' and resid 438 through 448 removed outlier: 3.548A pdb=" N THR b 442 " --> pdb=" O ARG b 438 " (cutoff:3.500A) Processing helix chain 'b' and resid 451 through 465 Processing helix chain 'b' and resid 482 through 486 Processing helix chain 'b' and resid 491 through 510 removed outlier: 3.794A pdb=" N LEU b 508 " --> pdb=" O ALA b 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 35 removed outlier: 3.853A pdb=" N ILE G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 39 removed outlier: 3.965A pdb=" N LEU G 39 " --> pdb=" O ARG G 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 36 through 39' Processing helix chain 'G' and resid 60 through 68 Processing helix chain 'G' and resid 72 through 89 Processing helix chain 'G' and resid 92 through 113 removed outlier: 4.055A pdb=" N ILE G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) Proline residue: G 109 - end of helix Processing helix chain 'G' and resid 117 through 139 Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'G' and resid 162 through 166 removed outlier: 4.022A pdb=" N HIS G 166 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 183 Processing helix chain 'G' and resid 199 through 204 Processing helix chain 'G' and resid 213 through 217 Processing helix chain 'G' and resid 266 through 290 removed outlier: 4.343A pdb=" N ASN G 270 " --> pdb=" O GLU G 266 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG G 271 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL G 290 " --> pdb=" O GLN G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 321 through 333 Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 385 through 408 removed outlier: 4.156A pdb=" N ASP G 398 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA G 399 " --> pdb=" O ASN G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 432 Processing helix chain 'G' and resid 438 through 449 removed outlier: 3.846A pdb=" N VAL G 445 " --> pdb=" O PRO G 441 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA G 446 " --> pdb=" O TYR G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 461 Processing helix chain 'G' and resid 465 through 478 Processing helix chain 'G' and resid 503 through 522 Processing helix chain 'g' and resid 17 through 35 removed outlier: 3.839A pdb=" N ILE g 35 " --> pdb=" O VAL g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 36 through 39 removed outlier: 4.169A pdb=" N LEU g 39 " --> pdb=" O ARG g 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 36 through 39' Processing helix chain 'g' and resid 60 through 67 Processing helix chain 'g' and resid 72 through 89 Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.631A pdb=" N ILE g 97 " --> pdb=" O THR g 93 " (cutoff:3.500A) Proline residue: g 109 - end of helix Processing helix chain 'g' and resid 117 through 139 Processing helix chain 'g' and resid 147 through 156 Processing helix chain 'g' and resid 157 through 159 No H-bonds generated for 'chain 'g' and resid 157 through 159' Processing helix chain 'g' and resid 162 through 166 removed outlier: 4.108A pdb=" N HIS g 166 " --> pdb=" O TYR g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 183 Processing helix chain 'g' and resid 213 through 217 Processing helix chain 'g' and resid 265 through 267 No H-bonds generated for 'chain 'g' and resid 265 through 267' Processing helix chain 'g' and resid 268 through 289 removed outlier: 4.035A pdb=" N ILE g 272 " --> pdb=" O ASP g 268 " (cutoff:3.500A) Processing helix chain 'g' and resid 302 through 311 Processing helix chain 'g' and resid 321 through 333 removed outlier: 3.972A pdb=" N ARG g 327 " --> pdb=" O SER g 323 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG g 330 " --> pdb=" O ASN g 326 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL g 331 " --> pdb=" O ARG g 327 " (cutoff:3.500A) Processing helix chain 'g' and resid 339 through 343 removed outlier: 3.582A pdb=" N LEU g 343 " --> pdb=" O VAL g 340 " (cutoff:3.500A) Processing helix chain 'g' and resid 385 through 408 Processing helix chain 'g' and resid 417 through 432 removed outlier: 3.729A pdb=" N LYS g 432 " --> pdb=" O ALA g 428 " (cutoff:3.500A) Processing helix chain 'g' and resid 438 through 449 removed outlier: 3.951A pdb=" N ALA g 444 " --> pdb=" O TRP g 440 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL g 445 " --> pdb=" O PRO g 441 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA g 446 " --> pdb=" O TYR g 442 " (cutoff:3.500A) Processing helix chain 'g' and resid 450 through 461 Processing helix chain 'g' and resid 465 through 478 Processing helix chain 'g' and resid 503 through 522 Processing helix chain 'D' and resid 17 through 37 removed outlier: 3.957A pdb=" N THR D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.588A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 113 Processing helix chain 'D' and resid 116 through 138 Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 166 through 180 Proline residue: D 172 - end of helix Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 256 through 281 removed outlier: 3.587A pdb=" N MET D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 281 " --> pdb=" O LYS D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 383 through 407 Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 430 through 433 removed outlier: 6.195A pdb=" N GLU D 433 " --> pdb=" O ARG D 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 430 through 433' Processing helix chain 'D' and resid 434 through 448 removed outlier: 3.578A pdb=" N PHE D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 461 through 473 Processing helix chain 'D' and resid 501 through 520 Processing helix chain 'd' and resid 17 through 37 removed outlier: 3.594A pdb=" N ARG d 21 " --> pdb=" O PRO d 17 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR d 37 " --> pdb=" O ASP d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 69 removed outlier: 4.068A pdb=" N ALA d 69 " --> pdb=" O LEU d 65 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 89 Processing helix chain 'd' and resid 94 through 113 Processing helix chain 'd' and resid 116 through 138 removed outlier: 3.591A pdb=" N MET d 138 " --> pdb=" O ILE d 134 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 159 removed outlier: 3.528A pdb=" N SER d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 166 through 180 Proline residue: d 172 - end of helix Processing helix chain 'd' and resid 190 through 192 No H-bonds generated for 'chain 'd' and resid 190 through 192' Processing helix chain 'd' and resid 256 through 281 Processing helix chain 'd' and resid 298 through 308 Processing helix chain 'd' and resid 317 through 328 removed outlier: 3.738A pdb=" N LYS d 326 " --> pdb=" O GLU d 322 " (cutoff:3.500A) Processing helix chain 'd' and resid 335 through 339 Processing helix chain 'd' and resid 340 through 344 Processing helix chain 'd' and resid 383 through 407 Processing helix chain 'd' and resid 415 through 430 removed outlier: 3.814A pdb=" N ARG d 430 " --> pdb=" O SER d 426 " (cutoff:3.500A) Processing helix chain 'd' and resid 431 through 433 No H-bonds generated for 'chain 'd' and resid 431 through 433' Processing helix chain 'd' and resid 434 through 448 removed outlier: 3.738A pdb=" N PHE d 438 " --> pdb=" O GLY d 434 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU d 442 " --> pdb=" O PHE d 438 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU d 448 " --> pdb=" O ALA d 444 " (cutoff:3.500A) Processing helix chain 'd' and resid 448 through 458 Processing helix chain 'd' and resid 461 through 476 Processing helix chain 'd' and resid 501 through 520 Processing helix chain 'E' and resid 43 through 59 Processing helix chain 'E' and resid 60 through 65 removed outlier: 4.663A pdb=" N THR E 63 " --> pdb=" O ILE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 98 through 115 removed outlier: 3.532A pdb=" N LEU E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 140 Processing helix chain 'E' and resid 142 through 164 Processing helix chain 'E' and resid 172 through 189 Processing helix chain 'E' and resid 190 through 195 removed outlier: 6.596A pdb=" N VAL E 193 " --> pdb=" O SER E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 210 removed outlier: 3.586A pdb=" N PHE E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 222 No H-bonds generated for 'chain 'E' and resid 220 through 222' Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 291 through 316 Processing helix chain 'E' and resid 328 through 338 Processing helix chain 'E' and resid 347 through 359 Processing helix chain 'E' and resid 365 through 369 Processing helix chain 'E' and resid 412 through 436 Processing helix chain 'E' and resid 444 through 459 removed outlier: 3.639A pdb=" N VAL E 448 " --> pdb=" O GLY E 444 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 462 No H-bonds generated for 'chain 'E' and resid 460 through 462' Processing helix chain 'E' and resid 463 through 464 No H-bonds generated for 'chain 'E' and resid 463 through 464' Processing helix chain 'E' and resid 465 through 487 removed outlier: 3.573A pdb=" N THR E 478 " --> pdb=" O GLN E 474 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE E 479 " --> pdb=" O ALA E 475 " (cutoff:3.500A) Proline residue: E 480 - end of helix Processing helix chain 'E' and resid 490 through 505 removed outlier: 3.631A pdb=" N GLU E 505 " --> pdb=" O LYS E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 550 Processing helix chain 'e' and resid 43 through 62 removed outlier: 3.564A pdb=" N ILE e 60 " --> pdb=" O SER e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 65 No H-bonds generated for 'chain 'e' and resid 63 through 65' Processing helix chain 'e' and resid 86 through 94 Processing helix chain 'e' and resid 98 through 115 Processing helix chain 'e' and resid 120 through 139 removed outlier: 3.513A pdb=" N GLU e 135 " --> pdb=" O ASP e 131 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 164 removed outlier: 3.957A pdb=" N GLU e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR e 164 " --> pdb=" O LYS e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 172 through 188 Processing helix chain 'e' and resid 189 through 195 removed outlier: 6.308A pdb=" N ILE e 192 " --> pdb=" O GLY e 189 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL e 193 " --> pdb=" O SER e 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 196 through 211 removed outlier: 4.226A pdb=" N PHE e 200 " --> pdb=" O ASP e 196 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL e 211 " --> pdb=" O ALA e 207 " (cutoff:3.500A) Processing helix chain 'e' and resid 220 through 222 No H-bonds generated for 'chain 'e' and resid 220 through 222' Processing helix chain 'e' and resid 233 through 237 Processing helix chain 'e' and resid 291 through 317 removed outlier: 3.630A pdb=" N GLN e 303 " --> pdb=" O GLN e 299 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS e 307 " --> pdb=" O GLN e 303 " (cutoff:3.500A) Processing helix chain 'e' and resid 328 through 338 Processing helix chain 'e' and resid 347 through 358 Processing helix chain 'e' and resid 412 through 436 Processing helix chain 'e' and resid 444 through 459 removed outlier: 3.750A pdb=" N ASP e 459 " --> pdb=" O SER e 455 " (cutoff:3.500A) Processing helix chain 'e' and resid 465 through 486 removed outlier: 3.632A pdb=" N THR e 478 " --> pdb=" O GLN e 474 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE e 479 " --> pdb=" O ALA e 475 " (cutoff:3.500A) Proline residue: e 480 - end of helix Processing helix chain 'e' and resid 490 through 505 Processing helix chain 'e' and resid 521 through 525 Processing helix chain 'e' and resid 531 through 550 Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.805A pdb=" N THR Z 35 " --> pdb=" O SER Z 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 66 Processing helix chain 'Z' and resid 70 through 88 Processing helix chain 'Z' and resid 90 through 110 Processing helix chain 'Z' and resid 114 through 137 Processing helix chain 'Z' and resid 146 through 160 removed outlier: 3.944A pdb=" N GLN Z 152 " --> pdb=" O GLU Z 148 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR Z 160 " --> pdb=" O SER Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 182 removed outlier: 3.999A pdb=" N VAL Z 169 " --> pdb=" O ASP Z 165 " (cutoff:3.500A) Proline residue: Z 172 - end of helix Processing helix chain 'Z' and resid 190 through 192 No H-bonds generated for 'chain 'Z' and resid 190 through 192' Processing helix chain 'Z' and resid 203 through 207 Processing helix chain 'Z' and resid 255 through 284 removed outlier: 3.777A pdb=" N ARG Z 259 " --> pdb=" O SER Z 255 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP Z 260 " --> pdb=" O ALA Z 256 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS Z 268 " --> pdb=" O ALA Z 264 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE Z 269 " --> pdb=" O SER Z 265 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL Z 270 " --> pdb=" O GLU Z 266 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS Z 273 " --> pdb=" O PHE Z 269 " (cutoff:3.500A) Processing helix chain 'Z' and resid 302 through 312 removed outlier: 3.743A pdb=" N HIS Z 312 " --> pdb=" O VAL Z 308 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 333 removed outlier: 3.576A pdb=" N LEU Z 330 " --> pdb=" O GLU Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 339 through 343 Processing helix chain 'Z' and resid 384 through 408 Processing helix chain 'Z' and resid 416 through 434 Processing helix chain 'Z' and resid 440 through 451 Processing helix chain 'Z' and resid 452 through 462 removed outlier: 3.558A pdb=" N SER Z 462 " --> pdb=" O LEU Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 465 through 483 removed outlier: 3.969A pdb=" N ALA Z 471 " --> pdb=" O LEU Z 467 " (cutoff:3.500A) Processing helix chain 'Z' and resid 500 through 505 Processing helix chain 'Z' and resid 510 through 529 Processing helix chain 'z' and resid 16 through 34 Processing helix chain 'z' and resid 35 through 37 No H-bonds generated for 'chain 'z' and resid 35 through 37' Processing helix chain 'z' and resid 58 through 66 Processing helix chain 'z' and resid 70 through 82 Processing helix chain 'z' and resid 83 through 85 No H-bonds generated for 'chain 'z' and resid 83 through 85' Processing helix chain 'z' and resid 90 through 110 Processing helix chain 'z' and resid 114 through 137 Processing helix chain 'z' and resid 146 through 162 removed outlier: 3.764A pdb=" N THR z 160 " --> pdb=" O SER z 156 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS z 161 " --> pdb=" O SER z 157 " (cutoff:3.500A) Processing helix chain 'z' and resid 164 through 182 removed outlier: 4.012A pdb=" N GLU z 168 " --> pdb=" O ALA z 164 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL z 169 " --> pdb=" O ASP z 165 " (cutoff:3.500A) Proline residue: z 172 - end of helix Processing helix chain 'z' and resid 190 through 192 No H-bonds generated for 'chain 'z' and resid 190 through 192' Processing helix chain 'z' and resid 203 through 207 Processing helix chain 'z' and resid 255 through 284 removed outlier: 4.302A pdb=" N PHE z 269 " --> pdb=" O SER z 265 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL z 270 " --> pdb=" O GLU z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 302 through 312 Processing helix chain 'z' and resid 321 through 333 Processing helix chain 'z' and resid 339 through 343 Processing helix chain 'z' and resid 344 through 348 Processing helix chain 'z' and resid 384 through 408 Processing helix chain 'z' and resid 416 through 434 removed outlier: 3.727A pdb=" N MET z 431 " --> pdb=" O ARG z 427 " (cutoff:3.500A) Processing helix chain 'z' and resid 440 through 451 removed outlier: 3.589A pdb=" N ILE z 444 " --> pdb=" O THR z 440 " (cutoff:3.500A) Processing helix chain 'z' and resid 452 through 463 Processing helix chain 'z' and resid 465 through 483 removed outlier: 3.718A pdb=" N LEU z 470 " --> pdb=" O PRO z 466 " (cutoff:3.500A) Processing helix chain 'z' and resid 500 through 505 Processing helix chain 'z' and resid 510 through 529 Processing helix chain 'H' and resid 22 through 41 Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 77 through 94 Processing helix chain 'H' and resid 97 through 118 Proline residue: H 114 - end of helix Processing helix chain 'H' and resid 121 through 143 Processing helix chain 'H' and resid 153 through 166 removed outlier: 3.852A pdb=" N LEU H 158 " --> pdb=" O GLY H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 188 removed outlier: 4.447A pdb=" N LYS H 180 " --> pdb=" O ASP H 176 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET H 181 " --> pdb=" O PHE H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 208 through 212 Processing helix chain 'H' and resid 263 through 289 removed outlier: 3.639A pdb=" N GLY H 289 " --> pdb=" O VAL H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 310 Processing helix chain 'H' and resid 319 through 331 Processing helix chain 'H' and resid 342 through 346 Processing helix chain 'H' and resid 356 through 360 Processing helix chain 'H' and resid 382 through 406 removed outlier: 3.633A pdb=" N LEU H 404 " --> pdb=" O VAL H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 428 Processing helix chain 'H' and resid 429 through 431 No H-bonds generated for 'chain 'H' and resid 429 through 431' Processing helix chain 'H' and resid 433 through 446 removed outlier: 4.045A pdb=" N MET H 437 " --> pdb=" O GLY H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 457 removed outlier: 3.528A pdb=" N ALA H 457 " --> pdb=" O LEU H 453 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 473 Processing helix chain 'H' and resid 500 through 519 Processing helix chain 'h' and resid 22 through 41 removed outlier: 3.529A pdb=" N ILE h 26 " --> pdb=" O GLY h 22 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL h 36 " --> pdb=" O ALA h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 44 No H-bonds generated for 'chain 'h' and resid 42 through 44' Processing helix chain 'h' and resid 65 through 74 Processing helix chain 'h' and resid 80 through 94 removed outlier: 3.604A pdb=" N VAL h 84 " --> pdb=" O ALA h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 118 removed outlier: 3.524A pdb=" N THR h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) Proline residue: h 114 - end of helix Processing helix chain 'h' and resid 121 through 144 Processing helix chain 'h' and resid 153 through 166 Processing helix chain 'h' and resid 174 through 188 removed outlier: 4.345A pdb=" N LYS h 180 " --> pdb=" O ASP h 176 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET h 181 " --> pdb=" O PHE h 177 " (cutoff:3.500A) Processing helix chain 'h' and resid 195 through 197 No H-bonds generated for 'chain 'h' and resid 195 through 197' Processing helix chain 'h' and resid 208 through 212 Processing helix chain 'h' and resid 265 through 289 removed outlier: 4.188A pdb=" N ALA h 269 " --> pdb=" O GLU h 265 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL h 271 " --> pdb=" O TYR h 267 " (cutoff:3.500A) Processing helix chain 'h' and resid 300 through 310 Processing helix chain 'h' and resid 319 through 331 Processing helix chain 'h' and resid 342 through 346 Processing helix chain 'h' and resid 356 through 360 removed outlier: 3.522A pdb=" N GLU h 360 " --> pdb=" O ILE h 357 " (cutoff:3.500A) Processing helix chain 'h' and resid 382 through 406 Processing helix chain 'h' and resid 414 through 429 removed outlier: 3.561A pdb=" N LYS h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) Processing helix chain 'h' and resid 433 through 447 removed outlier: 3.989A pdb=" N MET h 437 " --> pdb=" O GLY h 433 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU h 447 " --> pdb=" O ALA h 443 " (cutoff:3.500A) Processing helix chain 'h' and resid 447 through 457 Processing helix chain 'h' and resid 460 through 474 Processing helix chain 'h' and resid 500 through 519 Processing helix chain 'Q' and resid 22 through 25 Processing helix chain 'Q' and resid 26 through 44 removed outlier: 3.596A pdb=" N ILE Q 32 " --> pdb=" O ILE Q 28 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU Q 37 " --> pdb=" O ALA Q 33 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 74 Processing helix chain 'Q' and resid 79 through 96 removed outlier: 3.968A pdb=" N LEU Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 121 removed outlier: 4.314A pdb=" N LYS Q 116 " --> pdb=" O ASN Q 112 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU Q 117 " --> pdb=" O VAL Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 145 Processing helix chain 'Q' and resid 155 through 168 removed outlier: 3.604A pdb=" N MET Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) Proline residue: Q 165 - end of helix Processing helix chain 'Q' and resid 174 through 190 removed outlier: 3.838A pdb=" N GLU Q 180 " --> pdb=" O ASP Q 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 216 through 220 Processing helix chain 'Q' and resid 269 through 294 removed outlier: 3.510A pdb=" N GLU Q 281 " --> pdb=" O SER Q 277 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 316 Processing helix chain 'Q' and resid 325 through 337 removed outlier: 3.751A pdb=" N ARG Q 334 " --> pdb=" O ARG Q 330 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL Q 335 " --> pdb=" O ARG Q 331 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 352 Processing helix chain 'Q' and resid 390 through 410 removed outlier: 3.838A pdb=" N GLY Q 410 " --> pdb=" O ALA Q 406 " (cutoff:3.500A) Processing helix chain 'Q' and resid 424 through 441 Processing helix chain 'Q' and resid 444 through 456 removed outlier: 4.236A pdb=" N ALA Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE Q 456 " --> pdb=" O PHE Q 452 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 467 removed outlier: 3.540A pdb=" N ALA Q 467 " --> pdb=" O LEU Q 463 " (cutoff:3.500A) Processing helix chain 'Q' and resid 470 through 483 Proline residue: Q 476 - end of helix removed outlier: 3.541A pdb=" N HIS Q 482 " --> pdb=" O LEU Q 478 " (cutoff:3.500A) Processing helix chain 'Q' and resid 511 through 516 removed outlier: 3.960A pdb=" N GLU Q 515 " --> pdb=" O ASP Q 511 " (cutoff:3.500A) Processing helix chain 'Q' and resid 521 through 540 Processing helix chain 'q' and resid 22 through 25 Processing helix chain 'q' and resid 26 through 44 removed outlier: 3.695A pdb=" N GLU q 37 " --> pdb=" O ALA q 33 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU q 38 " --> pdb=" O ALA q 34 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR q 44 " --> pdb=" O GLN q 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 75 Processing helix chain 'q' and resid 79 through 94 removed outlier: 4.210A pdb=" N LEU q 85 " --> pdb=" O ALA q 81 " (cutoff:3.500A) Processing helix chain 'q' and resid 99 through 119 Processing helix chain 'q' and resid 123 through 143 removed outlier: 3.817A pdb=" N ASP q 143 " --> pdb=" O LEU q 139 " (cutoff:3.500A) Processing helix chain 'q' and resid 155 through 168 removed outlier: 3.740A pdb=" N MET q 162 " --> pdb=" O GLU q 158 " (cutoff:3.500A) Proline residue: q 165 - end of helix Processing helix chain 'q' and resid 174 through 190 Processing helix chain 'q' and resid 203 through 205 No H-bonds generated for 'chain 'q' and resid 203 through 205' Processing helix chain 'q' and resid 216 through 220 Processing helix chain 'q' and resid 269 through 294 removed outlier: 3.548A pdb=" N MET q 294 " --> pdb=" O GLU q 290 " (cutoff:3.500A) Processing helix chain 'q' and resid 306 through 316 Processing helix chain 'q' and resid 325 through 333 Processing helix chain 'q' and resid 348 through 352 Processing helix chain 'q' and resid 390 through 410 Processing helix chain 'q' and resid 424 through 440 Processing helix chain 'q' and resid 444 through 455 removed outlier: 4.057A pdb=" N ALA q 448 " --> pdb=" O LEU q 444 " (cutoff:3.500A) Processing helix chain 'q' and resid 457 through 467 Processing helix chain 'q' and resid 470 through 483 Proline residue: q 476 - end of helix Processing helix chain 'q' and resid 492 through 495 Processing helix chain 'q' and resid 512 through 516 Processing helix chain 'q' and resid 521 through 540 Processing helix chain 'P' and resid 106 through 111 Processing helix chain 'P' and resid 111 through 117 removed outlier: 3.775A pdb=" N GLN P 116 " --> pdb=" O THR P 112 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY P 117 " --> pdb=" O LEU P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 162 removed outlier: 3.698A pdb=" N ARG P 151 " --> pdb=" O LYS P 147 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS P 162 " --> pdb=" O GLN P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 178 Processing helix chain 'P' and resid 182 through 186 Processing helix chain 'P' and resid 208 through 212 removed outlier: 3.539A pdb=" N ASN P 211 " --> pdb=" O GLY P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 223 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.326A pdb=" N ILE A 541 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N MET D 47 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR A 543 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LYS D 49 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 545 " --> pdb=" O LYS D 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 207 removed outlier: 6.257A pdb=" N ASN A 204 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU A 387 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 206 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 225 removed outlier: 6.426A pdb=" N THR A 377 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS A 358 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 361 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 222 through 225 removed outlier: 6.426A pdb=" N THR A 377 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS A 358 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS A 243 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 297 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA A 245 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 296 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA7, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.548A pdb=" N LYS A 508 " --> pdb=" O ASP A 503 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 18 through 21 removed outlier: 4.733A pdb=" N ILE a 541 " --> pdb=" O ASP d 45 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET d 47 " --> pdb=" O ILE a 541 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR a 543 " --> pdb=" O MET d 47 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LYS d 49 " --> pdb=" O THR a 543 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE a 545 " --> pdb=" O LYS d 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 60 through 63 Processing sheet with id=AB1, first strand: chain 'a' and resid 204 through 208 Processing sheet with id=AB2, first strand: chain 'a' and resid 223 through 224 removed outlier: 4.216A pdb=" N VAL a 361 " --> pdb=" O ILE a 237 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE a 237 " --> pdb=" O VAL a 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 316 through 319 removed outlier: 6.444A pdb=" N VAL a 296 " --> pdb=" O VAL a 318 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 418 through 420 Processing sheet with id=AB5, first strand: chain 'a' and resid 500 through 503 removed outlier: 3.550A pdb=" N LYS a 508 " --> pdb=" O ASP a 503 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 11 through 13 removed outlier: 4.031A pdb=" N VAL B 511 " --> pdb=" O ASP E 71 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE E 73 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN B 513 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE E 75 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE B 515 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 55 through 57 removed outlier: 7.349A pdb=" N ASP B 43 " --> pdb=" O ASP D 523 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ALA D 525 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU B 45 " --> pdb=" O ALA D 525 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AB9, first strand: chain 'B' and resid 193 through 199 removed outlier: 6.545A pdb=" N GLN B 194 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU B 369 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 196 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLY B 371 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 198 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 304 through 306 removed outlier: 6.497A pdb=" N PHE B 284 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B 225 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU B 344 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU B 227 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 342 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 470 through 473 Processing sheet with id=AC3, first strand: chain 'b' and resid 12 through 13 removed outlier: 6.615A pdb=" N ASP e 71 " --> pdb=" O VAL b 511 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN b 513 " --> pdb=" O ASP e 71 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 55 through 57 removed outlier: 7.533A pdb=" N ASP b 43 " --> pdb=" O ASP d 523 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ALA d 525 " --> pdb=" O ASP b 43 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU b 45 " --> pdb=" O ALA d 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'b' and resid 140 through 141 Processing sheet with id=AC6, first strand: chain 'b' and resid 193 through 199 removed outlier: 6.438A pdb=" N GLN b 194 " --> pdb=" O ILE b 367 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU b 369 " --> pdb=" O GLN b 194 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE b 196 " --> pdb=" O LEU b 369 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY b 371 " --> pdb=" O ILE b 196 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE b 198 " --> pdb=" O GLY b 371 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 304 through 306 removed outlier: 6.942A pdb=" N ARG b 225 " --> pdb=" O GLU b 344 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU b 344 " --> pdb=" O ARG b 225 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU b 227 " --> pdb=" O VAL b 342 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL b 342 " --> pdb=" O GLU b 227 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 470 through 473 removed outlier: 3.504A pdb=" N THR b 478 " --> pdb=" O ASP b 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 55 through 56 removed outlier: 7.251A pdb=" N LEU G 45 " --> pdb=" O GLU Z 532 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU Z 534 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N MET G 47 " --> pdb=" O LEU Z 534 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA Z 536 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU G 49 " --> pdb=" O ALA Z 536 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU Z 533 " --> pdb=" O LEU Z 13 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AD2, first strand: chain 'G' and resid 206 through 210 removed outlier: 3.927A pdb=" N GLY G 383 " --> pdb=" O ILE G 209 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 224 through 225 Processing sheet with id=AD4, first strand: chain 'G' and resid 315 through 318 removed outlier: 6.238A pdb=" N VAL G 295 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL G 244 " --> pdb=" O ILE G 296 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N VAL G 337 " --> pdb=" O VAL G 243 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU G 245 " --> pdb=" O VAL G 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 482 through 484 Processing sheet with id=AD6, first strand: chain 'g' and resid 55 through 56 removed outlier: 7.437A pdb=" N LEU g 45 " --> pdb=" O GLU z 532 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU z 534 " --> pdb=" O LEU g 45 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N MET g 47 " --> pdb=" O LEU z 534 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA z 536 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU g 49 " --> pdb=" O ALA z 536 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'g' and resid 141 through 142 Processing sheet with id=AD8, first strand: chain 'g' and resid 206 through 210 removed outlier: 4.079A pdb=" N GLY g 383 " --> pdb=" O ILE g 209 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'g' and resid 224 through 225 Processing sheet with id=AE1, first strand: chain 'g' and resid 237 through 238 Processing sheet with id=AE2, first strand: chain 'g' and resid 315 through 317 removed outlier: 6.385A pdb=" N VAL g 295 " --> pdb=" O LEU g 317 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL g 244 " --> pdb=" O ILE g 296 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N VAL g 337 " --> pdb=" O VAL g 243 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU g 245 " --> pdb=" O VAL g 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'g' and resid 482 through 484 Processing sheet with id=AE4, first strand: chain 'D' and resid 194 through 200 removed outlier: 6.659A pdb=" N ARG D 195 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE D 379 " --> pdb=" O ARG D 195 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL D 197 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLY D 381 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS D 199 " --> pdb=" O GLY D 381 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 213 through 215 removed outlier: 3.837A pdb=" N VAL D 361 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU D 349 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU D 230 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU D 351 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG D 228 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL D 285 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS D 233 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU D 287 " --> pdb=" O LYS D 233 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY D 235 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLN D 289 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE D 237 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 213 through 215 removed outlier: 3.837A pdb=" N VAL D 361 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU D 349 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU D 230 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU D 351 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG D 228 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ILE D 333 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU D 236 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AE8, first strand: chain 'D' and resid 480 through 483 Processing sheet with id=AE9, first strand: chain 'd' and resid 194 through 200 removed outlier: 6.601A pdb=" N ARG d 195 " --> pdb=" O VAL d 377 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE d 379 " --> pdb=" O ARG d 195 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL d 197 " --> pdb=" O ILE d 379 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLY d 381 " --> pdb=" O VAL d 197 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS d 199 " --> pdb=" O GLY d 381 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU d 208 " --> pdb=" O VAL d 378 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'd' and resid 213 through 214 removed outlier: 6.721A pdb=" N ASP d 348 " --> pdb=" O LYS d 231 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'd' and resid 311 through 316 removed outlier: 3.617A pdb=" N ASP d 315 " --> pdb=" O ILE d 288 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY d 235 " --> pdb=" O LEU d 287 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLN d 289 " --> pdb=" O GLY d 235 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE d 237 " --> pdb=" O GLN d 289 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ILE d 333 " --> pdb=" O ILE d 234 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU d 236 " --> pdb=" O ILE d 333 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 410 through 412 Processing sheet with id=AF4, first strand: chain 'd' and resid 480 through 483 Processing sheet with id=AF5, first strand: chain 'E' and resid 39 through 42 removed outlier: 6.250A pdb=" N ASP H 50 " --> pdb=" O ILE E 551 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN E 553 " --> pdb=" O ASP H 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AF7, first strand: chain 'E' and resid 224 through 228 Processing sheet with id=AF8, first strand: chain 'E' and resid 242 through 244 removed outlier: 7.101A pdb=" N ASP E 390 " --> pdb=" O PHE E 385 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N PHE E 385 " --> pdb=" O ASP E 390 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE E 380 " --> pdb=" O VAL E 258 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 342 through 343 removed outlier: 6.651A pdb=" N VAL E 321 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 320 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'e' and resid 39 through 42 removed outlier: 7.124A pdb=" N ASP h 50 " --> pdb=" O ILE e 551 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN e 553 " --> pdb=" O ASP h 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 166 through 167 Processing sheet with id=AG3, first strand: chain 'e' and resid 224 through 230 removed outlier: 7.003A pdb=" N LYS e 225 " --> pdb=" O CYS e 406 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL e 408 " --> pdb=" O LYS e 225 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN e 227 " --> pdb=" O VAL e 408 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLY e 410 " --> pdb=" O GLN e 227 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG e 229 " --> pdb=" O GLY e 410 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'e' and resid 243 through 245 removed outlier: 6.802A pdb=" N ASP e 390 " --> pdb=" O PHE e 385 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N PHE e 385 " --> pdb=" O ASP e 390 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'e' and resid 342 through 343 removed outlier: 6.852A pdb=" N VAL e 321 " --> pdb=" O VAL e 343 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS e 268 " --> pdb=" O VAL e 320 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE e 322 " --> pdb=" O LYS e 268 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA e 270 " --> pdb=" O ILE e 322 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Z' and resid 53 through 56 removed outlier: 6.756A pdb=" N LEU Z 43 " --> pdb=" O ILE Q 541 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN Q 543 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET Z 45 " --> pdb=" O GLN Q 543 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AG8, first strand: chain 'Z' and resid 194 through 199 removed outlier: 6.257A pdb=" N GLU Z 195 " --> pdb=" O ILE Z 378 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE Z 380 " --> pdb=" O GLU Z 195 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET Z 197 " --> pdb=" O ILE Z 380 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 213 through 215 removed outlier: 3.891A pdb=" N LEU Z 213 " --> pdb=" O VAL Z 367 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 315 through 317 removed outlier: 6.814A pdb=" N PHE Z 293 " --> pdb=" O LEU Z 315 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU Z 317 " --> pdb=" O PHE Z 293 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE Z 295 " --> pdb=" O LEU Z 317 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR Z 232 " --> pdb=" O VAL Z 294 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE Z 296 " --> pdb=" O TYR Z 232 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU Z 234 " --> pdb=" O ILE Z 296 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N GLN Z 337 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE Z 235 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'Z' and resid 315 through 317 removed outlier: 6.814A pdb=" N PHE Z 293 " --> pdb=" O LEU Z 315 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU Z 317 " --> pdb=" O PHE Z 293 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE Z 295 " --> pdb=" O LEU Z 317 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR Z 232 " --> pdb=" O VAL Z 294 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE Z 296 " --> pdb=" O TYR Z 232 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU Z 234 " --> pdb=" O ILE Z 296 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 490 through 491 Processing sheet with id=AH4, first strand: chain 'z' and resid 53 through 56 removed outlier: 7.371A pdb=" N LEU z 43 " --> pdb=" O GLN q 543 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ILE q 545 " --> pdb=" O LEU z 43 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N MET z 45 " --> pdb=" O ILE q 545 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'z' and resid 138 through 139 Processing sheet with id=AH6, first strand: chain 'z' and resid 194 through 200 Processing sheet with id=AH7, first strand: chain 'z' and resid 214 through 215 Processing sheet with id=AH8, first strand: chain 'z' and resid 314 through 317 removed outlier: 6.945A pdb=" N PHE z 293 " --> pdb=" O LEU z 315 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU z 317 " --> pdb=" O PHE z 293 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE z 295 " --> pdb=" O LEU z 317 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU z 236 " --> pdb=" O ILE z 296 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N GLN z 337 " --> pdb=" O VAL z 233 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE z 235 " --> pdb=" O GLN z 337 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'z' and resid 314 through 317 removed outlier: 6.945A pdb=" N PHE z 293 " --> pdb=" O LEU z 315 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU z 317 " --> pdb=" O PHE z 293 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE z 295 " --> pdb=" O LEU z 317 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU z 236 " --> pdb=" O ILE z 296 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'z' and resid 490 through 491 Processing sheet with id=AI2, first strand: chain 'H' and resid 18 through 21 removed outlier: 3.526A pdb=" N ASP H 18 " --> pdb=" O THR H 525 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASN Q 52 " --> pdb=" O VAL H 520 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU H 522 " --> pdb=" O ASN Q 52 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 145 through 146 Processing sheet with id=AI4, first strand: chain 'H' and resid 199 through 205 Processing sheet with id=AI5, first strand: chain 'H' and resid 219 through 220 Processing sheet with id=AI6, first strand: chain 'H' and resid 313 through 315 removed outlier: 8.556A pdb=" N GLN H 335 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER H 243 " --> pdb=" O GLN H 335 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 313 through 315 Processing sheet with id=AI8, first strand: chain 'H' and resid 479 through 482 removed outlier: 4.117A pdb=" N ASN H 487 " --> pdb=" O VAL H 482 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'h' and resid 17 through 21 removed outlier: 6.386A pdb=" N ASN q 52 " --> pdb=" O VAL h 520 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU h 522 " --> pdb=" O ASN q 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS q 61 " --> pdb=" O ASN q 57 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'h' and resid 145 through 146 Processing sheet with id=AJ2, first strand: chain 'h' and resid 199 through 203 Processing sheet with id=AJ3, first strand: chain 'h' and resid 313 through 315 Processing sheet with id=AJ4, first strand: chain 'h' and resid 351 through 355 Processing sheet with id=AJ5, first strand: chain 'h' and resid 479 through 482 removed outlier: 4.258A pdb=" N ASN h 487 " --> pdb=" O VAL h 482 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Q' and resid 148 through 149 Processing sheet with id=AJ7, first strand: chain 'Q' and resid 207 through 213 Processing sheet with id=AJ8, first strand: chain 'Q' and resid 226 through 228 Processing sheet with id=AJ9, first strand: chain 'Q' and resid 319 through 322 removed outlier: 6.397A pdb=" N LYS Q 246 " --> pdb=" O CYS Q 298 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL Q 300 " --> pdb=" O LYS Q 246 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA Q 248 " --> pdb=" O VAL Q 300 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'q' and resid 207 through 213 removed outlier: 6.782A pdb=" N ARG q 208 " --> pdb=" O ILE q 384 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU q 386 " --> pdb=" O ARG q 208 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL q 210 " --> pdb=" O LEU q 386 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLY q 388 " --> pdb=" O VAL q 210 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE q 212 " --> pdb=" O GLY q 388 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR q 221 " --> pdb=" O ILE q 385 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'q' and resid 225 through 228 Processing sheet with id=AK3, first strand: chain 'q' and resid 319 through 322 removed outlier: 6.467A pdb=" N LYS q 246 " --> pdb=" O CYS q 298 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL q 300 " --> pdb=" O LYS q 246 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA q 248 " --> pdb=" O VAL q 300 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'q' and resid 419 through 421 Processing sheet with id=AK5, first strand: chain 'q' and resid 497 through 498 Processing sheet with id=AK6, first strand: chain 'P' and resid 100 through 101 removed outlier: 6.537A pdb=" N TYR P 137 " --> pdb=" O LYS P 168 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL P 170 " --> pdb=" O TYR P 137 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE P 139 " --> pdb=" O VAL P 170 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE P 172 " --> pdb=" O PHE P 139 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS P 141 " --> pdb=" O ILE P 172 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR P 188 " --> pdb=" O LEU P 142 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU P 189 " --> pdb=" O ASN P 200 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN P 200 " --> pdb=" O LEU P 189 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL P 191 " --> pdb=" O ILE P 198 " (cutoff:3.500A) 3792 hydrogen bonds defined for protein. 10839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.87 Time building geometry restraints manager: 14.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13037 1.33 - 1.45: 13166 1.45 - 1.57: 39504 1.57 - 1.69: 0 1.69 - 1.81: 526 Bond restraints: 66233 Sorted by residual: bond pdb=" C LYS q 413 " pdb=" N PRO q 414 " ideal model delta sigma weight residual 1.334 1.553 -0.219 2.34e-02 1.83e+03 8.75e+01 bond pdb=" C LYS Q 413 " pdb=" N PRO Q 414 " ideal model delta sigma weight residual 1.334 1.552 -0.218 2.34e-02 1.83e+03 8.67e+01 bond pdb=" N PRO h 42 " pdb=" CD PRO h 42 " ideal model delta sigma weight residual 1.473 1.556 -0.083 1.40e-02 5.10e+03 3.52e+01 bond pdb=" CA ASP Z 187 " pdb=" C ASP Z 187 " ideal model delta sigma weight residual 1.517 1.534 -0.017 6.30e-03 2.52e+04 6.97e+00 bond pdb=" N PRO e 143 " pdb=" CD PRO e 143 " ideal model delta sigma weight residual 1.473 1.510 -0.037 1.40e-02 5.10e+03 6.82e+00 ... (remaining 66228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 87554 2.05 - 4.11: 1688 4.11 - 6.16: 91 6.16 - 8.21: 3 8.21 - 10.27: 2 Bond angle restraints: 89338 Sorted by residual: angle pdb=" N GLY q 508 " pdb=" CA GLY q 508 " pdb=" C GLY q 508 " ideal model delta sigma weight residual 111.85 118.78 -6.93 1.20e+00 6.94e-01 3.33e+01 angle pdb=" N THR b 469 " pdb=" CA THR b 469 " pdb=" C THR b 469 " ideal model delta sigma weight residual 114.56 109.29 5.27 1.27e+00 6.20e-01 1.72e+01 angle pdb=" C ASP Z 163 " pdb=" N ALA Z 164 " pdb=" CA ALA Z 164 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N THR B 469 " pdb=" CA THR B 469 " pdb=" C THR B 469 " ideal model delta sigma weight residual 114.56 109.68 4.88 1.27e+00 6.20e-01 1.48e+01 angle pdb=" CA THR b 469 " pdb=" C THR b 469 " pdb=" N SER b 470 " ideal model delta sigma weight residual 119.26 114.92 4.34 1.14e+00 7.69e-01 1.45e+01 ... (remaining 89333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 39868 18.00 - 36.00: 870 36.00 - 54.00: 239 54.00 - 72.00: 100 72.00 - 90.00: 45 Dihedral angle restraints: 41122 sinusoidal: 16507 harmonic: 24615 Sorted by residual: dihedral pdb=" CA ALA Z 231 " pdb=" C ALA Z 231 " pdb=" N TYR Z 232 " pdb=" CA TYR Z 232 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA PHE B 218 " pdb=" C PHE B 218 " pdb=" N GLY B 219 " pdb=" CA GLY B 219 " ideal model delta harmonic sigma weight residual 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA THR P 203 " pdb=" C THR P 203 " pdb=" N LEU P 204 " pdb=" CA LEU P 204 " ideal model delta harmonic sigma weight residual 180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 41119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 7569 0.045 - 0.090: 1573 0.090 - 0.135: 1123 0.135 - 0.181: 401 0.181 - 0.226: 17 Chirality restraints: 10683 Sorted by residual: chirality pdb=" CA VAL H 496 " pdb=" N VAL H 496 " pdb=" C VAL H 496 " pdb=" CB VAL H 496 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL h 496 " pdb=" N VAL h 496 " pdb=" C VAL h 496 " pdb=" CB VAL h 496 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL a 517 " pdb=" N VAL a 517 " pdb=" C VAL a 517 " pdb=" CB VAL a 517 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 10680 not shown) Planarity restraints: 11517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Q 413 " 0.029 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO Q 414 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO Q 414 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO Q 414 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 41 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO H 42 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO H 42 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 42 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS q 413 " -0.021 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO q 414 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO q 414 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO q 414 " -0.020 5.00e-02 4.00e+02 ... (remaining 11514 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 11140 2.77 - 3.30: 65981 3.30 - 3.84: 104750 3.84 - 4.37: 128755 4.37 - 4.90: 215629 Nonbonded interactions: 526255 Sorted by model distance: nonbonded pdb=" N ILE H 10 " pdb=" OH TYR Q 21 " model vdw 2.239 3.120 nonbonded pdb=" CG2 ILE a 57 " pdb=" CD1 LEU P 148 " model vdw 2.289 3.880 nonbonded pdb=" O LEU a 357 " pdb=" OG1 THR a 377 " model vdw 2.296 3.040 nonbonded pdb=" O PHE E 249 " pdb=" OG SER E 250 " model vdw 2.329 3.040 nonbonded pdb=" NZ LYS q 170 " pdb=" OD2 ASP q 403 " model vdw 2.330 3.120 ... (remaining 526250 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 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } 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=1.00 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: 0.880 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: 0.070 Extract box with map and model: 1.860 Check model and map are aligned: 0.380 Set scattering table: 0.490 Process input model: 117.860 Find NCS groups from input model: 4.480 Set up NCS constraints: 0.390 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:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4192 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 : 0.009 0.219 66233 Z= 0.604 Angle : 0.685 10.267 89338 Z= 0.454 Chirality : 0.057 0.226 10683 Planarity : 0.002 0.047 11517 Dihedral : 10.356 89.999 25176 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.25 % Favored : 97.58 % Rotamer: Outliers : 0.03 % Allowed : 0.68 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.08), residues: 8528 helix: 0.26 (0.07), residues: 4301 sheet: -0.06 (0.16), residues: 979 loop : -0.46 (0.11), residues: 3248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP g 500 HIS 0.001 0.000 HIS E 251 PHE 0.002 0.000 PHE P 96 TYR 0.010 0.000 TYR E 517 ARG 0.002 0.000 ARG P 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3232 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 3230 time to evaluate : 5.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 84 VAL cc_start: 0.5945 (t) cc_final: 0.5479 (t) REVERT: A 110 LYS cc_start: 0.5803 (tttt) cc_final: 0.5533 (tttt) REVERT: A 111 ARG cc_start: 0.6246 (mmt180) cc_final: 0.5744 (mmt90) REVERT: A 456 LEU cc_start: 0.6580 (mt) cc_final: 0.6309 (mt) REVERT: A 457 ILE cc_start: 0.6057 (tp) cc_final: 0.4981 (tp) REVERT: A 473 LEU cc_start: 0.6080 (mt) cc_final: 0.5799 (mt) REVERT: A 499 ASN cc_start: 0.5688 (m-40) cc_final: 0.4994 (m110) REVERT: A 509 ILE cc_start: 0.6664 (mm) cc_final: 0.6309 (mm) REVERT: A 517 VAL cc_start: 0.7692 (t) cc_final: 0.7367 (t) REVERT: A 532 LEU cc_start: 0.6285 (tt) cc_final: 0.5634 (tt) REVERT: A 541 ILE cc_start: 0.6507 (mm) cc_final: 0.5374 (mm) REVERT: a 40 VAL cc_start: 0.7083 (m) cc_final: 0.6779 (p) REVERT: a 86 LEU cc_start: 0.5558 (tp) cc_final: 0.5175 (tp) REVERT: a 282 LEU cc_start: 0.2805 (mt) cc_final: 0.2265 (mp) REVERT: a 433 LEU cc_start: 0.6379 (mt) cc_final: 0.5742 (mt) REVERT: B 98 LEU cc_start: 0.4915 (tp) cc_final: 0.4669 (tp) REVERT: B 113 SER cc_start: 0.5868 (m) cc_final: 0.5086 (t) REVERT: B 459 LEU cc_start: 0.6644 (tp) cc_final: 0.6363 (tp) REVERT: B 487 ILE cc_start: 0.8240 (mm) cc_final: 0.7921 (tt) REVERT: b 67 ILE cc_start: 0.7099 (mm) cc_final: 0.6804 (mm) REVERT: b 181 ILE cc_start: 0.5580 (mm) cc_final: 0.5278 (mm) REVERT: b 190 LEU cc_start: 0.6944 (mt) cc_final: 0.6446 (mt) REVERT: b 402 LEU cc_start: 0.6384 (mt) cc_final: 0.5925 (mt) REVERT: b 479 ILE cc_start: 0.7682 (mm) cc_final: 0.7407 (mm) REVERT: b 481 ASP cc_start: 0.4020 (t70) cc_final: 0.3767 (p0) REVERT: G 81 LEU cc_start: 0.5913 (tp) cc_final: 0.5563 (tp) REVERT: G 94 THR cc_start: 0.5087 (p) cc_final: 0.4824 (p) REVERT: G 97 ILE cc_start: 0.6438 (mm) cc_final: 0.6193 (mm) REVERT: G 102 GLU cc_start: 0.5319 (tp30) cc_final: 0.4868 (tp30) REVERT: G 113 GLU cc_start: 0.5316 (mt-10) cc_final: 0.5114 (mt-10) REVERT: G 139 VAL cc_start: 0.6465 (m) cc_final: 0.6064 (p) REVERT: G 437 ILE cc_start: 0.7811 (tp) cc_final: 0.7577 (tp) REVERT: G 445 VAL cc_start: 0.6879 (t) cc_final: 0.6574 (p) REVERT: G 465 ILE cc_start: 0.6205 (mm) cc_final: 0.5988 (mp) REVERT: G 467 LEU cc_start: 0.6495 (mp) cc_final: 0.5936 (mp) REVERT: G 512 THR cc_start: 0.5193 (p) cc_final: 0.4453 (m) REVERT: G 514 ILE cc_start: 0.6429 (mt) cc_final: 0.6210 (mt) REVERT: g 57 LEU cc_start: 0.5937 (mt) cc_final: 0.5723 (mm) REVERT: g 102 GLU cc_start: 0.4511 (tp30) cc_final: 0.4180 (tp30) REVERT: g 103 ILE cc_start: 0.6347 (mt) cc_final: 0.6073 (mt) REVERT: g 112 ILE cc_start: 0.6879 (mm) cc_final: 0.6624 (mm) REVERT: g 234 MET cc_start: -0.1328 (tpt) cc_final: -0.2453 (tmm) REVERT: g 283 MET cc_start: -0.0583 (mtt) cc_final: -0.1077 (mtp) REVERT: g 456 LEU cc_start: 0.7205 (mt) cc_final: 0.6677 (mm) REVERT: g 457 ILE cc_start: 0.6803 (mt) cc_final: 0.6525 (mt) REVERT: g 512 THR cc_start: 0.5677 (p) cc_final: 0.5093 (m) REVERT: D 70 ILE cc_start: 0.5513 (mt) cc_final: 0.5224 (pt) REVERT: D 142 VAL cc_start: 0.6105 (m) cc_final: 0.5774 (p) REVERT: D 229 LYS cc_start: 0.0024 (mmmt) cc_final: -0.0257 (mmtp) REVERT: D 260 MET cc_start: -0.2933 (tpp) cc_final: -0.4325 (mtt) REVERT: D 421 ILE cc_start: 0.5740 (mt) cc_final: 0.5365 (mt) REVERT: D 425 LEU cc_start: 0.5858 (mt) cc_final: 0.5386 (mt) REVERT: D 439 ILE cc_start: 0.5896 (mt) cc_final: 0.5435 (mt) REVERT: D 449 VAL cc_start: 0.6033 (p) cc_final: 0.5657 (p) REVERT: D 453 THR cc_start: 0.5402 (m) cc_final: 0.5172 (p) REVERT: D 466 VAL cc_start: 0.5931 (t) cc_final: 0.5127 (t) REVERT: d 36 ARG cc_start: 0.5871 (ttp80) cc_final: 0.4809 (tmm160) REVERT: d 86 ASP cc_start: 0.4789 (t70) cc_final: 0.4580 (t0) REVERT: d 103 LEU cc_start: 0.6202 (tp) cc_final: 0.5882 (tp) REVERT: d 124 PHE cc_start: 0.5417 (m-10) cc_final: 0.5154 (m-10) REVERT: d 395 HIS cc_start: 0.4541 (t70) cc_final: 0.4152 (t70) REVERT: d 510 LEU cc_start: 0.6354 (mt) cc_final: 0.6005 (mm) REVERT: E 51 ILE cc_start: 0.5443 (mt) cc_final: 0.5205 (mt) REVERT: E 129 LEU cc_start: 0.6819 (mt) cc_final: 0.6189 (mt) REVERT: E 150 PHE cc_start: 0.5521 (m-10) cc_final: 0.5021 (m-10) REVERT: E 211 VAL cc_start: 0.3645 (m) cc_final: 0.3093 (m) REVERT: E 490 ASP cc_start: 0.2685 (t0) cc_final: 0.2054 (t70) REVERT: E 552 ASP cc_start: 0.4980 (t70) cc_final: 0.4561 (t0) REVERT: e 134 LEU cc_start: 0.6371 (tp) cc_final: 0.6118 (tp) REVERT: e 225 LYS cc_start: 0.4587 (mmtt) cc_final: 0.4058 (mmtt) REVERT: e 528 VAL cc_start: 0.6102 (t) cc_final: 0.5841 (p) REVERT: e 552 ASP cc_start: 0.4607 (t70) cc_final: 0.4317 (t0) REVERT: Z 46 LEU cc_start: 0.6951 (mp) cc_final: 0.6745 (mp) REVERT: Z 93 THR cc_start: 0.7010 (m) cc_final: 0.6726 (p) REVERT: Z 196 ILE cc_start: 0.7269 (mm) cc_final: 0.6924 (mm) REVERT: Z 306 LEU cc_start: 0.5028 (mt) cc_final: 0.4723 (mt) REVERT: Z 422 LEU cc_start: 0.7413 (mt) cc_final: 0.6630 (tt) REVERT: Z 447 PHE cc_start: 0.6567 (t80) cc_final: 0.6265 (t80) REVERT: Z 458 LEU cc_start: 0.6886 (mt) cc_final: 0.6501 (mt) REVERT: z 63 LEU cc_start: 0.6385 (mt) cc_final: 0.5767 (mt) REVERT: z 128 GLU cc_start: 0.5516 (mm-30) cc_final: 0.4807 (mm-30) REVERT: z 133 LEU cc_start: 0.6790 (tp) cc_final: 0.6408 (tp) REVERT: z 422 LEU cc_start: 0.7483 (tp) cc_final: 0.6786 (tt) REVERT: z 513 LEU cc_start: 0.6467 (mt) cc_final: 0.6256 (mt) REVERT: H 27 ILE cc_start: 0.7674 (mt) cc_final: 0.7438 (mt) REVERT: H 104 LEU cc_start: 0.6414 (mt) cc_final: 0.6154 (mm) REVERT: H 108 LEU cc_start: 0.6270 (mt) cc_final: 0.6003 (mt) REVERT: H 293 VAL cc_start: 0.6066 (t) cc_final: 0.5851 (m) REVERT: H 409 ILE cc_start: 0.6221 (pt) cc_final: 0.5937 (pt) REVERT: H 421 SER cc_start: 0.6161 (t) cc_final: 0.4086 (p) REVERT: H 426 ASP cc_start: 0.3725 (m-30) cc_final: 0.2192 (m-30) REVERT: H 465 LEU cc_start: 0.5422 (mt) cc_final: 0.5104 (mt) REVERT: h 26 ILE cc_start: 0.6487 (mt) cc_final: 0.5910 (mt) REVERT: h 65 ASP cc_start: 0.4578 (t70) cc_final: 0.3819 (t0) REVERT: h 94 VAL cc_start: 0.6402 (t) cc_final: 0.5880 (t) REVERT: h 108 LEU cc_start: 0.6375 (mt) cc_final: 0.6131 (mt) REVERT: h 389 VAL cc_start: 0.7078 (t) cc_final: 0.6556 (t) REVERT: h 502 VAL cc_start: 0.6450 (t) cc_final: 0.6178 (p) REVERT: h 516 LEU cc_start: 0.7338 (tp) cc_final: 0.6882 (tp) REVERT: Q 39 HIS cc_start: 0.7073 (t70) cc_final: 0.5878 (t-90) REVERT: Q 49 CYS cc_start: 0.7053 (m) cc_final: 0.5827 (m) REVERT: Q 71 MET cc_start: 0.3652 (tmm) cc_final: 0.3168 (tmm) REVERT: Q 83 LYS cc_start: 0.6680 (mmmt) cc_final: 0.6433 (tppp) REVERT: Q 86 VAL cc_start: 0.6112 (t) cc_final: 0.5788 (p) REVERT: Q 96 MET cc_start: 0.5709 (tpp) cc_final: 0.5428 (tpp) REVERT: Q 105 ILE cc_start: 0.7204 (mt) cc_final: 0.6514 (mt) REVERT: Q 142 LEU cc_start: 0.6923 (mt) cc_final: 0.6217 (mm) REVERT: Q 150 ILE cc_start: 0.6587 (mm) cc_final: 0.6360 (mm) REVERT: Q 167 ILE cc_start: 0.5859 (mm) cc_final: 0.5648 (mm) REVERT: Q 207 ILE cc_start: 0.6951 (mt) cc_final: 0.6709 (tp) REVERT: Q 396 ASP cc_start: 0.3743 (t70) cc_final: 0.3320 (t70) REVERT: Q 452 PHE cc_start: 0.6764 (t80) cc_final: 0.6542 (t80) REVERT: Q 478 LEU cc_start: 0.7583 (mt) cc_final: 0.7001 (mm) REVERT: Q 530 VAL cc_start: 0.7408 (t) cc_final: 0.6844 (t) REVERT: q 35 ILE cc_start: 0.7750 (mt) cc_final: 0.7518 (tp) REVERT: q 71 MET cc_start: 0.5884 (ttp) cc_final: 0.3895 (ttp) REVERT: q 111 LEU cc_start: 0.7121 (mt) cc_final: 0.6507 (mt) REVERT: q 112 ASN cc_start: 0.6618 (m-40) cc_final: 0.5962 (m110) REVERT: q 132 ASN cc_start: 0.5806 (m-40) cc_final: 0.5433 (m110) REVERT: q 142 LEU cc_start: 0.6822 (mt) cc_final: 0.6105 (mt) REVERT: q 160 LEU cc_start: 0.6316 (mt) cc_final: 0.6108 (mt) REVERT: q 444 LEU cc_start: 0.7735 (mp) cc_final: 0.7403 (mt) REVERT: q 447 LEU cc_start: 0.6592 (mt) cc_final: 0.6290 (mt) REVERT: q 544 ILE cc_start: 0.7445 (mt) cc_final: 0.6576 (mm) outliers start: 2 outliers final: 1 residues processed: 3231 average time/residue: 0.6864 time to fit residues: 3649.0295 Evaluate side-chains 2245 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2244 time to evaluate : 5.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 411 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 715 optimal weight: 0.9980 chunk 641 optimal weight: 9.9990 chunk 356 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 433 optimal weight: 6.9990 chunk 342 optimal weight: 6.9990 chunk 663 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 403 optimal weight: 5.9990 chunk 494 optimal weight: 7.9990 chunk 769 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 485 GLN ** a 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 158 ASN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 435 ASN ** a 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 168 GLN b 282 ASN b 296 GLN b 308 HIS b 385 HIS b 465 ASN G 395 ASN G 443 GLN g 72 HIS g 395 ASN g 443 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN D 192 ASN D 273 ASN D 395 HIS ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 GLN ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 GLN ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN ** E 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 GLN ** e 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 353 HIS ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 110 GLN Z 192 HIS ** Z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 67 GLN z 110 GLN z 185 GLN ** z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 356 GLN ** z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 515 ASN ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 370 GLN h 29 ASN ** h 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 HIS h 238 ASN ** h 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 472 HIS ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 494 HIS ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 27 GLN q 52 ASN ** q 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 203 ASN q 283 GLN ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 477 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4630 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 66233 Z= 0.285 Angle : 0.781 17.107 89338 Z= 0.410 Chirality : 0.048 0.279 10683 Planarity : 0.005 0.061 11517 Dihedral : 4.482 34.766 9055 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.04 % Favored : 97.87 % Rotamer: Outliers : 3.08 % Allowed : 13.22 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.09), residues: 8528 helix: 1.10 (0.07), residues: 4339 sheet: 0.28 (0.16), residues: 988 loop : -0.54 (0.11), residues: 3201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 440 HIS 0.021 0.002 HIS a 403 PHE 0.038 0.003 PHE E 179 TYR 0.028 0.002 TYR b 291 ARG 0.014 0.001 ARG b 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2688 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 2465 time to evaluate : 5.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 84 VAL cc_start: 0.6531 (t) cc_final: 0.5955 (t) REVERT: A 107 GLU cc_start: 0.4211 (tp30) cc_final: 0.3963 (tp30) REVERT: A 458 ILE cc_start: 0.6817 (mm) cc_final: 0.6548 (mm) REVERT: A 542 ASP cc_start: 0.4993 (p0) cc_final: 0.4597 (p0) REVERT: A 544 MET cc_start: 0.4051 (tpt) cc_final: 0.2990 (tpp) REVERT: a 60 PHE cc_start: 0.7277 (p90) cc_final: 0.6641 (p90) REVERT: a 94 ILE cc_start: 0.5955 (mm) cc_final: 0.5381 (tp) REVERT: a 118 ASN cc_start: 0.6589 (m110) cc_final: 0.6362 (m110) REVERT: a 282 LEU cc_start: 0.2759 (mt) cc_final: 0.1997 (mp) REVERT: a 530 SER cc_start: 0.6107 (m) cc_final: 0.5862 (m) REVERT: B 113 SER cc_start: 0.5960 (m) cc_final: 0.5412 (t) REVERT: B 152 ASP cc_start: 0.2531 (m-30) cc_final: 0.2220 (m-30) REVERT: B 418 GLU cc_start: 0.4406 (tp30) cc_final: 0.4053 (tp30) REVERT: B 487 ILE cc_start: 0.7932 (mm) cc_final: 0.7672 (tt) REVERT: b 43 ASP cc_start: 0.5241 (m-30) cc_final: 0.3438 (m-30) REVERT: b 67 ILE cc_start: 0.7019 (mm) cc_final: 0.6747 (mm) REVERT: b 191 GLU cc_start: 0.4661 (tp30) cc_final: 0.4428 (tp30) REVERT: b 307 GLU cc_start: 0.4292 (OUTLIER) cc_final: 0.2994 (mm-30) REVERT: b 390 VAL cc_start: 0.6972 (m) cc_final: 0.6591 (p) REVERT: b 433 PHE cc_start: 0.7066 (t80) cc_final: 0.6716 (t80) REVERT: b 455 LEU cc_start: 0.5659 (pp) cc_final: 0.5358 (pp) REVERT: b 515 ILE cc_start: 0.5709 (mm) cc_final: 0.4711 (mm) REVERT: G 44 MET cc_start: 0.5652 (mmm) cc_final: 0.5263 (mmm) REVERT: G 113 GLU cc_start: 0.5367 (mt-10) cc_final: 0.5062 (mt-10) REVERT: G 234 MET cc_start: 0.0617 (ptp) cc_final: 0.0250 (ptp) REVERT: G 359 MET cc_start: 0.4356 (tpt) cc_final: 0.3739 (tpt) REVERT: G 445 VAL cc_start: 0.6945 (t) cc_final: 0.6592 (p) REVERT: G 475 HIS cc_start: 0.5775 (OUTLIER) cc_final: 0.5276 (m170) REVERT: G 487 ASP cc_start: 0.6286 (p0) cc_final: 0.5577 (p0) REVERT: g 29 LYS cc_start: 0.6519 (ttmt) cc_final: 0.6274 (tttt) REVERT: g 99 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5640 (tp) REVERT: g 203 TYR cc_start: 0.3437 (m-80) cc_final: 0.3225 (m-80) REVERT: g 283 MET cc_start: -0.0769 (mtt) cc_final: -0.1753 (mtp) REVERT: g 327 ARG cc_start: 0.5851 (mmp80) cc_final: 0.3981 (mtt180) REVERT: g 447 ASP cc_start: 0.5773 (t0) cc_final: 0.4833 (t0) REVERT: g 472 ARG cc_start: 0.5236 (mtm180) cc_final: 0.5013 (mtm180) REVERT: D 91 ASP cc_start: 0.4593 (t0) cc_final: 0.4207 (t0) REVERT: D 96 VAL cc_start: 0.5783 (m) cc_final: 0.5541 (p) REVERT: D 108 GLU cc_start: 0.4964 (tt0) cc_final: 0.4675 (tt0) REVERT: D 124 PHE cc_start: 0.5468 (m-10) cc_final: 0.5253 (m-10) REVERT: D 149 GLN cc_start: 0.5337 (mm-40) cc_final: 0.4925 (mm-40) REVERT: D 260 MET cc_start: -0.2738 (tpp) cc_final: -0.4714 (mtm) REVERT: D 419 ILE cc_start: 0.5568 (mm) cc_final: 0.5241 (mm) REVERT: D 524 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7176 (tt) REVERT: d 125 GLN cc_start: 0.5381 (tm-30) cc_final: 0.4498 (tm-30) REVERT: d 137 GLU cc_start: 0.5432 (tm-30) cc_final: 0.5117 (tm-30) REVERT: d 420 GLU cc_start: 0.3627 (tp30) cc_final: 0.3330 (tp30) REVERT: d 464 LYS cc_start: 0.6545 (tttm) cc_final: 0.6117 (tttm) REVERT: E 52 LEU cc_start: 0.6261 (pp) cc_final: 0.5755 (pp) REVERT: E 124 VAL cc_start: 0.6249 (m) cc_final: 0.6032 (m) REVERT: E 129 LEU cc_start: 0.6876 (mt) cc_final: 0.6444 (mt) REVERT: E 472 PHE cc_start: 0.6108 (t80) cc_final: 0.5877 (t80) REVERT: E 486 ASN cc_start: 0.6630 (t0) cc_final: 0.6221 (t0) REVERT: E 552 ASP cc_start: 0.4940 (t70) cc_final: 0.4472 (t0) REVERT: e 136 LEU cc_start: 0.5847 (mt) cc_final: 0.5596 (mt) REVERT: Z 29 LEU cc_start: 0.7578 (tp) cc_final: 0.7332 (tt) REVERT: Z 104 GLN cc_start: 0.5256 (mm-40) cc_final: 0.4766 (mm-40) REVERT: Z 127 LYS cc_start: 0.6746 (ptpt) cc_final: 0.6308 (ptpp) REVERT: Z 224 MET cc_start: 0.3001 (OUTLIER) cc_final: 0.2783 (ptm) REVERT: Z 402 VAL cc_start: 0.6951 (m) cc_final: 0.6511 (t) REVERT: Z 422 LEU cc_start: 0.7655 (mt) cc_final: 0.7106 (tt) REVERT: Z 454 ILE cc_start: 0.8208 (mm) cc_final: 0.7795 (mm) REVERT: Z 513 LEU cc_start: 0.7210 (mm) cc_final: 0.6891 (mm) REVERT: Z 526 ASN cc_start: 0.6953 (m-40) cc_final: 0.6724 (m-40) REVERT: Z 529 LEU cc_start: 0.5676 (mt) cc_final: 0.5244 (mt) REVERT: z 63 LEU cc_start: 0.6039 (mt) cc_final: 0.5729 (mt) REVERT: z 108 PHE cc_start: 0.5827 (m-80) cc_final: 0.5591 (m-10) REVERT: z 140 LYS cc_start: 0.6284 (tppt) cc_final: 0.6069 (tppt) REVERT: z 181 VAL cc_start: 0.6351 (m) cc_final: 0.6120 (p) REVERT: z 513 LEU cc_start: 0.6540 (mt) cc_final: 0.6269 (mp) REVERT: H 75 VAL cc_start: 0.7485 (t) cc_final: 0.7225 (p) REVERT: H 108 LEU cc_start: 0.6462 (mt) cc_final: 0.6250 (mt) REVERT: H 465 LEU cc_start: 0.5739 (mt) cc_final: 0.5421 (mt) REVERT: h 37 GLN cc_start: 0.6786 (tm-30) cc_final: 0.6442 (tm-30) REVERT: h 108 LEU cc_start: 0.7048 (mt) cc_final: 0.6782 (mm) REVERT: h 123 HIS cc_start: 0.5555 (t70) cc_final: 0.5147 (t-90) REVERT: h 282 LEU cc_start: 0.6744 (mt) cc_final: 0.6222 (mp) REVERT: h 453 LEU cc_start: 0.7134 (mt) cc_final: 0.6838 (mt) REVERT: h 502 VAL cc_start: 0.6362 (t) cc_final: 0.6090 (p) REVERT: Q 49 CYS cc_start: 0.6662 (m) cc_final: 0.6280 (m) REVERT: Q 96 MET cc_start: 0.5974 (tpp) cc_final: 0.5733 (tpp) REVERT: Q 109 GLU cc_start: 0.5546 (mm-30) cc_final: 0.5125 (mm-30) REVERT: Q 129 GLN cc_start: 0.6333 (tp-100) cc_final: 0.5579 (tp-100) REVERT: Q 142 LEU cc_start: 0.7018 (mt) cc_final: 0.6559 (mm) REVERT: Q 171 LYS cc_start: 0.6237 (mtmm) cc_final: 0.6027 (mttt) REVERT: Q 524 LYS cc_start: 0.7625 (mmmm) cc_final: 0.7361 (mmmm) REVERT: q 27 GLN cc_start: 0.6133 (tp40) cc_final: 0.5690 (tp-100) REVERT: q 444 LEU cc_start: 0.7450 (mp) cc_final: 0.7117 (mt) REVERT: q 494 HIS cc_start: 0.5205 (p90) cc_final: 0.4894 (p90) outliers start: 223 outliers final: 114 residues processed: 2560 average time/residue: 0.6811 time to fit residues: 2913.6584 Evaluate side-chains 2262 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 2143 time to evaluate : 5.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 85 GLU Chi-restraints excluded: chain a residue 115 LEU Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 123 THR Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 535 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 307 GLU Chi-restraints excluded: chain b residue 385 HIS Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 430 VAL Chi-restraints excluded: chain b residue 454 GLU Chi-restraints excluded: chain b residue 502 SER Chi-restraints excluded: chain G residue 62 HIS Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 395 ASN Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain g residue 50 ASP Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain d residue 149 GLN Chi-restraints excluded: chain d residue 169 PHE Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 411 ILE Chi-restraints excluded: chain d residue 419 ILE Chi-restraints excluded: chain d residue 512 SER Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 142 HIS Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain e residue 156 LEU Chi-restraints excluded: chain e residue 457 GLU Chi-restraints excluded: chain e residue 469 PHE Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 156 SER Chi-restraints excluded: chain Z residue 194 VAL Chi-restraints excluded: chain Z residue 209 PHE Chi-restraints excluded: chain Z residue 224 MET Chi-restraints excluded: chain Z residue 317 LEU Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 94 VAL Chi-restraints excluded: chain z residue 157 SER Chi-restraints excluded: chain z residue 169 VAL Chi-restraints excluded: chain z residue 192 HIS Chi-restraints excluded: chain z residue 279 ASP Chi-restraints excluded: chain z residue 283 GLU Chi-restraints excluded: chain z residue 423 SER Chi-restraints excluded: chain z residue 479 ASP Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain H residue 472 HIS Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 214 PHE Chi-restraints excluded: chain h residue 279 PHE Chi-restraints excluded: chain h residue 409 ILE Chi-restraints excluded: chain h residue 444 LYS Chi-restraints excluded: chain h residue 525 THR Chi-restraints excluded: chain Q residue 58 HIS Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 174 SER Chi-restraints excluded: chain Q residue 472 ASN Chi-restraints excluded: chain Q residue 493 ASP Chi-restraints excluded: chain Q residue 506 ASP Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 46 MET Chi-restraints excluded: chain q residue 57 ASN Chi-restraints excluded: chain q residue 84 VAL Chi-restraints excluded: chain q residue 157 ASN Chi-restraints excluded: chain q residue 183 SER Chi-restraints excluded: chain q residue 207 ILE Chi-restraints excluded: chain q residue 219 ASN Chi-restraints excluded: chain q residue 245 HIS Chi-restraints excluded: chain q residue 329 LEU Chi-restraints excluded: chain q residue 475 LEU Chi-restraints excluded: chain q residue 499 VAL Chi-restraints excluded: chain q residue 519 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 427 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 640 optimal weight: 0.6980 chunk 523 optimal weight: 4.9990 chunk 212 optimal weight: 0.5980 chunk 770 optimal weight: 6.9990 chunk 832 optimal weight: 2.9990 chunk 686 optimal weight: 9.9990 chunk 764 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 618 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 77 HIS A 89 GLN A 481 HIS ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 194 GLN b 385 HIS G 21 GLN G 395 ASN ** G 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN g 459 ASN g 470 GLN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 GLN d 395 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN E 424 HIS E 509 ASN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 432 ASN ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN e 502 GLN ** Z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 324 ASN z 356 GLN ** z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 HIS ** H 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN ** h 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN ** q 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 219 ASN ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 477 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4680 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 66233 Z= 0.252 Angle : 0.777 14.745 89338 Z= 0.400 Chirality : 0.048 0.277 10683 Planarity : 0.005 0.098 11517 Dihedral : 4.475 31.122 9055 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 3.40 % Allowed : 17.09 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 8528 helix: 1.04 (0.07), residues: 4335 sheet: 0.32 (0.17), residues: 999 loop : -0.64 (0.11), residues: 3194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 167 HIS 0.018 0.002 HIS Q 39 PHE 0.042 0.003 PHE q 137 TYR 0.045 0.002 TYR A 432 ARG 0.015 0.001 ARG b 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2576 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 2330 time to evaluate : 5.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 110 LYS cc_start: 0.6120 (tmmt) cc_final: 0.5872 (tmmt) REVERT: A 458 ILE cc_start: 0.6759 (mm) cc_final: 0.6550 (mm) REVERT: A 545 ILE cc_start: 0.5178 (OUTLIER) cc_final: 0.4730 (tp) REVERT: a 115 LEU cc_start: 0.6829 (mt) cc_final: 0.6525 (mt) REVERT: a 137 ILE cc_start: 0.5688 (pt) cc_final: 0.5290 (pt) REVERT: a 282 LEU cc_start: 0.2874 (mt) cc_final: 0.2108 (mp) REVERT: a 436 PHE cc_start: 0.4602 (t80) cc_final: 0.4396 (t80) REVERT: a 474 VAL cc_start: 0.5393 (t) cc_final: 0.4903 (p) REVERT: a 530 SER cc_start: 0.5680 (m) cc_final: 0.5001 (m) REVERT: B 113 SER cc_start: 0.6337 (m) cc_final: 0.5605 (t) REVERT: b 67 ILE cc_start: 0.7108 (mm) cc_final: 0.6784 (mm) REVERT: b 122 GLU cc_start: 0.3683 (mt-10) cc_final: 0.3412 (mt-10) REVERT: b 144 HIS cc_start: 0.5892 (p-80) cc_final: 0.5598 (p-80) REVERT: b 381 GLU cc_start: 0.5048 (pp20) cc_final: 0.4091 (pp20) REVERT: b 390 VAL cc_start: 0.7135 (m) cc_final: 0.6456 (p) REVERT: b 433 PHE cc_start: 0.7074 (t80) cc_final: 0.6637 (t80) REVERT: b 493 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6527 (mm) REVERT: b 497 VAL cc_start: 0.7062 (t) cc_final: 0.6859 (t) REVERT: b 514 ILE cc_start: 0.6636 (mp) cc_final: 0.6292 (mm) REVERT: G 94 THR cc_start: 0.5479 (p) cc_final: 0.5260 (p) REVERT: G 126 LYS cc_start: 0.6601 (ptpt) cc_final: 0.6332 (ptpt) REVERT: G 234 MET cc_start: 0.0712 (ptp) cc_final: 0.0315 (ptp) REVERT: G 298 GLU cc_start: 0.1449 (tt0) cc_final: 0.0575 (tt0) REVERT: G 445 VAL cc_start: 0.7010 (t) cc_final: 0.6737 (p) REVERT: G 475 HIS cc_start: 0.5712 (OUTLIER) cc_final: 0.5042 (m170) REVERT: g 29 LYS cc_start: 0.6188 (ttmt) cc_final: 0.5966 (tttt) REVERT: g 79 LEU cc_start: 0.6573 (mt) cc_final: 0.6356 (mt) REVERT: g 80 GLU cc_start: 0.4490 (tm-30) cc_final: 0.4276 (tm-30) REVERT: g 234 MET cc_start: -0.0004 (tpp) cc_final: -0.1425 (tmm) REVERT: g 283 MET cc_start: -0.0963 (mtt) cc_final: -0.1567 (mtm) REVERT: g 522 ARG cc_start: 0.7046 (ttp80) cc_final: 0.6762 (ttp-170) REVERT: D 37 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.6421 (m) REVERT: D 45 ASP cc_start: 0.3740 (t0) cc_final: 0.3009 (t0) REVERT: D 260 MET cc_start: -0.2668 (tpp) cc_final: -0.4303 (mtt) REVERT: d 103 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6608 (mp) REVERT: d 311 MET cc_start: 0.2824 (mmt) cc_final: 0.2410 (mmt) REVERT: E 124 VAL cc_start: 0.6216 (m) cc_final: 0.6008 (m) REVERT: E 129 LEU cc_start: 0.6868 (mt) cc_final: 0.6292 (mt) REVERT: E 136 LEU cc_start: 0.6360 (mm) cc_final: 0.5924 (mm) REVERT: E 212 MET cc_start: 0.4286 (ppp) cc_final: 0.3638 (ppp) REVERT: E 452 LEU cc_start: 0.6184 (pp) cc_final: 0.5557 (pp) REVERT: E 552 ASP cc_start: 0.4809 (t70) cc_final: 0.4418 (t0) REVERT: e 114 GLU cc_start: 0.4257 (pp20) cc_final: 0.3806 (pp20) REVERT: e 164 THR cc_start: 0.6687 (p) cc_final: 0.6291 (m) REVERT: e 509 ASN cc_start: 0.4998 (p0) cc_final: 0.4771 (p0) REVERT: Z 108 PHE cc_start: 0.5799 (OUTLIER) cc_final: 0.5486 (t80) REVERT: Z 422 LEU cc_start: 0.7707 (mt) cc_final: 0.7050 (tt) REVERT: Z 473 VAL cc_start: 0.6014 (m) cc_final: 0.5782 (p) REVERT: z 205 LYS cc_start: 0.7473 (mmtm) cc_final: 0.7261 (mmtm) REVERT: z 467 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5213 (mt) REVERT: H 75 VAL cc_start: 0.7582 (t) cc_final: 0.7254 (p) REVERT: H 107 GLU cc_start: 0.4423 (tp30) cc_final: 0.3301 (tp30) REVERT: H 108 LEU cc_start: 0.6350 (mt) cc_final: 0.6059 (mt) REVERT: H 111 GLU cc_start: 0.4596 (mm-30) cc_final: 0.3600 (mm-30) REVERT: H 116 LEU cc_start: 0.7843 (mp) cc_final: 0.7464 (mt) REVERT: H 485 THR cc_start: 0.4733 (m) cc_final: 0.4046 (m) REVERT: h 30 ILE cc_start: 0.6614 (mt) cc_final: 0.6413 (mt) REVERT: h 108 LEU cc_start: 0.7050 (mt) cc_final: 0.6713 (mt) REVERT: h 116 LEU cc_start: 0.7383 (mt) cc_final: 0.7035 (mm) REVERT: h 488 ILE cc_start: 0.7431 (pt) cc_final: 0.7079 (pt) REVERT: Q 52 ASN cc_start: 0.6065 (t0) cc_final: 0.5826 (t0) REVERT: Q 109 GLU cc_start: 0.5163 (mm-30) cc_final: 0.4946 (mm-30) REVERT: Q 118 ILE cc_start: 0.8463 (mt) cc_final: 0.8091 (mm) REVERT: Q 129 GLN cc_start: 0.6260 (tp-100) cc_final: 0.5314 (tp-100) REVERT: Q 133 MET cc_start: 0.5314 (mmp) cc_final: 0.4946 (mmp) REVERT: Q 526 PHE cc_start: 0.6162 (t80) cc_final: 0.5700 (t80) REVERT: q 457 GLU cc_start: 0.5159 (pt0) cc_final: 0.4781 (pt0) outliers start: 246 outliers final: 144 residues processed: 2428 average time/residue: 0.6891 time to fit residues: 2797.3749 Evaluate side-chains 2256 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 2105 time to evaluate : 5.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 113 ASN Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 123 THR Chi-restraints excluded: chain a residue 295 VAL Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 401 SER Chi-restraints excluded: chain a residue 424 CYS Chi-restraints excluded: chain a residue 479 SER Chi-restraints excluded: chain a residue 497 TYR Chi-restraints excluded: chain a residue 502 LEU Chi-restraints excluded: chain a residue 524 LYS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 HIS Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 146 LYS Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 292 ASP Chi-restraints excluded: chain b residue 311 PHE Chi-restraints excluded: chain b residue 385 HIS Chi-restraints excluded: chain b residue 413 LYS Chi-restraints excluded: chain b residue 493 LEU Chi-restraints excluded: chain b residue 502 SER Chi-restraints excluded: chain G residue 62 HIS Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 395 ASN Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain g residue 35 ILE Chi-restraints excluded: chain g residue 50 ASP Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 98 ILE Chi-restraints excluded: chain g residue 412 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 129 LYS Chi-restraints excluded: chain d residue 149 GLN Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 411 ILE Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 512 SER Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 547 MET Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 107 LEU Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain e residue 151 ASP Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain e residue 312 ASP Chi-restraints excluded: chain e residue 321 VAL Chi-restraints excluded: chain e residue 407 PHE Chi-restraints excluded: chain e residue 457 GLU Chi-restraints excluded: chain e residue 469 PHE Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 108 PHE Chi-restraints excluded: chain Z residue 194 VAL Chi-restraints excluded: chain Z residue 209 PHE Chi-restraints excluded: chain Z residue 317 LEU Chi-restraints excluded: chain Z residue 533 LEU Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 145 ASN Chi-restraints excluded: chain z residue 157 SER Chi-restraints excluded: chain z residue 166 LEU Chi-restraints excluded: chain z residue 169 VAL Chi-restraints excluded: chain z residue 174 VAL Chi-restraints excluded: chain z residue 192 HIS Chi-restraints excluded: chain z residue 279 ASP Chi-restraints excluded: chain z residue 298 GLN Chi-restraints excluded: chain z residue 385 HIS Chi-restraints excluded: chain z residue 423 SER Chi-restraints excluded: chain z residue 467 LEU Chi-restraints excluded: chain z residue 479 ASP Chi-restraints excluded: chain z residue 509 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 141 ASN Chi-restraints excluded: chain H residue 293 VAL Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 73 LEU Chi-restraints excluded: chain h residue 127 LYS Chi-restraints excluded: chain h residue 214 PHE Chi-restraints excluded: chain h residue 279 PHE Chi-restraints excluded: chain h residue 444 LYS Chi-restraints excluded: chain h residue 446 LEU Chi-restraints excluded: chain h residue 525 THR Chi-restraints excluded: chain Q residue 40 GLN Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 58 HIS Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 115 GLU Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 174 SER Chi-restraints excluded: chain Q residue 201 TYR Chi-restraints excluded: chain Q residue 405 VAL Chi-restraints excluded: chain Q residue 472 ASN Chi-restraints excluded: chain Q residue 506 ASP Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 62 ILE Chi-restraints excluded: chain q residue 84 VAL Chi-restraints excluded: chain q residue 101 ASN Chi-restraints excluded: chain q residue 157 ASN Chi-restraints excluded: chain q residue 207 ILE Chi-restraints excluded: chain q residue 219 ASN Chi-restraints excluded: chain q residue 245 HIS Chi-restraints excluded: chain q residue 499 VAL Chi-restraints excluded: chain q residue 519 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 761 optimal weight: 0.0570 chunk 579 optimal weight: 4.9990 chunk 399 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 367 optimal weight: 10.0000 chunk 517 optimal weight: 5.9990 chunk 773 optimal weight: 0.8980 chunk 818 optimal weight: 5.9990 chunk 404 optimal weight: 10.0000 chunk 732 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN a 89 GLN a 241 ASN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 435 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN G 123 GLN G 395 ASN ** G 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 395 ASN g 470 GLN ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 138 GLN ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 299 GLN ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 GLN ** Z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 237 ASN Z 526 ASN ** z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN ** H 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 436 GLN H 456 ASN ** h 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 466 ASN ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 27 GLN q 101 ASN q 112 ASN q 154 ASN q 472 ASN ** q 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 543 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4731 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 66233 Z= 0.253 Angle : 0.787 15.245 89338 Z= 0.406 Chirality : 0.048 0.453 10683 Planarity : 0.005 0.085 11517 Dihedral : 4.533 30.435 9055 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 3.63 % Allowed : 19.22 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.09), residues: 8528 helix: 0.91 (0.07), residues: 4338 sheet: 0.26 (0.16), residues: 1024 loop : -0.78 (0.11), residues: 3166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP g 440 HIS 0.022 0.002 HIS e 50 PHE 0.052 0.002 PHE E 179 TYR 0.048 0.002 TYR a 432 ARG 0.017 0.001 ARG d 424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2518 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 2255 time to evaluate : 5.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 75 VAL cc_start: 0.7149 (m) cc_final: 0.6907 (m) REVERT: A 520 PRO cc_start: 0.7579 (Cg_exo) cc_final: 0.7284 (Cg_endo) REVERT: a 137 ILE cc_start: 0.5831 (pt) cc_final: 0.5602 (pt) REVERT: a 282 LEU cc_start: 0.2690 (mt) cc_final: 0.1822 (mp) REVERT: a 509 ILE cc_start: 0.7429 (mt) cc_final: 0.6187 (mt) REVERT: a 539 LEU cc_start: 0.7360 (tt) cc_final: 0.7149 (tt) REVERT: B 64 LEU cc_start: 0.5761 (pp) cc_final: 0.5425 (pp) REVERT: B 113 SER cc_start: 0.6425 (m) cc_final: 0.5991 (t) REVERT: B 115 ILE cc_start: 0.7709 (mm) cc_final: 0.7010 (mm) REVERT: B 438 ARG cc_start: 0.5689 (ptp-170) cc_final: 0.5396 (ptp-170) REVERT: B 460 ARG cc_start: 0.6753 (ttt-90) cc_final: 0.6475 (ttt-90) REVERT: b 67 ILE cc_start: 0.7161 (mm) cc_final: 0.6917 (mm) REVERT: b 292 ASP cc_start: 0.4170 (OUTLIER) cc_final: 0.3583 (p0) REVERT: b 347 MET cc_start: 0.2923 (mmp) cc_final: 0.2509 (mmp) REVERT: b 390 VAL cc_start: 0.6970 (m) cc_final: 0.6594 (p) REVERT: b 408 GLU cc_start: 0.5569 (mp0) cc_final: 0.5259 (mp0) REVERT: b 433 PHE cc_start: 0.7302 (t80) cc_final: 0.7031 (t80) REVERT: b 455 LEU cc_start: 0.5980 (pp) cc_final: 0.5663 (pp) REVERT: G 146 GLU cc_start: 0.6297 (mp0) cc_final: 0.4332 (mm-30) REVERT: G 234 MET cc_start: 0.0609 (ptp) cc_final: 0.0353 (ptp) REVERT: G 475 HIS cc_start: 0.5609 (OUTLIER) cc_final: 0.4079 (m170) REVERT: g 29 LYS cc_start: 0.5977 (ttmt) cc_final: 0.5717 (tttt) REVERT: g 80 GLU cc_start: 0.4546 (tm-30) cc_final: 0.4307 (tm-30) REVERT: g 234 MET cc_start: -0.0139 (tpp) cc_final: -0.0887 (tmm) REVERT: g 283 MET cc_start: -0.0915 (mtt) cc_final: -0.1445 (mtm) REVERT: D 37 THR cc_start: 0.7008 (OUTLIER) cc_final: 0.6756 (m) REVERT: D 260 MET cc_start: -0.2702 (tpp) cc_final: -0.4461 (mtt) REVERT: E 124 VAL cc_start: 0.6242 (m) cc_final: 0.5976 (m) REVERT: E 129 LEU cc_start: 0.6795 (mt) cc_final: 0.6519 (mt) REVERT: E 212 MET cc_start: 0.4295 (ppp) cc_final: 0.3336 (ppp) REVERT: E 498 LEU cc_start: 0.6371 (mm) cc_final: 0.6146 (mm) REVERT: E 537 GLN cc_start: 0.5497 (pp30) cc_final: 0.5064 (pp30) REVERT: E 552 ASP cc_start: 0.4923 (t70) cc_final: 0.4570 (t0) REVERT: e 115 ILE cc_start: 0.4838 (mt) cc_final: 0.4327 (mm) REVERT: e 119 THR cc_start: 0.6771 (p) cc_final: 0.6558 (p) REVERT: e 221 PHE cc_start: 0.5321 (m-10) cc_final: 0.4964 (m-10) REVERT: e 309 MET cc_start: 0.2207 (tpt) cc_final: 0.1729 (tpp) REVERT: e 543 GLN cc_start: 0.5384 (tm-30) cc_final: 0.4750 (tm-30) REVERT: Z 109 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8305 (tt) REVERT: Z 131 LYS cc_start: 0.6849 (pttm) cc_final: 0.6358 (ptpp) REVERT: Z 431 MET cc_start: 0.0705 (ptt) cc_final: 0.0458 (ptt) REVERT: Z 473 VAL cc_start: 0.6226 (m) cc_final: 0.6000 (p) REVERT: Z 510 TYR cc_start: 0.5452 (OUTLIER) cc_final: 0.4754 (t80) REVERT: Z 526 ASN cc_start: 0.6741 (m110) cc_final: 0.6367 (m-40) REVERT: z 34 GLU cc_start: 0.5660 (pp20) cc_final: 0.5417 (pp20) REVERT: z 329 GLN cc_start: 0.5274 (tp-100) cc_final: 0.5019 (tp-100) REVERT: H 75 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7402 (p) REVERT: H 108 LEU cc_start: 0.6440 (mt) cc_final: 0.6154 (mt) REVERT: H 116 LEU cc_start: 0.7767 (mp) cc_final: 0.6908 (mp) REVERT: H 146 ASP cc_start: 0.4695 (p0) cc_final: 0.4335 (p0) REVERT: H 468 LEU cc_start: 0.7519 (mt) cc_final: 0.7079 (mt) REVERT: h 180 LYS cc_start: 0.4147 (mmtm) cc_final: 0.3727 (mmtm) REVERT: h 181 MET cc_start: 0.5447 (mmp) cc_final: 0.5164 (mmp) REVERT: h 279 PHE cc_start: 0.5630 (OUTLIER) cc_final: 0.5341 (t80) REVERT: Q 46 MET cc_start: 0.2419 (tpt) cc_final: 0.2145 (tpt) REVERT: Q 61 LYS cc_start: 0.3807 (tttp) cc_final: 0.3586 (tttp) REVERT: Q 118 ILE cc_start: 0.8424 (mt) cc_final: 0.8191 (mm) REVERT: Q 129 GLN cc_start: 0.6498 (tp-100) cc_final: 0.5779 (tp-100) REVERT: Q 135 ARG cc_start: 0.7272 (tmm-80) cc_final: 0.6930 (tmm-80) REVERT: Q 294 MET cc_start: 0.2390 (mmm) cc_final: 0.1522 (mpp) REVERT: q 27 GLN cc_start: 0.5418 (OUTLIER) cc_final: 0.5145 (tp-100) REVERT: q 180 GLU cc_start: 0.4787 (pp20) cc_final: 0.4368 (pp20) REVERT: q 451 GLN cc_start: 0.5957 (mm110) cc_final: 0.5725 (mm110) outliers start: 263 outliers final: 164 residues processed: 2373 average time/residue: 0.6514 time to fit residues: 2573.3096 Evaluate side-chains 2236 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 2064 time to evaluate : 5.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain a residue 113 ASN Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 256 MET Chi-restraints excluded: chain a residue 295 VAL Chi-restraints excluded: chain a residue 401 SER Chi-restraints excluded: chain a residue 424 CYS Chi-restraints excluded: chain a residue 474 VAL Chi-restraints excluded: chain a residue 477 LEU Chi-restraints excluded: chain a residue 497 TYR Chi-restraints excluded: chain a residue 517 VAL Chi-restraints excluded: chain a residue 532 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 385 HIS Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain b residue 36 THR Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 146 LYS Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 292 ASP Chi-restraints excluded: chain b residue 413 LYS Chi-restraints excluded: chain b residue 502 SER Chi-restraints excluded: chain G residue 62 HIS Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 395 ASN Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain g residue 50 ASP Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 125 LEU Chi-restraints excluded: chain g residue 393 ASP Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 311 MET Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 182 SER Chi-restraints excluded: chain d residue 285 VAL Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 411 ILE Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 512 SER Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 547 MET Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 107 LEU Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain e residue 312 ASP Chi-restraints excluded: chain e residue 321 VAL Chi-restraints excluded: chain e residue 407 PHE Chi-restraints excluded: chain e residue 545 CYS Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 107 ARG Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 194 VAL Chi-restraints excluded: chain Z residue 209 PHE Chi-restraints excluded: chain Z residue 317 LEU Chi-restraints excluded: chain Z residue 367 VAL Chi-restraints excluded: chain Z residue 412 ILE Chi-restraints excluded: chain Z residue 509 SER Chi-restraints excluded: chain Z residue 510 TYR Chi-restraints excluded: chain Z residue 533 LEU Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 55 LEU Chi-restraints excluded: chain z residue 145 ASN Chi-restraints excluded: chain z residue 150 LEU Chi-restraints excluded: chain z residue 157 SER Chi-restraints excluded: chain z residue 169 VAL Chi-restraints excluded: chain z residue 174 VAL Chi-restraints excluded: chain z residue 192 HIS Chi-restraints excluded: chain z residue 209 PHE Chi-restraints excluded: chain z residue 279 ASP Chi-restraints excluded: chain z residue 283 GLU Chi-restraints excluded: chain z residue 298 GLN Chi-restraints excluded: chain z residue 385 HIS Chi-restraints excluded: chain z residue 423 SER Chi-restraints excluded: chain z residue 479 ASP Chi-restraints excluded: chain z residue 498 SER Chi-restraints excluded: chain z residue 509 SER Chi-restraints excluded: chain z residue 527 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain H residue 141 ASN Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain H residue 472 HIS Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 73 LEU Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain h residue 147 ILE Chi-restraints excluded: chain h residue 199 ILE Chi-restraints excluded: chain h residue 214 PHE Chi-restraints excluded: chain h residue 279 PHE Chi-restraints excluded: chain h residue 394 HIS Chi-restraints excluded: chain h residue 444 LYS Chi-restraints excluded: chain h residue 446 LEU Chi-restraints excluded: chain h residue 466 ASN Chi-restraints excluded: chain h residue 501 LEU Chi-restraints excluded: chain h residue 525 THR Chi-restraints excluded: chain Q residue 49 CYS Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 58 HIS Chi-restraints excluded: chain Q residue 115 GLU Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 201 TYR Chi-restraints excluded: chain Q residue 405 VAL Chi-restraints excluded: chain Q residue 472 ASN Chi-restraints excluded: chain Q residue 506 ASP Chi-restraints excluded: chain q residue 27 GLN Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 101 ASN Chi-restraints excluded: chain q residue 139 LEU Chi-restraints excluded: chain q residue 157 ASN Chi-restraints excluded: chain q residue 207 ILE Chi-restraints excluded: chain q residue 245 HIS Chi-restraints excluded: chain q residue 249 VAL Chi-restraints excluded: chain q residue 329 LEU Chi-restraints excluded: chain q residue 471 VAL Chi-restraints excluded: chain q residue 499 VAL Chi-restraints excluded: chain q residue 519 ASP Chi-restraints excluded: chain q residue 539 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 681 optimal weight: 10.0000 chunk 464 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 609 optimal weight: 5.9990 chunk 337 optimal weight: 0.9990 chunk 698 optimal weight: 30.0000 chunk 565 optimal weight: 0.6980 chunk 0 optimal weight: 50.0000 chunk 418 optimal weight: 0.4980 chunk 734 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** b 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 HIS G 395 ASN G 477 GLN ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 106 GLN g 458 GLN g 470 GLN ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 238 GLN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 GLN ** E 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 520 ASN ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN e 543 GLN Z 104 GLN ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 110 GLN ** z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN ** H 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS q 27 GLN q 101 ASN ** q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 219 ASN ** q 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 543 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4701 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 66233 Z= 0.232 Angle : 0.813 18.984 89338 Z= 0.410 Chirality : 0.048 0.338 10683 Planarity : 0.004 0.083 11517 Dihedral : 4.532 29.526 9055 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.91 % Favored : 96.99 % Rotamer: Outliers : 3.45 % Allowed : 21.37 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.09), residues: 8528 helix: 0.88 (0.07), residues: 4349 sheet: 0.29 (0.17), residues: 998 loop : -0.80 (0.11), residues: 3181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 497 HIS 0.018 0.001 HIS a 403 PHE 0.039 0.002 PHE D 304 TYR 0.041 0.002 TYR a 432 ARG 0.015 0.001 ARG d 424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2465 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 2215 time to evaluate : 5.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 533 GLU cc_start: 0.6326 (mm-30) cc_final: 0.6079 (mp0) REVERT: a 93 GLU cc_start: 0.4343 (pp20) cc_final: 0.4080 (pp20) REVERT: a 282 LEU cc_start: 0.2569 (mt) cc_final: 0.1545 (mp) REVERT: a 509 ILE cc_start: 0.7277 (mt) cc_final: 0.6629 (mt) REVERT: B 33 VAL cc_start: 0.5568 (m) cc_final: 0.5171 (p) REVERT: B 113 SER cc_start: 0.6831 (m) cc_final: 0.6432 (t) REVERT: B 460 ARG cc_start: 0.6796 (ttt-90) cc_final: 0.6386 (ttt-90) REVERT: b 67 ILE cc_start: 0.7326 (mm) cc_final: 0.6973 (mm) REVERT: b 109 LEU cc_start: 0.6030 (mt) cc_final: 0.5715 (mt) REVERT: b 390 VAL cc_start: 0.6574 (m) cc_final: 0.6326 (p) REVERT: b 433 PHE cc_start: 0.7319 (t80) cc_final: 0.6969 (t80) REVERT: b 458 LYS cc_start: 0.5495 (pttp) cc_final: 0.5069 (pttm) REVERT: G 298 GLU cc_start: 0.1738 (tt0) cc_final: 0.1217 (tt0) REVERT: g 29 LYS cc_start: 0.6001 (ttmt) cc_final: 0.5588 (tttt) REVERT: g 79 LEU cc_start: 0.6306 (mt) cc_final: 0.6074 (mt) REVERT: g 99 LEU cc_start: 0.6838 (tp) cc_final: 0.6165 (mp) REVERT: g 110 TYR cc_start: 0.6241 (m-80) cc_final: 0.5460 (m-10) REVERT: g 138 GLN cc_start: 0.6288 (pp30) cc_final: 0.6018 (pp30) REVERT: g 234 MET cc_start: -0.0683 (tpp) cc_final: -0.1093 (tmm) REVERT: g 283 MET cc_start: -0.0898 (mtt) cc_final: -0.1459 (mtm) REVERT: g 459 ASN cc_start: 0.6666 (t0) cc_final: 0.6202 (t0) REVERT: g 507 GLN cc_start: 0.5843 (pp30) cc_final: 0.5069 (pp30) REVERT: D 37 THR cc_start: 0.6914 (OUTLIER) cc_final: 0.6638 (m) REVERT: D 260 MET cc_start: -0.2511 (tpp) cc_final: -0.4408 (mtt) REVERT: D 285 VAL cc_start: 0.2337 (OUTLIER) cc_final: 0.1160 (p) REVERT: E 85 ASN cc_start: 0.7192 (OUTLIER) cc_final: 0.6647 (m-40) REVERT: E 124 VAL cc_start: 0.5762 (m) cc_final: 0.5493 (m) REVERT: E 129 LEU cc_start: 0.6756 (mt) cc_final: 0.6467 (mt) REVERT: E 161 LEU cc_start: 0.7038 (mt) cc_final: 0.6665 (mt) REVERT: E 212 MET cc_start: 0.4243 (ppp) cc_final: 0.4035 (ppp) REVERT: E 552 ASP cc_start: 0.4848 (t70) cc_final: 0.4513 (t0) REVERT: e 109 LYS cc_start: 0.5050 (tppt) cc_final: 0.4705 (tppt) REVERT: e 115 ILE cc_start: 0.6062 (mt) cc_final: 0.5800 (mm) REVERT: e 309 MET cc_start: 0.2096 (tpt) cc_final: 0.1665 (tpp) REVERT: e 543 GLN cc_start: 0.5115 (tm130) cc_final: 0.4388 (tm-30) REVERT: Z 101 LEU cc_start: 0.6213 (mm) cc_final: 0.5818 (mm) REVERT: Z 109 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8376 (tt) REVERT: Z 131 LYS cc_start: 0.6622 (pttm) cc_final: 0.5888 (ptpp) REVERT: Z 323 ARG cc_start: 0.3452 (tpp-160) cc_final: 0.2072 (tpp-160) REVERT: Z 469 VAL cc_start: 0.7654 (m) cc_final: 0.7104 (p) REVERT: z 478 ASP cc_start: 0.4927 (t0) cc_final: 0.4105 (t0) REVERT: z 506 ILE cc_start: 0.7980 (mp) cc_final: 0.7375 (tt) REVERT: H 75 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7437 (p) REVERT: H 108 LEU cc_start: 0.6302 (mt) cc_final: 0.6075 (mt) REVERT: H 116 LEU cc_start: 0.7696 (mp) cc_final: 0.7142 (mp) REVERT: H 508 ASN cc_start: 0.5272 (m-40) cc_final: 0.4918 (m-40) REVERT: H 518 LEU cc_start: 0.6695 (mp) cc_final: 0.6422 (mt) REVERT: Q 39 HIS cc_start: 0.6647 (t-90) cc_final: 0.6374 (t-90) REVERT: Q 82 VAL cc_start: 0.6310 (OUTLIER) cc_final: 0.6062 (m) REVERT: Q 118 ILE cc_start: 0.8235 (mt) cc_final: 0.8022 (mm) REVERT: Q 129 GLN cc_start: 0.6666 (tp-100) cc_final: 0.6059 (tp-100) REVERT: Q 133 MET cc_start: 0.5227 (mmp) cc_final: 0.5014 (mmp) REVERT: Q 142 LEU cc_start: 0.6880 (tp) cc_final: 0.6658 (tp) REVERT: Q 536 THR cc_start: 0.6170 (p) cc_final: 0.5880 (p) REVERT: q 154 ASN cc_start: 0.5888 (t0) cc_final: 0.5616 (m-40) outliers start: 250 outliers final: 174 residues processed: 2323 average time/residue: 0.6408 time to fit residues: 2486.3611 Evaluate side-chains 2251 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 2071 time to evaluate : 5.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain a residue 15 LEU Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain a residue 113 ASN Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 256 MET Chi-restraints excluded: chain a residue 295 VAL Chi-restraints excluded: chain a residue 424 CYS Chi-restraints excluded: chain a residue 497 TYR Chi-restraints excluded: chain a residue 517 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 385 HIS Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain b residue 36 THR Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 146 LYS Chi-restraints excluded: chain b residue 184 LEU Chi-restraints excluded: chain b residue 308 HIS Chi-restraints excluded: chain b residue 502 SER Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 62 HIS Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 382 ARG Chi-restraints excluded: chain G residue 395 ASN Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 479 ASN Chi-restraints excluded: chain g residue 50 ASP Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 125 LEU Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 182 SER Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 411 ILE Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 512 SER Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 547 MET Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 107 LEU Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain e residue 312 ASP Chi-restraints excluded: chain e residue 321 VAL Chi-restraints excluded: chain e residue 407 PHE Chi-restraints excluded: chain e residue 499 LYS Chi-restraints excluded: chain e residue 512 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 194 VAL Chi-restraints excluded: chain Z residue 209 PHE Chi-restraints excluded: chain Z residue 406 LEU Chi-restraints excluded: chain Z residue 412 ILE Chi-restraints excluded: chain Z residue 533 LEU Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 110 GLN Chi-restraints excluded: chain z residue 145 ASN Chi-restraints excluded: chain z residue 169 VAL Chi-restraints excluded: chain z residue 174 VAL Chi-restraints excluded: chain z residue 192 HIS Chi-restraints excluded: chain z residue 209 PHE Chi-restraints excluded: chain z residue 210 ILE Chi-restraints excluded: chain z residue 279 ASP Chi-restraints excluded: chain z residue 283 GLU Chi-restraints excluded: chain z residue 385 HIS Chi-restraints excluded: chain z residue 423 SER Chi-restraints excluded: chain z residue 479 ASP Chi-restraints excluded: chain z residue 509 SER Chi-restraints excluded: chain z residue 513 LEU Chi-restraints excluded: chain z residue 527 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 141 ASN Chi-restraints excluded: chain H residue 334 ILE Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain H residue 472 HIS Chi-restraints excluded: chain H residue 496 VAL Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 73 LEU Chi-restraints excluded: chain h residue 74 ASP Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain h residue 214 PHE Chi-restraints excluded: chain h residue 279 PHE Chi-restraints excluded: chain h residue 376 LEU Chi-restraints excluded: chain h residue 394 HIS Chi-restraints excluded: chain h residue 446 LEU Chi-restraints excluded: chain h residue 449 ILE Chi-restraints excluded: chain h residue 466 ASN Chi-restraints excluded: chain h residue 501 LEU Chi-restraints excluded: chain h residue 523 THR Chi-restraints excluded: chain h residue 525 THR Chi-restraints excluded: chain Q residue 49 CYS Chi-restraints excluded: chain Q residue 58 HIS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 115 GLU Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 201 TYR Chi-restraints excluded: chain Q residue 440 ARG Chi-restraints excluded: chain Q residue 472 ASN Chi-restraints excluded: chain Q residue 499 VAL Chi-restraints excluded: chain Q residue 539 LEU Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 62 ILE Chi-restraints excluded: chain q residue 101 ASN Chi-restraints excluded: chain q residue 127 ILE Chi-restraints excluded: chain q residue 157 ASN Chi-restraints excluded: chain q residue 207 ILE Chi-restraints excluded: chain q residue 245 HIS Chi-restraints excluded: chain q residue 249 VAL Chi-restraints excluded: chain q residue 471 VAL Chi-restraints excluded: chain q residue 475 LEU Chi-restraints excluded: chain q residue 499 VAL Chi-restraints excluded: chain q residue 517 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 275 optimal weight: 6.9990 chunk 737 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 480 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 819 optimal weight: 7.9990 chunk 680 optimal weight: 10.0000 chunk 379 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 430 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 385 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS G 395 ASN ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 106 GLN g 123 GLN ** g 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 470 GLN ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 140 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 41 GLN ** e 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 466 GLN e 537 GLN ** Z 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 410 ASN z 110 GLN z 329 GLN ** z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN ** q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 391 GLN ** q 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4845 moved from start: 0.6715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 66233 Z= 0.283 Angle : 0.840 17.594 89338 Z= 0.434 Chirality : 0.049 0.357 10683 Planarity : 0.005 0.089 11517 Dihedral : 4.717 47.645 9055 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 4.13 % Allowed : 22.88 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.09), residues: 8528 helix: 0.61 (0.07), residues: 4359 sheet: 0.13 (0.16), residues: 1041 loop : -0.99 (0.11), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP G 500 HIS 0.022 0.002 HIS e 50 PHE 0.054 0.002 PHE E 179 TYR 0.036 0.002 TYR a 432 ARG 0.016 0.001 ARG H 469 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2487 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 2188 time to evaluate : 5.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 114 GLU cc_start: 0.5737 (mt-10) cc_final: 0.5332 (mt-10) REVERT: A 121 HIS cc_start: 0.6268 (t-90) cc_final: 0.5971 (t-90) REVERT: a 18 GLU cc_start: 0.4502 (tp30) cc_final: 0.4119 (tp30) REVERT: a 28 GLN cc_start: 0.6218 (mm-40) cc_final: 0.6006 (mm-40) REVERT: a 282 LEU cc_start: 0.2961 (mt) cc_final: 0.2123 (mp) REVERT: a 476 LYS cc_start: 0.7164 (tttt) cc_final: 0.6657 (tttt) REVERT: a 509 ILE cc_start: 0.7494 (mt) cc_final: 0.6765 (mt) REVERT: B 265 GLU cc_start: 0.2152 (OUTLIER) cc_final: 0.1337 (mt-10) REVERT: b 64 LEU cc_start: 0.6439 (mm) cc_final: 0.6209 (mm) REVERT: b 433 PHE cc_start: 0.7305 (t80) cc_final: 0.6999 (t80) REVERT: G 29 LYS cc_start: 0.6789 (tttt) cc_final: 0.6464 (tttt) REVERT: G 126 LYS cc_start: 0.6841 (ptpt) cc_final: 0.6586 (ptpt) REVERT: G 234 MET cc_start: 0.1602 (ptp) cc_final: 0.0991 (ttp) REVERT: g 29 LYS cc_start: 0.6220 (ttmt) cc_final: 0.5655 (tttt) REVERT: g 110 TYR cc_start: 0.6054 (m-80) cc_final: 0.5332 (m-10) REVERT: g 234 MET cc_start: -0.0410 (tpp) cc_final: -0.0683 (tmm) REVERT: g 283 MET cc_start: -0.0814 (mtt) cc_final: -0.1433 (mtm) REVERT: g 420 GLU cc_start: 0.5248 (mp0) cc_final: 0.5044 (mp0) REVERT: g 455 THR cc_start: 0.6202 (p) cc_final: 0.5925 (p) REVERT: g 494 MET cc_start: 0.3550 (mmt) cc_final: 0.3333 (mmt) REVERT: g 499 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6545 (mt) REVERT: g 506 LYS cc_start: 0.7071 (mmmm) cc_final: 0.6593 (mmmm) REVERT: g 507 GLN cc_start: 0.5687 (pp30) cc_final: 0.5427 (pp30) REVERT: D 26 ILE cc_start: 0.7840 (pt) cc_final: 0.7517 (pt) REVERT: D 125 GLN cc_start: 0.5696 (pt0) cc_final: 0.5479 (pt0) REVERT: D 260 MET cc_start: -0.2519 (tpp) cc_final: -0.4465 (mtt) REVERT: D 418 GLU cc_start: 0.5982 (mp0) cc_final: 0.5744 (mp0) REVERT: d 113 LYS cc_start: 0.6324 (ptpt) cc_final: 0.5942 (mtmm) REVERT: d 305 LEU cc_start: 0.4317 (mt) cc_final: 0.4006 (mt) REVERT: d 420 GLU cc_start: 0.4770 (tp30) cc_final: 0.3945 (tp30) REVERT: E 85 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.6721 (m-40) REVERT: E 129 LEU cc_start: 0.6816 (mt) cc_final: 0.6601 (mt) REVERT: E 136 LEU cc_start: 0.6120 (mm) cc_final: 0.5903 (mm) REVERT: E 212 MET cc_start: 0.4437 (ppp) cc_final: 0.3518 (ppp) REVERT: E 309 MET cc_start: 0.4741 (mtt) cc_final: 0.4449 (mtt) REVERT: E 534 LYS cc_start: 0.6178 (mmmt) cc_final: 0.5821 (mmmm) REVERT: E 537 GLN cc_start: 0.5557 (pp30) cc_final: 0.5309 (pp30) REVERT: E 552 ASP cc_start: 0.4755 (t70) cc_final: 0.4475 (t0) REVERT: e 83 ILE cc_start: 0.7076 (tp) cc_final: 0.6806 (tp) REVERT: e 164 THR cc_start: 0.7001 (p) cc_final: 0.6569 (m) REVERT: e 309 MET cc_start: 0.2029 (tpt) cc_final: 0.1661 (tpp) REVERT: e 543 GLN cc_start: 0.5529 (tm130) cc_final: 0.5035 (tm-30) REVERT: Z 101 LEU cc_start: 0.6259 (mm) cc_final: 0.5964 (mm) REVERT: Z 108 PHE cc_start: 0.6018 (m-80) cc_final: 0.5444 (m-80) REVERT: Z 109 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8421 (tt) REVERT: Z 295 ILE cc_start: 0.2869 (tp) cc_final: 0.2356 (tp) REVERT: Z 469 VAL cc_start: 0.7908 (m) cc_final: 0.7626 (p) REVERT: z 506 ILE cc_start: 0.7990 (mp) cc_final: 0.7218 (tt) REVERT: H 116 LEU cc_start: 0.7992 (mp) cc_final: 0.7749 (mt) REVERT: H 438 ILE cc_start: 0.7398 (mm) cc_final: 0.7189 (mt) REVERT: H 459 PHE cc_start: 0.5604 (m-10) cc_final: 0.5248 (m-80) REVERT: Q 82 VAL cc_start: 0.6164 (OUTLIER) cc_final: 0.5837 (m) REVERT: Q 83 LYS cc_start: 0.7487 (mmmm) cc_final: 0.6663 (mmmm) REVERT: Q 86 VAL cc_start: 0.6545 (p) cc_final: 0.6235 (p) REVERT: Q 118 ILE cc_start: 0.8431 (mt) cc_final: 0.8186 (mm) REVERT: Q 294 MET cc_start: 0.2525 (mmm) cc_final: 0.1770 (mpp) REVERT: Q 461 ARG cc_start: 0.6640 (ttp80) cc_final: 0.6328 (ttp80) REVERT: Q 465 GLU cc_start: 0.5585 (mm-30) cc_final: 0.5338 (mm-30) REVERT: Q 506 ASP cc_start: 0.4796 (OUTLIER) cc_final: 0.4440 (m-30) REVERT: Q 525 LYS cc_start: 0.7382 (pptt) cc_final: 0.7101 (pptt) REVERT: q 46 MET cc_start: 0.1620 (OUTLIER) cc_final: 0.1131 (tpt) REVERT: q 104 MET cc_start: 0.6440 (mmm) cc_final: 0.6222 (mmm) outliers start: 299 outliers final: 228 residues processed: 2316 average time/residue: 0.6605 time to fit residues: 2550.1443 Evaluate side-chains 2262 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 2027 time to evaluate : 5.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain a residue 15 LEU Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 106 SER Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain a residue 113 ASN Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 249 LEU Chi-restraints excluded: chain a residue 256 MET Chi-restraints excluded: chain a residue 295 VAL Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 479 SER Chi-restraints excluded: chain a residue 497 TYR Chi-restraints excluded: chain a residue 517 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 385 HIS Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain b residue 36 THR Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 102 LEU Chi-restraints excluded: chain b residue 133 ASP Chi-restraints excluded: chain b residue 146 LYS Chi-restraints excluded: chain b residue 172 HIS Chi-restraints excluded: chain b residue 184 LEU Chi-restraints excluded: chain b residue 292 ASP Chi-restraints excluded: chain b residue 308 HIS Chi-restraints excluded: chain b residue 346 ILE Chi-restraints excluded: chain b residue 402 LEU Chi-restraints excluded: chain b residue 418 GLU Chi-restraints excluded: chain b residue 467 ILE Chi-restraints excluded: chain b residue 502 SER Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 62 HIS Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 382 ARG Chi-restraints excluded: chain G residue 395 ASN Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 445 VAL Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain G residue 479 ASN Chi-restraints excluded: chain g residue 35 ILE Chi-restraints excluded: chain g residue 50 ASP Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 123 GLN Chi-restraints excluded: chain g residue 393 ASP Chi-restraints excluded: chain g residue 398 ASP Chi-restraints excluded: chain g residue 499 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 311 MET Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 133 ASP Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain d residue 140 HIS Chi-restraints excluded: chain d residue 182 SER Chi-restraints excluded: chain d residue 204 ILE Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 411 ILE Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 512 SER Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 517 TYR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 107 LEU Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain e residue 151 ASP Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain e residue 312 ASP Chi-restraints excluded: chain e residue 321 VAL Chi-restraints excluded: chain e residue 407 PHE Chi-restraints excluded: chain e residue 512 VAL Chi-restraints excluded: chain e residue 527 VAL Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 46 LEU Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 106 HIS Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 194 VAL Chi-restraints excluded: chain Z residue 209 PHE Chi-restraints excluded: chain Z residue 317 LEU Chi-restraints excluded: chain Z residue 365 THR Chi-restraints excluded: chain Z residue 367 VAL Chi-restraints excluded: chain Z residue 384 THR Chi-restraints excluded: chain Z residue 410 ASN Chi-restraints excluded: chain Z residue 412 ILE Chi-restraints excluded: chain Z residue 420 ILE Chi-restraints excluded: chain Z residue 521 THR Chi-restraints excluded: chain Z residue 533 LEU Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 55 LEU Chi-restraints excluded: chain z residue 87 THR Chi-restraints excluded: chain z residue 93 THR Chi-restraints excluded: chain z residue 111 GLU Chi-restraints excluded: chain z residue 145 ASN Chi-restraints excluded: chain z residue 160 THR Chi-restraints excluded: chain z residue 169 VAL Chi-restraints excluded: chain z residue 174 VAL Chi-restraints excluded: chain z residue 192 HIS Chi-restraints excluded: chain z residue 209 PHE Chi-restraints excluded: chain z residue 279 ASP Chi-restraints excluded: chain z residue 283 GLU Chi-restraints excluded: chain z residue 385 HIS Chi-restraints excluded: chain z residue 423 SER Chi-restraints excluded: chain z residue 479 ASP Chi-restraints excluded: chain z residue 509 SER Chi-restraints excluded: chain z residue 527 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain H residue 141 ASN Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain H residue 472 HIS Chi-restraints excluded: chain H residue 479 TYR Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain h residue 199 ILE Chi-restraints excluded: chain h residue 214 PHE Chi-restraints excluded: chain h residue 279 PHE Chi-restraints excluded: chain h residue 376 LEU Chi-restraints excluded: chain h residue 446 LEU Chi-restraints excluded: chain h residue 449 ILE Chi-restraints excluded: chain h residue 466 ASN Chi-restraints excluded: chain h residue 472 HIS Chi-restraints excluded: chain h residue 501 LEU Chi-restraints excluded: chain h residue 511 THR Chi-restraints excluded: chain h residue 523 THR Chi-restraints excluded: chain h residue 525 THR Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 49 CYS Chi-restraints excluded: chain Q residue 58 HIS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 115 GLU Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 201 TYR Chi-restraints excluded: chain Q residue 333 CYS Chi-restraints excluded: chain Q residue 369 THR Chi-restraints excluded: chain Q residue 420 LEU Chi-restraints excluded: chain Q residue 440 ARG Chi-restraints excluded: chain Q residue 472 ASN Chi-restraints excluded: chain Q residue 499 VAL Chi-restraints excluded: chain Q residue 506 ASP Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 46 MET Chi-restraints excluded: chain q residue 62 ILE Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain q residue 127 ILE Chi-restraints excluded: chain q residue 157 ASN Chi-restraints excluded: chain q residue 204 VAL Chi-restraints excluded: chain q residue 207 ILE Chi-restraints excluded: chain q residue 245 HIS Chi-restraints excluded: chain q residue 308 LEU Chi-restraints excluded: chain q residue 327 PHE Chi-restraints excluded: chain q residue 329 LEU Chi-restraints excluded: chain q residue 471 VAL Chi-restraints excluded: chain q residue 475 LEU Chi-restraints excluded: chain q residue 499 VAL Chi-restraints excluded: chain q residue 500 ASP Chi-restraints excluded: chain q residue 517 ILE Chi-restraints excluded: chain q residue 519 ASP Chi-restraints excluded: chain q residue 538 VAL Chi-restraints excluded: chain q residue 539 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 790 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 466 optimal weight: 0.9990 chunk 598 optimal weight: 50.0000 chunk 463 optimal weight: 9.9990 chunk 689 optimal weight: 3.9990 chunk 457 optimal weight: 0.9980 chunk 816 optimal weight: 10.0000 chunk 510 optimal weight: 4.9990 chunk 497 optimal weight: 6.9990 chunk 376 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 27 ASN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 191 ASN a 435 ASN B 47 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN G 395 ASN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN ** g 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 470 GLN ** g 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 140 HIS ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 410 ASN z 312 HIS ** z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 ASN ** H 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 27 GLN ** q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4875 moved from start: 0.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 66233 Z= 0.286 Angle : 0.877 18.063 89338 Z= 0.453 Chirality : 0.050 0.362 10683 Planarity : 0.005 0.086 11517 Dihedral : 4.799 55.895 9055 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 3.92 % Allowed : 24.61 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.09), residues: 8528 helix: 0.54 (0.07), residues: 4340 sheet: 0.12 (0.17), residues: 993 loop : -1.03 (0.11), residues: 3195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP d 440 HIS 0.037 0.002 HIS d 140 PHE 0.043 0.002 PHE D 304 TYR 0.041 0.002 TYR q 312 ARG 0.025 0.001 ARG Z 323 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2455 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 2171 time to evaluate : 5.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 43 SER cc_start: 0.6959 (p) cc_final: 0.6631 (t) REVERT: A 84 VAL cc_start: 0.6927 (t) cc_final: 0.6680 (t) REVERT: a 93 GLU cc_start: 0.4814 (pp20) cc_final: 0.4605 (pp20) REVERT: a 282 LEU cc_start: 0.2841 (mt) cc_final: 0.1928 (mp) REVERT: a 476 LYS cc_start: 0.7081 (tttt) cc_final: 0.6453 (tttt) REVERT: a 509 ILE cc_start: 0.7572 (mt) cc_final: 0.6797 (mp) REVERT: B 265 GLU cc_start: 0.2326 (OUTLIER) cc_final: 0.1636 (mt-10) REVERT: b 467 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.7013 (mm) REVERT: G 29 LYS cc_start: 0.6778 (tttt) cc_final: 0.6548 (tttt) REVERT: G 102 GLU cc_start: 0.4700 (tp30) cc_final: 0.4391 (tp30) REVERT: G 234 MET cc_start: 0.1961 (ptp) cc_final: 0.1521 (ttm) REVERT: G 421 MET cc_start: 0.5792 (tmm) cc_final: 0.4789 (tmm) REVERT: G 475 HIS cc_start: 0.5430 (OUTLIER) cc_final: 0.4823 (m170) REVERT: G 508 GLN cc_start: 0.5909 (mm-40) cc_final: 0.5603 (mm-40) REVERT: g 29 LYS cc_start: 0.6310 (ttmt) cc_final: 0.5991 (tttt) REVERT: g 79 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.6139 (tt) REVERT: g 110 TYR cc_start: 0.6136 (m-80) cc_final: 0.5581 (m-10) REVERT: g 234 MET cc_start: -0.0324 (tpp) cc_final: -0.0572 (tmm) REVERT: g 283 MET cc_start: -0.0739 (mtt) cc_final: -0.1057 (mtm) REVERT: g 455 THR cc_start: 0.6230 (p) cc_final: 0.5958 (p) REVERT: g 499 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6198 (mt) REVERT: g 506 LYS cc_start: 0.7124 (mmmm) cc_final: 0.6577 (mmmm) REVERT: D 260 MET cc_start: -0.2198 (tpp) cc_final: -0.3977 (mpp) REVERT: D 350 VAL cc_start: 0.0739 (OUTLIER) cc_final: -0.1128 (t) REVERT: d 113 LYS cc_start: 0.6490 (ptpt) cc_final: 0.5939 (mtmm) REVERT: d 146 ASP cc_start: 0.3759 (t0) cc_final: 0.3479 (t70) REVERT: d 314 LYS cc_start: 0.4453 (OUTLIER) cc_final: 0.4127 (ptpp) REVERT: E 85 ASN cc_start: 0.7094 (m110) cc_final: 0.6573 (m-40) REVERT: E 129 LEU cc_start: 0.6770 (mt) cc_final: 0.6494 (mt) REVERT: E 145 LYS cc_start: 0.6871 (mtmt) cc_final: 0.6668 (mtmm) REVERT: E 212 MET cc_start: 0.4434 (ppp) cc_final: 0.3355 (ppp) REVERT: E 309 MET cc_start: 0.5707 (mtt) cc_final: 0.5312 (mtt) REVERT: E 531 PHE cc_start: 0.6446 (t80) cc_final: 0.5210 (t80) REVERT: E 537 GLN cc_start: 0.5504 (pp30) cc_final: 0.5238 (pp30) REVERT: E 552 ASP cc_start: 0.4764 (t70) cc_final: 0.4507 (t0) REVERT: e 45 GLU cc_start: 0.5564 (OUTLIER) cc_final: 0.4520 (pm20) REVERT: e 309 MET cc_start: 0.2078 (tpt) cc_final: 0.1648 (tpp) REVERT: e 543 GLN cc_start: 0.5528 (tm130) cc_final: 0.4648 (tm-30) REVERT: Z 101 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5922 (mm) REVERT: Z 107 ARG cc_start: 0.6824 (ttp80) cc_final: 0.6616 (ttp80) REVERT: Z 108 PHE cc_start: 0.6266 (m-80) cc_final: 0.5915 (m-80) REVERT: Z 109 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8524 (tt) REVERT: Z 295 ILE cc_start: 0.2462 (tp) cc_final: 0.1973 (tp) REVERT: Z 418 PHE cc_start: 0.6578 (t80) cc_final: 0.6303 (t80) REVERT: z 16 ASP cc_start: 0.5742 (m-30) cc_final: 0.5339 (m-30) REVERT: z 161 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7759 (mmmm) REVERT: z 451 LEU cc_start: 0.7238 (mt) cc_final: 0.6886 (mt) REVERT: H 113 LYS cc_start: 0.7480 (tttm) cc_final: 0.7215 (tttm) REVERT: H 317 ARG cc_start: 0.4386 (tpm170) cc_final: 0.4075 (tpp-160) REVERT: H 452 GLN cc_start: 0.6370 (mt0) cc_final: 0.6149 (mt0) REVERT: H 486 GLU cc_start: 0.5780 (mm-30) cc_final: 0.5492 (mm-30) REVERT: H 490 ASP cc_start: 0.4868 (m-30) cc_final: 0.4361 (m-30) REVERT: h 113 LYS cc_start: 0.6627 (ttpp) cc_final: 0.6299 (ttpp) REVERT: h 437 MET cc_start: 0.5155 (mmm) cc_final: 0.4639 (mmm) REVERT: Q 129 GLN cc_start: 0.6481 (tp-100) cc_final: 0.6023 (tp-100) REVERT: Q 133 MET cc_start: 0.5361 (mmp) cc_final: 0.5035 (mmp) REVERT: Q 294 MET cc_start: 0.2711 (mmm) cc_final: 0.2278 (mpp) REVERT: Q 506 ASP cc_start: 0.5125 (OUTLIER) cc_final: 0.3421 (p0) REVERT: q 39 HIS cc_start: 0.6577 (t70) cc_final: 0.6132 (t70) REVERT: q 46 MET cc_start: 0.1446 (OUTLIER) cc_final: -0.0341 (tpp) REVERT: q 164 LYS cc_start: 0.6648 (pptt) cc_final: 0.6417 (pptt) REVERT: q 256 ILE cc_start: 0.0214 (OUTLIER) cc_final: -0.0643 (mp) REVERT: q 287 MET cc_start: 0.5273 (tmm) cc_final: 0.4901 (tmm) REVERT: q 436 LYS cc_start: 0.6788 (ptpp) cc_final: 0.5892 (mttp) outliers start: 284 outliers final: 211 residues processed: 2299 average time/residue: 0.6396 time to fit residues: 2448.5020 Evaluate side-chains 2268 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 2044 time to evaluate : 5.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain a residue 15 LEU Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 106 SER Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain a residue 113 ASN Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 249 LEU Chi-restraints excluded: chain a residue 256 MET Chi-restraints excluded: chain a residue 295 VAL Chi-restraints excluded: chain a residue 341 MET Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 460 LYS Chi-restraints excluded: chain a residue 535 CYS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 385 HIS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain b residue 36 THR Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 146 LYS Chi-restraints excluded: chain b residue 172 HIS Chi-restraints excluded: chain b residue 176 LEU Chi-restraints excluded: chain b residue 184 LEU Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 292 ASP Chi-restraints excluded: chain b residue 346 ILE Chi-restraints excluded: chain b residue 402 LEU Chi-restraints excluded: chain b residue 418 GLU Chi-restraints excluded: chain b residue 467 ILE Chi-restraints excluded: chain b residue 468 SER Chi-restraints excluded: chain b residue 502 SER Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 62 HIS Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 395 ASN Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain G residue 479 ASN Chi-restraints excluded: chain g residue 35 ILE Chi-restraints excluded: chain g residue 50 ASP Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 393 ASP Chi-restraints excluded: chain g residue 398 ASP Chi-restraints excluded: chain g residue 450 GLU Chi-restraints excluded: chain g residue 499 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 311 MET Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 133 ASP Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain d residue 204 ILE Chi-restraints excluded: chain d residue 253 ILE Chi-restraints excluded: chain d residue 314 LYS Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 411 ILE Chi-restraints excluded: chain d residue 492 THR Chi-restraints excluded: chain d residue 510 LEU Chi-restraints excluded: chain d residue 512 SER Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 517 TYR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain e residue 45 GLU Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 107 LEU Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain e residue 312 ASP Chi-restraints excluded: chain e residue 321 VAL Chi-restraints excluded: chain e residue 407 PHE Chi-restraints excluded: chain e residue 499 LYS Chi-restraints excluded: chain e residue 512 VAL Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 209 PHE Chi-restraints excluded: chain Z residue 224 MET Chi-restraints excluded: chain Z residue 317 LEU Chi-restraints excluded: chain Z residue 365 THR Chi-restraints excluded: chain Z residue 367 VAL Chi-restraints excluded: chain Z residue 406 LEU Chi-restraints excluded: chain Z residue 412 ILE Chi-restraints excluded: chain Z residue 533 LEU Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 55 LEU Chi-restraints excluded: chain z residue 87 THR Chi-restraints excluded: chain z residue 145 ASN Chi-restraints excluded: chain z residue 169 VAL Chi-restraints excluded: chain z residue 174 VAL Chi-restraints excluded: chain z residue 192 HIS Chi-restraints excluded: chain z residue 209 PHE Chi-restraints excluded: chain z residue 279 ASP Chi-restraints excluded: chain z residue 283 GLU Chi-restraints excluded: chain z residue 296 ILE Chi-restraints excluded: chain z residue 385 HIS Chi-restraints excluded: chain z residue 423 SER Chi-restraints excluded: chain z residue 479 ASP Chi-restraints excluded: chain z residue 509 SER Chi-restraints excluded: chain z residue 513 LEU Chi-restraints excluded: chain z residue 527 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain H residue 141 ASN Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 422 LYS Chi-restraints excluded: chain H residue 453 LEU Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain H residue 472 HIS Chi-restraints excluded: chain H residue 496 VAL Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain h residue 214 PHE Chi-restraints excluded: chain h residue 279 PHE Chi-restraints excluded: chain h residue 376 LEU Chi-restraints excluded: chain h residue 420 VAL Chi-restraints excluded: chain h residue 446 LEU Chi-restraints excluded: chain h residue 449 ILE Chi-restraints excluded: chain h residue 453 LEU Chi-restraints excluded: chain h residue 466 ASN Chi-restraints excluded: chain h residue 511 THR Chi-restraints excluded: chain h residue 523 THR Chi-restraints excluded: chain h residue 525 THR Chi-restraints excluded: chain Q residue 49 CYS Chi-restraints excluded: chain Q residue 58 HIS Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 115 GLU Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 174 SER Chi-restraints excluded: chain Q residue 201 TYR Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 298 CYS Chi-restraints excluded: chain Q residue 333 CYS Chi-restraints excluded: chain Q residue 472 ASN Chi-restraints excluded: chain Q residue 475 LEU Chi-restraints excluded: chain Q residue 499 VAL Chi-restraints excluded: chain Q residue 506 ASP Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 46 MET Chi-restraints excluded: chain q residue 62 ILE Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain q residue 127 ILE Chi-restraints excluded: chain q residue 157 ASN Chi-restraints excluded: chain q residue 207 ILE Chi-restraints excluded: chain q residue 256 ILE Chi-restraints excluded: chain q residue 308 LEU Chi-restraints excluded: chain q residue 327 PHE Chi-restraints excluded: chain q residue 370 VAL Chi-restraints excluded: chain q residue 429 GLU Chi-restraints excluded: chain q residue 471 VAL Chi-restraints excluded: chain q residue 475 LEU Chi-restraints excluded: chain q residue 499 VAL Chi-restraints excluded: chain q residue 500 ASP Chi-restraints excluded: chain q residue 517 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 505 optimal weight: 3.9990 chunk 326 optimal weight: 8.9990 chunk 487 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 158 optimal weight: 8.9990 chunk 519 optimal weight: 7.9990 chunk 556 optimal weight: 10.0000 chunk 403 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 641 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN ** b 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 393 GLN ** b 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 GLN G 395 ASN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 470 GLN D 67 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 HIS ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 165 GLN ** d 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 HIS e 106 GLN e 397 GLN ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 69 GLN ** Z 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 230 ASN Z 282 ASN ** Z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 410 ASN ** z 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** Q 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 ASN ** Q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 92 GLN ** q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 373 GLN ** q 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 moved from start: 0.7721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 66233 Z= 0.427 Angle : 0.990 19.677 89338 Z= 0.527 Chirality : 0.054 0.338 10683 Planarity : 0.006 0.088 11517 Dihedral : 5.242 46.095 9055 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 28.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 4.45 % Allowed : 25.85 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.09), residues: 8528 helix: 0.02 (0.07), residues: 4335 sheet: -0.24 (0.16), residues: 1051 loop : -1.38 (0.11), residues: 3142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP Z 507 HIS 0.023 0.002 HIS e 50 PHE 0.057 0.003 PHE D 304 TYR 0.039 0.003 TYR z 419 ARG 0.020 0.001 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2497 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 2175 time to evaluate : 5.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 43 SER cc_start: 0.7035 (p) cc_final: 0.6565 (t) REVERT: A 84 VAL cc_start: 0.6893 (t) cc_final: 0.5688 (t) REVERT: a 18 GLU cc_start: 0.3824 (tp30) cc_final: 0.3478 (tp30) REVERT: a 111 ARG cc_start: 0.5386 (mmt90) cc_final: 0.5016 (mmt90) REVERT: a 282 LEU cc_start: 0.3525 (mt) cc_final: 0.2379 (mp) REVERT: a 476 LYS cc_start: 0.6693 (tttt) cc_final: 0.6346 (tttt) REVERT: a 509 ILE cc_start: 0.7613 (mt) cc_final: 0.6952 (mt) REVERT: B 90 ASP cc_start: 0.3467 (t0) cc_final: 0.3172 (t0) REVERT: B 101 GLU cc_start: 0.5033 (mm-30) cc_final: 0.3871 (mm-30) REVERT: B 265 GLU cc_start: 0.2804 (OUTLIER) cc_final: 0.1965 (mt-10) REVERT: b 105 GLU cc_start: 0.3534 (tp30) cc_final: 0.3090 (tp30) REVERT: b 118 GLN cc_start: 0.5753 (tt0) cc_final: 0.5406 (tp40) REVERT: G 102 GLU cc_start: 0.4936 (tp30) cc_final: 0.4723 (tp30) REVERT: G 234 MET cc_start: 0.2015 (ptp) cc_final: 0.1552 (ttm) REVERT: G 421 MET cc_start: 0.6473 (tmm) cc_final: 0.5163 (tmm) REVERT: G 451 CYS cc_start: 0.5094 (p) cc_final: 0.4849 (p) REVERT: G 475 HIS cc_start: 0.5548 (OUTLIER) cc_final: 0.5014 (m170) REVERT: g 29 LYS cc_start: 0.5791 (ttmt) cc_final: 0.5421 (tttt) REVERT: g 79 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.6080 (tt) REVERT: g 234 MET cc_start: -0.0220 (tpp) cc_final: -0.0483 (tmm) REVERT: g 283 MET cc_start: -0.0795 (mtt) cc_final: -0.1062 (mtm) REVERT: g 420 GLU cc_start: 0.5296 (mp0) cc_final: 0.4957 (mp0) REVERT: g 506 LYS cc_start: 0.7240 (mmmm) cc_final: 0.6979 (mmmm) REVERT: D 86 ASP cc_start: 0.4797 (t70) cc_final: 0.4427 (t0) REVERT: D 138 MET cc_start: 0.4326 (mmp) cc_final: 0.4119 (mmp) REVERT: D 260 MET cc_start: -0.2175 (tpp) cc_final: -0.5322 (ptt) REVERT: D 350 VAL cc_start: 0.1056 (OUTLIER) cc_final: -0.1150 (t) REVERT: d 125 GLN cc_start: 0.5722 (OUTLIER) cc_final: 0.5272 (tm-30) REVERT: d 314 LYS cc_start: 0.4832 (OUTLIER) cc_final: 0.4518 (ptpp) REVERT: d 513 GLU cc_start: 0.5774 (pp20) cc_final: 0.5441 (pp20) REVERT: E 85 ASN cc_start: 0.7415 (OUTLIER) cc_final: 0.6956 (m-40) REVERT: E 129 LEU cc_start: 0.6997 (mt) cc_final: 0.6778 (mt) REVERT: E 134 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6770 (tt) REVERT: E 145 LYS cc_start: 0.7320 (mtmt) cc_final: 0.7107 (mtmm) REVERT: E 212 MET cc_start: 0.5097 (ppp) cc_final: 0.3751 (ppp) REVERT: e 45 GLU cc_start: 0.5699 (OUTLIER) cc_final: 0.4811 (pm20) REVERT: e 309 MET cc_start: 0.2376 (tpt) cc_final: 0.2140 (tpp) REVERT: e 543 GLN cc_start: 0.5649 (tm130) cc_final: 0.5160 (tm-30) REVERT: Z 101 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.5949 (mm) REVERT: Z 134 ASP cc_start: 0.5322 (p0) cc_final: 0.5016 (p0) REVERT: Z 295 ILE cc_start: 0.2822 (tp) cc_final: 0.2453 (tp) REVERT: Z 392 LYS cc_start: 0.7086 (ptmm) cc_final: 0.6782 (ptmm) REVERT: Z 437 LYS cc_start: 0.5080 (tttt) cc_final: 0.4831 (tttt) REVERT: Z 469 VAL cc_start: 0.7806 (m) cc_final: 0.7210 (p) REVERT: Z 470 LEU cc_start: 0.7271 (pp) cc_final: 0.6991 (pp) REVERT: z 16 ASP cc_start: 0.5888 (OUTLIER) cc_final: 0.5590 (m-30) REVERT: z 37 LEU cc_start: 0.3676 (tp) cc_final: 0.2391 (tt) REVERT: z 102 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7799 (mm) REVERT: z 161 LYS cc_start: 0.8264 (mmmt) cc_final: 0.7968 (mmmm) REVERT: z 451 LEU cc_start: 0.7194 (mt) cc_final: 0.6977 (mt) REVERT: z 506 ILE cc_start: 0.8003 (mp) cc_final: 0.7669 (tt) REVERT: z 513 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6521 (mp) REVERT: H 452 GLN cc_start: 0.6510 (mt0) cc_final: 0.6293 (mt0) REVERT: h 113 LYS cc_start: 0.6976 (ttpp) cc_final: 0.6595 (ttpp) REVERT: h 341 ILE cc_start: 0.3183 (mm) cc_final: 0.2370 (mm) REVERT: Q 86 VAL cc_start: 0.6853 (p) cc_final: 0.6652 (p) REVERT: Q 129 GLN cc_start: 0.6797 (tp-100) cc_final: 0.6369 (tp-100) REVERT: Q 294 MET cc_start: 0.2624 (mmm) cc_final: 0.2148 (mpp) REVERT: Q 429 GLU cc_start: 0.4606 (tm-30) cc_final: 0.4375 (tm-30) REVERT: Q 506 ASP cc_start: 0.6516 (OUTLIER) cc_final: 0.5654 (p0) REVERT: q 71 MET cc_start: 0.6119 (ppp) cc_final: 0.5918 (ppp) REVERT: q 96 MET cc_start: 0.5832 (tpp) cc_final: 0.4387 (tpp) REVERT: q 129 GLN cc_start: 0.6318 (tp-100) cc_final: 0.6062 (tm-30) REVERT: q 256 ILE cc_start: 0.1075 (OUTLIER) cc_final: 0.0105 (mp) outliers start: 322 outliers final: 229 residues processed: 2328 average time/residue: 0.6443 time to fit residues: 2509.5983 Evaluate side-chains 2321 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 2077 time to evaluate : 5.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain a residue 15 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 113 ASN Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 117 LYS Chi-restraints excluded: chain a residue 249 LEU Chi-restraints excluded: chain a residue 295 VAL Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 401 SER Chi-restraints excluded: chain a residue 424 CYS Chi-restraints excluded: chain a residue 460 LYS Chi-restraints excluded: chain a residue 497 TYR Chi-restraints excluded: chain a residue 535 CYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 385 HIS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain b residue 36 THR Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 99 SER Chi-restraints excluded: chain b residue 146 LYS Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 172 HIS Chi-restraints excluded: chain b residue 176 LEU Chi-restraints excluded: chain b residue 184 LEU Chi-restraints excluded: chain b residue 207 PHE Chi-restraints excluded: chain b residue 292 ASP Chi-restraints excluded: chain b residue 346 ILE Chi-restraints excluded: chain b residue 347 MET Chi-restraints excluded: chain b residue 418 GLU Chi-restraints excluded: chain b residue 464 TYR Chi-restraints excluded: chain b residue 468 SER Chi-restraints excluded: chain b residue 502 SER Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 62 HIS Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 395 ASN Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain g residue 35 ILE Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 50 ASP Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 139 VAL Chi-restraints excluded: chain g residue 203 TYR Chi-restraints excluded: chain g residue 393 ASP Chi-restraints excluded: chain g residue 398 ASP Chi-restraints excluded: chain g residue 499 ILE Chi-restraints excluded: chain g residue 520 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 311 MET Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 133 ASP Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain d residue 166 TYR Chi-restraints excluded: chain d residue 314 LYS Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 411 ILE Chi-restraints excluded: chain d residue 492 THR Chi-restraints excluded: chain d residue 501 VAL Chi-restraints excluded: chain d residue 512 SER Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain e residue 45 GLU Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 107 LEU Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain e residue 131 ASP Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain e residue 151 ASP Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain e residue 312 ASP Chi-restraints excluded: chain e residue 407 PHE Chi-restraints excluded: chain e residue 499 LYS Chi-restraints excluded: chain e residue 512 VAL Chi-restraints excluded: chain e residue 527 VAL Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 209 PHE Chi-restraints excluded: chain Z residue 210 ILE Chi-restraints excluded: chain Z residue 304 MET Chi-restraints excluded: chain Z residue 367 VAL Chi-restraints excluded: chain Z residue 384 THR Chi-restraints excluded: chain Z residue 406 LEU Chi-restraints excluded: chain Z residue 410 ASN Chi-restraints excluded: chain Z residue 412 ILE Chi-restraints excluded: chain Z residue 492 ASP Chi-restraints excluded: chain Z residue 493 LEU Chi-restraints excluded: chain Z residue 521 THR Chi-restraints excluded: chain Z residue 533 LEU Chi-restraints excluded: chain z residue 16 ASP Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 55 LEU Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 145 ASN Chi-restraints excluded: chain z residue 169 VAL Chi-restraints excluded: chain z residue 174 VAL Chi-restraints excluded: chain z residue 192 HIS Chi-restraints excluded: chain z residue 209 PHE Chi-restraints excluded: chain z residue 269 PHE Chi-restraints excluded: chain z residue 279 ASP Chi-restraints excluded: chain z residue 283 GLU Chi-restraints excluded: chain z residue 296 ILE Chi-restraints excluded: chain z residue 385 HIS Chi-restraints excluded: chain z residue 423 SER Chi-restraints excluded: chain z residue 479 ASP Chi-restraints excluded: chain z residue 509 SER Chi-restraints excluded: chain z residue 513 LEU Chi-restraints excluded: chain z residue 527 LEU Chi-restraints excluded: chain z residue 528 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain H residue 141 ASN Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 422 LYS Chi-restraints excluded: chain H residue 453 LEU Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain H residue 472 HIS Chi-restraints excluded: chain H residue 496 VAL Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain h residue 199 ILE Chi-restraints excluded: chain h residue 214 PHE Chi-restraints excluded: chain h residue 279 PHE Chi-restraints excluded: chain h residue 376 LEU Chi-restraints excluded: chain h residue 395 ASP Chi-restraints excluded: chain h residue 446 LEU Chi-restraints excluded: chain h residue 449 ILE Chi-restraints excluded: chain h residue 453 LEU Chi-restraints excluded: chain h residue 466 ASN Chi-restraints excluded: chain h residue 501 LEU Chi-restraints excluded: chain h residue 523 THR Chi-restraints excluded: chain h residue 525 THR Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 49 CYS Chi-restraints excluded: chain Q residue 58 HIS Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 91 GLN Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 174 SER Chi-restraints excluded: chain Q residue 201 TYR Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 298 CYS Chi-restraints excluded: chain Q residue 333 CYS Chi-restraints excluded: chain Q residue 420 LEU Chi-restraints excluded: chain Q residue 432 SER Chi-restraints excluded: chain Q residue 472 ASN Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain Q residue 499 VAL Chi-restraints excluded: chain Q residue 506 ASP Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 62 ILE Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain q residue 117 LEU Chi-restraints excluded: chain q residue 127 ILE Chi-restraints excluded: chain q residue 157 ASN Chi-restraints excluded: chain q residue 207 ILE Chi-restraints excluded: chain q residue 256 ILE Chi-restraints excluded: chain q residue 308 LEU Chi-restraints excluded: chain q residue 310 LEU Chi-restraints excluded: chain q residue 327 PHE Chi-restraints excluded: chain q residue 370 VAL Chi-restraints excluded: chain q residue 395 ASP Chi-restraints excluded: chain q residue 420 LEU Chi-restraints excluded: chain q residue 429 GLU Chi-restraints excluded: chain q residue 475 LEU Chi-restraints excluded: chain q residue 499 VAL Chi-restraints excluded: chain q residue 517 ILE Chi-restraints excluded: chain q residue 519 ASP Chi-restraints excluded: chain q residue 538 VAL Chi-restraints excluded: chain q residue 539 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 742 optimal weight: 10.0000 chunk 782 optimal weight: 20.0000 chunk 713 optimal weight: 20.0000 chunk 760 optimal weight: 9.9990 chunk 781 optimal weight: 1.9990 chunk 457 optimal weight: 0.6980 chunk 331 optimal weight: 2.9990 chunk 597 optimal weight: 10.0000 chunk 233 optimal weight: 0.1980 chunk 687 optimal weight: 4.9990 chunk 719 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 GLN a 27 ASN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 ASN a 430 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 393 GLN G 395 ASN ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 GLN ** Z 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 230 ASN Z 410 ASN ** z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 ASN ** h 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 276 GLN ** h 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN Q 101 ASN ** Q 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 ASN ** Q 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 101 ASN ** q 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4898 moved from start: 0.7859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 66233 Z= 0.277 Angle : 0.994 20.861 89338 Z= 0.504 Chirality : 0.053 0.370 10683 Planarity : 0.005 0.105 11517 Dihedral : 5.028 27.696 9055 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.12 % Rotamer: Outliers : 3.26 % Allowed : 28.63 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.09), residues: 8528 helix: 0.25 (0.07), residues: 4353 sheet: -0.05 (0.16), residues: 1002 loop : -1.29 (0.11), residues: 3173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G 440 HIS 0.014 0.002 HIS a 403 PHE 0.061 0.003 PHE Z 108 TYR 0.034 0.002 TYR q 312 ARG 0.017 0.001 ARG g 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17056 Ramachandran restraints generated. 8528 Oldfield, 0 Emsley, 8528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2437 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 2201 time to evaluate : 6.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.4822 (mp) cc_final: 0.4297 (mp) REVERT: A 43 SER cc_start: 0.6966 (p) cc_final: 0.6595 (t) REVERT: A 130 ARG cc_start: 0.5858 (ptt-90) cc_final: 0.5633 (ptp90) REVERT: A 408 VAL cc_start: 0.6547 (t) cc_final: 0.5314 (p) REVERT: A 518 LEU cc_start: 0.6096 (mt) cc_final: 0.5494 (mt) REVERT: A 526 LYS cc_start: 0.6016 (mttp) cc_final: 0.5685 (mttp) REVERT: A 540 ARG cc_start: 0.5867 (mtp85) cc_final: 0.5665 (mtp85) REVERT: a 18 GLU cc_start: 0.4056 (tp30) cc_final: 0.3801 (tp30) REVERT: a 111 ARG cc_start: 0.4891 (mmt90) cc_final: 0.4523 (mmt90) REVERT: a 282 LEU cc_start: 0.2971 (mt) cc_final: 0.2091 (mp) REVERT: a 476 LYS cc_start: 0.6972 (tttt) cc_final: 0.6748 (tttt) REVERT: a 509 ILE cc_start: 0.7514 (mt) cc_final: 0.6934 (mt) REVERT: a 542 ASP cc_start: 0.6280 (m-30) cc_final: 0.5925 (m-30) REVERT: G 102 GLU cc_start: 0.4721 (tp30) cc_final: 0.4505 (tp30) REVERT: G 131 ASP cc_start: 0.4395 (m-30) cc_final: 0.3934 (m-30) REVERT: G 234 MET cc_start: 0.2020 (ptp) cc_final: 0.1623 (ttm) REVERT: G 421 MET cc_start: 0.6292 (tmm) cc_final: 0.5216 (tmm) REVERT: G 475 HIS cc_start: 0.5049 (OUTLIER) cc_final: 0.4546 (m170) REVERT: g 29 LYS cc_start: 0.5819 (ttmt) cc_final: 0.5157 (tttt) REVERT: g 283 MET cc_start: -0.0894 (mtt) cc_final: -0.1142 (mtm) REVERT: g 499 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6378 (mt) REVERT: g 506 LYS cc_start: 0.7459 (mmmm) cc_final: 0.7160 (mmmm) REVERT: D 36 ARG cc_start: 0.5960 (ttp80) cc_final: 0.5643 (ttp80) REVERT: D 135 LEU cc_start: 0.6443 (mt) cc_final: 0.6242 (mt) REVERT: D 209 MET cc_start: 0.4085 (mmm) cc_final: 0.2753 (mmm) REVERT: D 260 MET cc_start: -0.2556 (tpp) cc_final: -0.4807 (ptt) REVERT: D 350 VAL cc_start: 0.0731 (OUTLIER) cc_final: -0.1056 (t) REVERT: D 498 LEU cc_start: 0.4315 (mm) cc_final: 0.3812 (mm) REVERT: d 113 LYS cc_start: 0.6285 (OUTLIER) cc_final: 0.6031 (mtmm) REVERT: d 125 GLN cc_start: 0.5593 (OUTLIER) cc_final: 0.5348 (tm-30) REVERT: d 305 LEU cc_start: 0.3899 (mt) cc_final: 0.2830 (mt) REVERT: d 314 LYS cc_start: 0.4508 (OUTLIER) cc_final: 0.4117 (ptpp) REVERT: d 526 PHE cc_start: 0.4845 (OUTLIER) cc_final: 0.4472 (m-80) REVERT: E 85 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6909 (m-40) REVERT: E 129 LEU cc_start: 0.6987 (mt) cc_final: 0.6639 (mt) REVERT: E 145 LYS cc_start: 0.6915 (mtmt) cc_final: 0.6683 (mtmm) REVERT: E 212 MET cc_start: 0.4611 (ppp) cc_final: 0.3479 (ppp) REVERT: E 465 ASP cc_start: 0.5507 (m-30) cc_final: 0.5235 (m-30) REVERT: e 45 GLU cc_start: 0.5452 (OUTLIER) cc_final: 0.4339 (pm20) REVERT: e 244 ILE cc_start: 0.4409 (OUTLIER) cc_final: 0.4182 (mp) REVERT: e 309 MET cc_start: 0.2329 (OUTLIER) cc_final: 0.2090 (tpp) REVERT: e 537 GLN cc_start: 0.5868 (mt0) cc_final: 0.4976 (mt0) REVERT: e 543 GLN cc_start: 0.5828 (tm130) cc_final: 0.5352 (tm-30) REVERT: e 547 MET cc_start: 0.5752 (mmp) cc_final: 0.5459 (mmp) REVERT: Z 101 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5666 (mm) REVERT: Z 169 VAL cc_start: 0.7279 (t) cc_final: 0.6882 (t) REVERT: Z 392 LYS cc_start: 0.6981 (ptmm) cc_final: 0.5736 (ptmm) REVERT: Z 400 ARG cc_start: 0.5892 (ttt180) cc_final: 0.5660 (ttt-90) REVERT: Z 469 VAL cc_start: 0.7654 (m) cc_final: 0.7254 (p) REVERT: z 16 ASP cc_start: 0.5603 (m-30) cc_final: 0.5307 (m-30) REVERT: z 37 LEU cc_start: 0.3261 (tp) cc_final: 0.1870 (tt) REVERT: z 161 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7855 (mmmm) REVERT: z 451 LEU cc_start: 0.7091 (mt) cc_final: 0.6868 (mt) REVERT: z 506 ILE cc_start: 0.7942 (mp) cc_final: 0.7545 (tt) REVERT: z 513 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6186 (mp) REVERT: H 317 ARG cc_start: 0.4950 (tpm170) cc_final: 0.4617 (tpp-160) REVERT: H 438 ILE cc_start: 0.7943 (mt) cc_final: 0.7696 (mt) REVERT: h 113 LYS cc_start: 0.6689 (ttpp) cc_final: 0.6377 (ttpp) REVERT: h 341 ILE cc_start: 0.3067 (mm) cc_final: 0.2357 (mm) REVERT: Q 101 ASN cc_start: 0.3300 (m-40) cc_final: 0.3038 (m-40) REVERT: Q 145 MET cc_start: 0.7023 (mmm) cc_final: 0.6788 (mmm) REVERT: Q 294 MET cc_start: 0.2704 (mmm) cc_final: 0.2309 (mpp) REVERT: q 39 HIS cc_start: 0.6243 (t70) cc_final: 0.5735 (t70) REVERT: q 46 MET cc_start: 0.1508 (tpp) cc_final: 0.0460 (tpp) REVERT: q 109 GLU cc_start: 0.5779 (mm-30) cc_final: 0.5431 (mm-30) REVERT: q 256 ILE cc_start: 0.1023 (OUTLIER) cc_final: 0.0099 (mp) REVERT: q 287 MET cc_start: 0.4857 (tmm) cc_final: 0.4090 (tmm) outliers start: 236 outliers final: 185 residues processed: 2302 average time/residue: 0.6523 time to fit residues: 2506.6375 Evaluate side-chains 2289 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 2090 time to evaluate : 5.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 113 ASN Chi-restraints excluded: chain a residue 295 VAL Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 465 ASN Chi-restraints excluded: chain a residue 497 TYR Chi-restraints excluded: chain a residue 532 LEU Chi-restraints excluded: chain a residue 535 CYS Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 385 HIS Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain b residue 36 THR Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 146 LYS Chi-restraints excluded: chain b residue 176 LEU Chi-restraints excluded: chain b residue 184 LEU Chi-restraints excluded: chain b residue 207 PHE Chi-restraints excluded: chain b residue 292 ASP Chi-restraints excluded: chain b residue 346 ILE Chi-restraints excluded: chain b residue 347 MET Chi-restraints excluded: chain b residue 502 SER Chi-restraints excluded: chain b residue 514 ILE Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 62 HIS Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 395 ASN Chi-restraints excluded: chain G residue 475 HIS Chi-restraints excluded: chain g residue 35 ILE Chi-restraints excluded: chain g residue 50 ASP Chi-restraints excluded: chain g residue 62 HIS Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 393 ASP Chi-restraints excluded: chain g residue 499 ILE Chi-restraints excluded: chain g residue 520 LEU Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 311 MET Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 47 MET Chi-restraints excluded: chain d residue 74 VAL Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 113 LYS Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 166 TYR Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 314 LYS Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 492 THR Chi-restraints excluded: chain d residue 499 GLN Chi-restraints excluded: chain d residue 512 SER Chi-restraints excluded: chain d residue 526 PHE Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain e residue 45 GLU Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 107 LEU Chi-restraints excluded: chain e residue 148 ASN Chi-restraints excluded: chain e residue 176 PHE Chi-restraints excluded: chain e residue 244 ILE Chi-restraints excluded: chain e residue 309 MET Chi-restraints excluded: chain e residue 312 ASP Chi-restraints excluded: chain e residue 407 PHE Chi-restraints excluded: chain e residue 499 LYS Chi-restraints excluded: chain e residue 512 VAL Chi-restraints excluded: chain e residue 527 VAL Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 209 PHE Chi-restraints excluded: chain Z residue 304 MET Chi-restraints excluded: chain Z residue 367 VAL Chi-restraints excluded: chain Z residue 406 LEU Chi-restraints excluded: chain Z residue 410 ASN Chi-restraints excluded: chain Z residue 412 ILE Chi-restraints excluded: chain Z residue 420 ILE Chi-restraints excluded: chain Z residue 460 LYS Chi-restraints excluded: chain Z residue 492 ASP Chi-restraints excluded: chain Z residue 533 LEU Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 55 LEU Chi-restraints excluded: chain z residue 92 THR Chi-restraints excluded: chain z residue 145 ASN Chi-restraints excluded: chain z residue 153 VAL Chi-restraints excluded: chain z residue 169 VAL Chi-restraints excluded: chain z residue 192 HIS Chi-restraints excluded: chain z residue 209 PHE Chi-restraints excluded: chain z residue 279 ASP Chi-restraints excluded: chain z residue 283 GLU Chi-restraints excluded: chain z residue 385 HIS Chi-restraints excluded: chain z residue 423 SER Chi-restraints excluded: chain z residue 479 ASP Chi-restraints excluded: chain z residue 509 SER Chi-restraints excluded: chain z residue 513 LEU Chi-restraints excluded: chain z residue 527 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain H residue 406 ASN Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 453 LEU Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain H residue 472 HIS Chi-restraints excluded: chain H residue 479 TYR Chi-restraints excluded: chain H residue 496 VAL Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain h residue 214 PHE Chi-restraints excluded: chain h residue 276 GLN Chi-restraints excluded: chain h residue 279 PHE Chi-restraints excluded: chain h residue 376 LEU Chi-restraints excluded: chain h residue 408 LEU Chi-restraints excluded: chain h residue 446 LEU Chi-restraints excluded: chain h residue 449 ILE Chi-restraints excluded: chain h residue 453 LEU Chi-restraints excluded: chain h residue 466 ASN Chi-restraints excluded: chain h residue 523 THR Chi-restraints excluded: chain h residue 525 THR Chi-restraints excluded: chain Q residue 40 GLN Chi-restraints excluded: chain Q residue 49 CYS Chi-restraints excluded: chain Q residue 58 HIS Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 91 GLN Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 174 SER Chi-restraints excluded: chain Q residue 201 TYR Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 298 CYS Chi-restraints excluded: chain Q residue 333 CYS Chi-restraints excluded: chain Q residue 472 ASN Chi-restraints excluded: chain Q residue 499 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 GLU Chi-restraints excluded: chain q residue 62 ILE Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain q residue 118 ILE Chi-restraints excluded: chain q residue 127 ILE Chi-restraints excluded: chain q residue 157 ASN Chi-restraints excluded: chain q residue 207 ILE Chi-restraints excluded: chain q residue 228 PHE Chi-restraints excluded: chain q residue 256 ILE Chi-restraints excluded: chain q residue 308 LEU Chi-restraints excluded: chain q residue 310 LEU Chi-restraints excluded: chain q residue 327 PHE Chi-restraints excluded: chain q residue 370 VAL Chi-restraints excluded: chain q residue 384 ILE Chi-restraints excluded: chain q residue 420 LEU Chi-restraints excluded: chain q residue 429 GLU Chi-restraints excluded: chain q residue 475 LEU Chi-restraints excluded: chain q residue 499 VAL Chi-restraints excluded: chain q residue 500 ASP Chi-restraints excluded: chain q residue 517 ILE Chi-restraints excluded: chain q residue 538 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1282 > 50: distance: 8 - 10: 34.060 distance: 10 - 11: 40.404 distance: 10 - 172: 37.234 distance: 11 - 12: 39.711 distance: 11 - 14: 56.240 distance: 12 - 13: 58.789 distance: 12 - 18: 48.903 distance: 13 - 169: 27.840 distance: 14 - 15: 48.689 distance: 15 - 16: 42.197 distance: 16 - 17: 35.035 distance: 18 - 19: 41.433 distance: 19 - 20: 57.394 distance: 19 - 22: 69.456 distance: 20 - 21: 56.682 distance: 20 - 25: 40.569 distance: 22 - 23: 39.587 distance: 22 - 24: 42.156 distance: 25 - 26: 27.937 distance: 25 - 159: 35.004 distance: 26 - 27: 57.508 distance: 26 - 29: 41.137 distance: 27 - 28: 48.720 distance: 27 - 36: 41.052 distance: 28 - 156: 31.697 distance: 29 - 30: 23.597 distance: 30 - 31: 61.888 distance: 30 - 32: 61.200 distance: 31 - 33: 64.970 distance: 32 - 34: 39.161 distance: 33 - 35: 41.235 distance: 34 - 35: 39.128 distance: 36 - 37: 39.917 distance: 37 - 38: 44.135 distance: 37 - 40: 15.461 distance: 38 - 39: 44.912 distance: 38 - 44: 23.849 distance: 40 - 41: 46.617 distance: 41 - 42: 42.534 distance: 41 - 43: 39.362 distance: 44 - 45: 38.193 distance: 45 - 46: 53.601 distance: 45 - 48: 56.762 distance: 46 - 47: 69.649 distance: 46 - 55: 11.505 distance: 48 - 49: 43.582 distance: 49 - 50: 46.640 distance: 50 - 51: 27.507 distance: 51 - 52: 32.074 distance: 52 - 53: 26.245 distance: 52 - 54: 26.961 distance: 55 - 56: 9.004 distance: 56 - 57: 40.302 distance: 56 - 59: 57.871 distance: 57 - 58: 14.307 distance: 57 - 64: 34.729 distance: 59 - 60: 39.656 distance: 60 - 61: 69.819 distance: 61 - 63: 51.189 distance: 64 - 65: 56.335 distance: 64 - 70: 15.249 distance: 65 - 66: 40.669 distance: 65 - 68: 40.322 distance: 66 - 67: 58.061 distance: 66 - 71: 21.133 distance: 68 - 69: 41.158 distance: 69 - 70: 68.352 distance: 71 - 72: 44.681 distance: 72 - 75: 67.682 distance: 73 - 74: 57.191 distance: 73 - 80: 40.731 distance: 75 - 76: 69.755 distance: 77 - 78: 68.783 distance: 77 - 79: 56.919 distance: 80 - 81: 15.592 distance: 81 - 82: 60.516 distance: 82 - 83: 40.249 distance: 82 - 84: 40.780 distance: 84 - 85: 54.732 distance: 85 - 86: 4.458 distance: 85 - 88: 49.100 distance: 86 - 87: 56.614 distance: 86 - 94: 33.529 distance: 88 - 89: 65.408 distance: 89 - 90: 43.014 distance: 90 - 92: 55.679 distance: 91 - 93: 40.365 distance: 92 - 93: 17.888