Starting phenix.real_space_refine on Wed Mar 4 16:55:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yle_10836/03_2026/6yle_10836.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yle_10836/03_2026/6yle_10836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6yle_10836/03_2026/6yle_10836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yle_10836/03_2026/6yle_10836.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yle_10836/03_2026/6yle_10836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yle_10836/03_2026/6yle_10836.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 61 5.16 5 C 9933 2.51 5 N 2535 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15345 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3139 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 384} Chain breaks: 9 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3260 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 14, 'TRANS': 400} Chain breaks: 6 Chain: "C" Number of atoms: 4352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4352 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 27, 'TRANS': 517} Chain breaks: 4 Chain: "D" Number of atoms: 4380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4380 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 27, 'TRANS': 519} Chain breaks: 2 Chain: "K" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 214 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 4, 'TRANS': 19} Time building chain proxies: 3.13, per 1000 atoms: 0.20 Number of scatterers: 15345 At special positions: 0 Unit cell: (113.313, 114.372, 111.195, 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 61 16.00 O 2816 8.00 N 2535 7.00 C 9933 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: 1.38 Conformation dependent library (CDL) restraints added in 718.6 milliseconds 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3678 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 20 sheets defined 44.5% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 169 through 172 removed outlier: 3.921A pdb=" N VAL A 172 " --> pdb=" O VAL A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.574A pdb=" N GLU A 461 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 458 through 462' Processing helix chain 'A' and resid 472 through 485 removed outlier: 4.229A pdb=" N TYR A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 485 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.941A pdb=" N SER B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 485 removed outlier: 3.909A pdb=" N SER B 485 " --> pdb=" O LYS B 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 14 removed outlier: 3.687A pdb=" N LEU C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 4.823A pdb=" N THR C 25 " --> pdb=" O ASN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 6.077A pdb=" N VAL C 34 " --> pdb=" O ARG C 31 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 35 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 58 removed outlier: 3.764A pdb=" N SER C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 78 Processing helix chain 'C' and resid 78 through 103 removed outlier: 3.606A pdb=" N LEU C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN C 88 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE C 103 " --> pdb=" O GLN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 129 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 142 through 158 removed outlier: 4.485A pdb=" N LYS C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALA C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Proline residue: C 151 - end of helix Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.501A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Proline residue: C 166 - end of helix Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.886A pdb=" N VAL C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.661A pdb=" N GLU C 263 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 265 " --> pdb=" O CYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 removed outlier: 3.789A pdb=" N TYR C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 278 " --> pdb=" O TYR C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 308 Processing helix chain 'C' and resid 309 through 326 removed outlier: 4.244A pdb=" N LEU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 364 through 391 removed outlier: 4.046A pdb=" N THR C 372 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Proline residue: C 375 - end of helix removed outlier: 3.521A pdb=" N GLN C 380 " --> pdb=" O GLN C 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY C 381 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 387 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 401 through 411 removed outlier: 3.585A pdb=" N SER C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 430 through 448 removed outlier: 4.218A pdb=" N HIS C 446 " --> pdb=" O MET C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 468 removed outlier: 4.436A pdb=" N SER C 458 " --> pdb=" O ILE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 536 removed outlier: 4.020A pdb=" N GLU C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 562 removed outlier: 4.373A pdb=" N ILE C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 579 Processing helix chain 'C' and resid 587 through 595 Processing helix chain 'C' and resid 601 through 608 removed outlier: 3.596A pdb=" N LEU C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 3.666A pdb=" N LEU D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 31 removed outlier: 4.788A pdb=" N THR D 25 " --> pdb=" O ASN D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 42 removed outlier: 4.273A pdb=" N LYS D 42 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 58 Processing helix chain 'D' and resid 62 through 77 Processing helix chain 'D' and resid 78 through 102 removed outlier: 6.717A pdb=" N GLY D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.643A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 132 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 142 through 157 removed outlier: 3.682A pdb=" N LYS D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix removed outlier: 3.685A pdb=" N LEU D 156 " --> pdb=" O THR D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.935A pdb=" N VAL D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) Proline residue: D 166 - end of helix Processing helix chain 'D' and resid 176 through 181 Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.088A pdb=" N VAL D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 241 through 252 Processing helix chain 'D' and resid 254 through 261 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 307 through 325 removed outlier: 3.610A pdb=" N MET D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 349 removed outlier: 3.797A pdb=" N VAL D 349 " --> pdb=" O VAL D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 391 Proline residue: D 375 - end of helix removed outlier: 3.901A pdb=" N GLY D 381 " --> pdb=" O ILE D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 398 No H-bonds generated for 'chain 'D' and resid 396 through 398' Processing helix chain 'D' and resid 399 through 406 Processing helix chain 'D' and resid 407 through 411 Processing helix chain 'D' and resid 422 through 427 removed outlier: 3.794A pdb=" N VAL D 426 " --> pdb=" O ASP D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 445 removed outlier: 3.759A pdb=" N THR D 435 " --> pdb=" O PHE D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 469 removed outlier: 3.509A pdb=" N GLU D 462 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 537 Processing helix chain 'D' and resid 540 through 562 Processing helix chain 'D' and resid 566 through 579 Processing helix chain 'D' and resid 589 through 597 removed outlier: 3.626A pdb=" N SER D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN D 597 " --> pdb=" O SER D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 608 removed outlier: 3.738A pdb=" N LEU D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU D 606 " --> pdb=" O MET D 602 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS D 607 " --> pdb=" O PHE D 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 removed outlier: 4.600A pdb=" N GLY A 13 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN A 4 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR A 400 " --> pdb=" O GLN A 4 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 6 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 398 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR A 8 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.665A pdb=" N VAL A 57 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A 71 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 85 removed outlier: 3.637A pdb=" N VAL A 85 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 110 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU A 124 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU A 130 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 147 removed outlier: 3.582A pdb=" N CYS A 183 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 198 removed outlier: 3.987A pdb=" N THR A 210 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A 216 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP A 225 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU A 250 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N PHE A 312 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR A 253 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU A 314 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR A 255 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU A 337 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N SER A 313 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 265 Processing sheet with id=AA7, first strand: chain 'A' and resid 286 through 288 Processing sheet with id=AA8, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.816A pdb=" N LEU A 359 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 380 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU A 372 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE A 378 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 453 Processing sheet with id=AB1, first strand: chain 'B' and resid 23 through 26 removed outlier: 4.065A pdb=" N GLY B 13 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 401 " --> pdb=" O GLN B 4 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 40 Processing sheet with id=AB3, first strand: chain 'B' and resid 81 through 85 removed outlier: 3.628A pdb=" N VAL B 85 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 110 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 120 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL B 133 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE B 122 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 129 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 144 through 147 removed outlier: 3.859A pdb=" N CYS B 183 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.961A pdb=" N SER B 216 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B 252 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP B 225 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU B 250 " --> pdb=" O ASP B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 260 through 265 removed outlier: 6.603A pdb=" N CYS B 280 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 286 through 288 Processing sheet with id=AB8, first strand: chain 'B' and resid 314 through 315 Processing sheet with id=AB9, first strand: chain 'B' and resid 347 through 352 removed outlier: 6.692A pdb=" N GLY B 362 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU B 350 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 360 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE B 352 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 358 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS B 367 " --> pdb=" O ASP B 363 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU B 372 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE B 378 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 450 through 453 Processing sheet with id=AC2, first strand: chain 'C' and resid 471 through 472 673 hydrogen bonds defined for protein. 1926 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: 2.18 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4770 1.34 - 1.46: 2924 1.46 - 1.57: 7856 1.57 - 1.69: 1 1.69 - 1.81: 85 Bond restraints: 15636 Sorted by residual: bond pdb=" N SER C 110 " pdb=" CA SER C 110 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" C THR C 328 " pdb=" N PRO C 329 " ideal model delta sigma weight residual 1.331 1.355 -0.024 7.90e-03 1.60e+04 9.16e+00 bond pdb=" C LEU A 190 " pdb=" N PRO A 191 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.27e-02 6.20e+03 8.98e+00 bond pdb=" C LEU B 190 " pdb=" N PRO B 191 " ideal model delta sigma weight residual 1.331 1.366 -0.035 1.20e-02 6.94e+03 8.50e+00 bond pdb=" C ILE C 538 " pdb=" N LEU C 539 " ideal model delta sigma weight residual 1.331 1.293 0.039 1.54e-02 4.22e+03 6.28e+00 ... (remaining 15631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 20107 2.13 - 4.25: 918 4.25 - 6.38: 146 6.38 - 8.50: 23 8.50 - 10.63: 6 Bond angle restraints: 21200 Sorted by residual: angle pdb=" N GLN C 269 " pdb=" CA GLN C 269 " pdb=" C GLN C 269 " ideal model delta sigma weight residual 111.69 101.06 10.63 1.23e+00 6.61e-01 7.47e+01 angle pdb=" CA VAL B 303 " pdb=" CB VAL B 303 " pdb=" CG2 VAL B 303 " ideal model delta sigma weight residual 110.40 119.51 -9.11 1.70e+00 3.46e-01 2.87e+01 angle pdb=" N LEU B 149 " pdb=" CA LEU B 149 " pdb=" C LEU B 149 " ideal model delta sigma weight residual 110.17 103.03 7.14 1.51e+00 4.39e-01 2.24e+01 angle pdb=" N PRO B 191 " pdb=" CA PRO B 191 " pdb=" C PRO B 191 " ideal model delta sigma weight residual 111.03 118.26 -7.23 1.54e+00 4.22e-01 2.20e+01 angle pdb=" CA VAL B 303 " pdb=" CB VAL B 303 " pdb=" CG1 VAL B 303 " ideal model delta sigma weight residual 110.40 117.87 -7.47 1.70e+00 3.46e-01 1.93e+01 ... (remaining 21195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 8276 17.81 - 35.63: 926 35.63 - 53.44: 164 53.44 - 71.26: 44 71.26 - 89.07: 42 Dihedral angle restraints: 9452 sinusoidal: 3810 harmonic: 5642 Sorted by residual: dihedral pdb=" CA ALA A 268 " pdb=" C ALA A 268 " pdb=" N ASP A 269 " pdb=" CA ASP A 269 " ideal model delta harmonic sigma weight residual -180.00 -117.42 -62.58 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA LEU B 205 " pdb=" C LEU B 205 " pdb=" N SER B 206 " pdb=" CA SER B 206 " ideal model delta harmonic sigma weight residual 180.00 139.23 40.77 0 5.00e+00 4.00e-02 6.65e+01 dihedral pdb=" CA SER C 417 " pdb=" C SER C 417 " pdb=" N ASN C 418 " pdb=" CA ASN C 418 " ideal model delta harmonic sigma weight residual 180.00 -143.63 -36.37 0 5.00e+00 4.00e-02 5.29e+01 ... (remaining 9449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 2534 0.349 - 0.699: 0 0.699 - 1.048: 0 1.048 - 1.398: 0 1.398 - 1.747: 1 Chirality restraints: 2535 Sorted by residual: chirality pdb=" CB VAL B 303 " pdb=" CA VAL B 303 " pdb=" CG1 VAL B 303 " pdb=" CG2 VAL B 303 " both_signs ideal model delta sigma weight residual False -2.63 -0.88 -1.75 2.00e-01 2.50e+01 7.63e+01 chirality pdb=" CA GLN C 269 " pdb=" N GLN C 269 " pdb=" C GLN C 269 " pdb=" CB GLN C 269 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA LYS D 391 " pdb=" N LYS D 391 " pdb=" C LYS D 391 " pdb=" CB LYS D 391 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2532 not shown) Planarity restraints: 2642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 13 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.17e+01 pdb=" C GLY B 13 " -0.059 2.00e-02 2.50e+03 pdb=" O GLY B 13 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 14 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 542 " 0.054 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO C 543 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 543 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 543 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 268 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.67e+00 pdb=" C GLU C 268 " 0.054 2.00e-02 2.50e+03 pdb=" O GLU C 268 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN C 269 " -0.018 2.00e-02 2.50e+03 ... (remaining 2639 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 76 2.51 - 3.11: 10892 3.11 - 3.70: 22642 3.70 - 4.30: 31744 4.30 - 4.90: 55561 Nonbonded interactions: 120915 Sorted by model distance: nonbonded pdb=" OE1 GLU D 162 " pdb=" OG1 THR D 205 " model vdw 1.910 3.040 nonbonded pdb=" O MET C 131 " pdb=" OG SER C 138 " model vdw 2.137 3.040 nonbonded pdb=" O THR B 208 " pdb=" OG SER B 227 " model vdw 2.138 3.040 nonbonded pdb=" OH TYR D 94 " pdb=" O ALA D 148 " model vdw 2.138 3.040 nonbonded pdb=" OG1 THR B 189 " pdb=" OD2 ASP B 218 " model vdw 2.141 3.040 ... (remaining 120910 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' and (resid 1 through 229 or resid 246 through 460 or resid 472 throug \ h 489)) selection = (chain 'B' and (resid 1 through 60 or resid 67 through 299 or resid 310 through \ 317 or resid 331 through 385 or resid 394 through 403 or resid 431 through 442 o \ r resid 447 through 489)) } ncs_group { reference = (chain 'C' and (resid 4 through 469 or resid 520 through 617)) selection = (chain 'D' and (resid 4 through 281 or resid 291 through 351 or resid 363 throug \ h 617)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.860 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 0.080 15636 Z= 0.380 Angle : 1.051 10.629 21200 Z= 0.578 Chirality : 0.065 1.747 2535 Planarity : 0.007 0.082 2642 Dihedral : 16.797 89.071 5774 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.28 % Allowed : 14.87 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.16), residues: 1878 helix: -1.73 (0.15), residues: 762 sheet: -1.54 (0.26), residues: 289 loop : -2.60 (0.18), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 312 TYR 0.016 0.002 TYR C 550 PHE 0.020 0.002 PHE B 7 TRP 0.013 0.002 TRP B 123 HIS 0.008 0.002 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00940 (15636) covalent geometry : angle 1.05095 (21200) hydrogen bonds : bond 0.17942 ( 673) hydrogen bonds : angle 6.77978 ( 1926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 322 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.9153 (mp) cc_final: 0.8869 (mp) REVERT: B 119 LYS cc_start: 0.7876 (ttmm) cc_final: 0.7641 (ttpp) REVERT: B 121 TYR cc_start: 0.8279 (m-80) cc_final: 0.7462 (m-80) REVERT: B 154 ILE cc_start: 0.9067 (pt) cc_final: 0.8821 (pt) REVERT: B 364 THR cc_start: 0.8766 (p) cc_final: 0.8471 (m) REVERT: B 439 ILE cc_start: 0.8115 (mp) cc_final: 0.7821 (mp) REVERT: C 64 LEU cc_start: 0.8332 (tp) cc_final: 0.8053 (tp) REVERT: C 110 SER cc_start: 0.6201 (OUTLIER) cc_final: 0.5069 (t) REVERT: C 403 ILE cc_start: 0.8396 (tt) cc_final: 0.8195 (mt) REVERT: D 520 MET cc_start: 0.7131 (mmt) cc_final: 0.6881 (mmp) outliers start: 5 outliers final: 2 residues processed: 325 average time/residue: 0.1420 time to fit residues: 64.6547 Evaluate side-chains 193 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 397 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS B 138 HIS ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS B 201 GLN B 449 HIS C 158 GLN C 452 ASN C 554 GLN D 554 GLN D 597 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100110 restraints weight = 31682.919| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.72 r_work: 0.3244 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15636 Z= 0.125 Angle : 0.621 6.930 21200 Z= 0.318 Chirality : 0.045 0.160 2535 Planarity : 0.005 0.056 2642 Dihedral : 5.442 44.521 2032 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.43 % Allowed : 14.87 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.18), residues: 1878 helix: -0.12 (0.18), residues: 768 sheet: -1.15 (0.27), residues: 305 loop : -2.22 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.012 0.001 TYR A 224 PHE 0.013 0.001 PHE D 431 TRP 0.013 0.001 TRP C 65 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00277 (15636) covalent geometry : angle 0.62099 (21200) hydrogen bonds : bond 0.04256 ( 673) hydrogen bonds : angle 4.80795 ( 1926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 239 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8859 (mt) cc_final: 0.8628 (mt) REVERT: A 130 LEU cc_start: 0.8849 (tp) cc_final: 0.8618 (tp) REVERT: A 256 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7899 (p) REVERT: A 367 LYS cc_start: 0.6802 (ptmt) cc_final: 0.6449 (pttp) REVERT: B 334 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.6186 (pmm) REVERT: B 439 ILE cc_start: 0.8167 (mp) cc_final: 0.7896 (mp) REVERT: B 453 TYR cc_start: 0.8930 (t80) cc_final: 0.8724 (t80) REVERT: D 388 MET cc_start: 0.8610 (tmm) cc_final: 0.8295 (tmm) REVERT: K 261 LYS cc_start: 0.9305 (mtpt) cc_final: 0.8718 (mmtt) outliers start: 43 outliers final: 21 residues processed: 270 average time/residue: 0.1239 time to fit residues: 50.2677 Evaluate side-chains 198 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 611 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 143 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 56 optimal weight: 0.0770 chunk 59 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 100 HIS B 140 GLN B 454 GLN ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS D 60 ASN D 271 ASN D 371 ASN D 446 HIS D 449 HIS D 527 ASN K 259 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.090126 restraints weight = 33336.738| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.71 r_work: 0.3072 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15636 Z= 0.257 Angle : 0.700 8.654 21200 Z= 0.358 Chirality : 0.048 0.169 2535 Planarity : 0.005 0.053 2642 Dihedral : 5.565 48.631 2029 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.90 % Allowed : 16.11 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.18), residues: 1878 helix: 0.28 (0.19), residues: 779 sheet: -1.12 (0.27), residues: 317 loop : -1.99 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C 174 TYR 0.014 0.002 TYR A 224 PHE 0.018 0.002 PHE D 267 TRP 0.013 0.001 TRP C 65 HIS 0.005 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00610 (15636) covalent geometry : angle 0.69974 (21200) hydrogen bonds : bond 0.04826 ( 673) hydrogen bonds : angle 4.79575 ( 1926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 188 time to evaluate : 0.602 Fit side-chains REVERT: A 130 LEU cc_start: 0.8959 (tp) cc_final: 0.8753 (tp) REVERT: A 256 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8296 (p) REVERT: B 154 ILE cc_start: 0.9262 (pt) cc_final: 0.8974 (mp) REVERT: B 334 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.6139 (pmm) REVERT: B 439 ILE cc_start: 0.8299 (mp) cc_final: 0.7989 (mp) REVERT: C 408 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7947 (tm-30) REVERT: C 520 MET cc_start: 0.7860 (mmm) cc_final: 0.7626 (mmm) REVERT: D 140 GLU cc_start: 0.4812 (OUTLIER) cc_final: 0.4219 (mt-10) REVERT: D 399 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7855 (p90) REVERT: K 252 ASP cc_start: 0.8863 (p0) cc_final: 0.8542 (p0) REVERT: K 261 LYS cc_start: 0.9407 (mtpt) cc_final: 0.8766 (mmtt) REVERT: K 265 ARG cc_start: 0.3934 (OUTLIER) cc_final: 0.3664 (ppt170) outliers start: 69 outliers final: 45 residues processed: 243 average time/residue: 0.1045 time to fit residues: 39.8768 Evaluate side-chains 212 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 162 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain K residue 265 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 35 ASN ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.104245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.090923 restraints weight = 32905.763| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.71 r_work: 0.3081 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15636 Z= 0.184 Angle : 0.611 7.672 21200 Z= 0.313 Chirality : 0.046 0.169 2535 Planarity : 0.004 0.044 2642 Dihedral : 5.266 48.408 2029 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.73 % Allowed : 17.07 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.19), residues: 1878 helix: 0.70 (0.19), residues: 780 sheet: -0.90 (0.27), residues: 315 loop : -1.81 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 380 TYR 0.014 0.001 TYR A 224 PHE 0.012 0.001 PHE D 433 TRP 0.013 0.001 TRP C 65 HIS 0.003 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00438 (15636) covalent geometry : angle 0.61119 (21200) hydrogen bonds : bond 0.04193 ( 673) hydrogen bonds : angle 4.59327 ( 1926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 181 time to evaluate : 0.578 Fit side-chains REVERT: A 130 LEU cc_start: 0.8963 (tp) cc_final: 0.8749 (tp) REVERT: A 256 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8320 (p) REVERT: A 332 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.6312 (t80) REVERT: B 334 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.6317 (pmm) REVERT: B 439 ILE cc_start: 0.8133 (mp) cc_final: 0.7929 (mp) REVERT: C 408 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8011 (tm-30) REVERT: C 535 ASN cc_start: 0.9530 (OUTLIER) cc_final: 0.9325 (m110) REVERT: C 604 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8924 (tm-30) REVERT: D 131 MET cc_start: 0.8679 (mtm) cc_final: 0.8472 (ttm) REVERT: D 359 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7892 (pp20) REVERT: D 403 ILE cc_start: 0.9201 (pt) cc_final: 0.8994 (pt) REVERT: D 520 MET cc_start: 0.7368 (mmt) cc_final: 0.6648 (mmt) REVERT: D 564 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.6785 (p90) REVERT: K 261 LYS cc_start: 0.9424 (mtpt) cc_final: 0.8792 (mmtt) REVERT: K 265 ARG cc_start: 0.4278 (OUTLIER) cc_final: 0.3983 (ppt170) outliers start: 66 outliers final: 41 residues processed: 231 average time/residue: 0.1005 time to fit residues: 36.7394 Evaluate side-chains 209 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 564 TYR Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain K residue 265 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 19 optimal weight: 0.0000 chunk 171 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN D 378 GLN ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.088818 restraints weight = 33295.968| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.70 r_work: 0.3041 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15636 Z= 0.228 Angle : 0.649 8.184 21200 Z= 0.331 Chirality : 0.047 0.181 2535 Planarity : 0.004 0.045 2642 Dihedral : 5.277 49.128 2029 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.35 % Allowed : 17.69 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.19), residues: 1878 helix: 0.85 (0.19), residues: 779 sheet: -1.00 (0.27), residues: 323 loop : -1.66 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 380 TYR 0.016 0.002 TYR A 224 PHE 0.014 0.001 PHE D 433 TRP 0.012 0.001 TRP C 65 HIS 0.005 0.001 HIS A 19 Details of bonding type rmsd covalent geometry : bond 0.00543 (15636) covalent geometry : angle 0.64891 (21200) hydrogen bonds : bond 0.04416 ( 673) hydrogen bonds : angle 4.65515 ( 1926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 167 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.9002 (tp) cc_final: 0.8785 (tp) REVERT: A 256 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8401 (p) REVERT: A 332 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.6627 (t80) REVERT: A 367 LYS cc_start: 0.6807 (ptmt) cc_final: 0.6470 (pttp) REVERT: B 334 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.6323 (pmm) REVERT: C 408 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8096 (tm-30) REVERT: C 535 ASN cc_start: 0.9541 (OUTLIER) cc_final: 0.9339 (m110) REVERT: D 140 GLU cc_start: 0.4840 (OUTLIER) cc_final: 0.4258 (mt-10) REVERT: D 403 ILE cc_start: 0.9187 (pt) cc_final: 0.8969 (pt) REVERT: D 564 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.6920 (p90) REVERT: K 261 LYS cc_start: 0.9404 (mtpt) cc_final: 0.8804 (mmtt) REVERT: K 265 ARG cc_start: 0.4311 (OUTLIER) cc_final: 0.3991 (ppt170) outliers start: 77 outliers final: 54 residues processed: 229 average time/residue: 0.1101 time to fit residues: 39.0648 Evaluate side-chains 217 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 156 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 564 TYR Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain K residue 265 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 69 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 ASN C 85 HIS D 192 ASN ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.090847 restraints weight = 32828.044| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.68 r_work: 0.3079 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15636 Z= 0.146 Angle : 0.583 7.691 21200 Z= 0.297 Chirality : 0.044 0.185 2535 Planarity : 0.004 0.042 2642 Dihedral : 4.986 48.396 2029 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.50 % Allowed : 18.26 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.19), residues: 1878 helix: 1.11 (0.19), residues: 773 sheet: -0.84 (0.28), residues: 308 loop : -1.47 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 94 TYR 0.013 0.001 TYR B 139 PHE 0.012 0.001 PHE B 7 TRP 0.012 0.001 TRP C 65 HIS 0.003 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00346 (15636) covalent geometry : angle 0.58334 (21200) hydrogen bonds : bond 0.03850 ( 673) hydrogen bonds : angle 4.50041 ( 1926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 0.598 Fit side-chains REVERT: A 266 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: A 332 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.6535 (t80) REVERT: A 367 LYS cc_start: 0.6722 (ptmt) cc_final: 0.6379 (pttp) REVERT: A 372 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7925 (tm-30) REVERT: C 387 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.8980 (mp) REVERT: C 408 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8085 (tm-30) REVERT: D 140 GLU cc_start: 0.4627 (OUTLIER) cc_final: 0.4045 (mt-10) REVERT: D 520 MET cc_start: 0.7358 (mmt) cc_final: 0.6742 (mmt) REVERT: K 261 LYS cc_start: 0.9418 (mtpt) cc_final: 0.8792 (mmtt) REVERT: K 265 ARG cc_start: 0.4497 (OUTLIER) cc_final: 0.4214 (ppt170) outliers start: 62 outliers final: 39 residues processed: 238 average time/residue: 0.1089 time to fit residues: 40.0562 Evaluate side-chains 215 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain K residue 265 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 21 optimal weight: 8.9990 chunk 70 optimal weight: 0.0270 chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 ASN B 474 ASN D 271 ASN ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.091809 restraints weight = 32714.462| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.69 r_work: 0.3098 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15636 Z= 0.122 Angle : 0.570 8.680 21200 Z= 0.289 Chirality : 0.044 0.181 2535 Planarity : 0.004 0.042 2642 Dihedral : 4.795 48.474 2029 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.17 % Allowed : 19.11 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.19), residues: 1878 helix: 1.26 (0.19), residues: 773 sheet: -0.73 (0.28), residues: 305 loop : -1.33 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 244 TYR 0.015 0.001 TYR C 159 PHE 0.016 0.001 PHE D 431 TRP 0.012 0.001 TRP C 65 HIS 0.003 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00283 (15636) covalent geometry : angle 0.57003 (21200) hydrogen bonds : bond 0.03630 ( 673) hydrogen bonds : angle 4.37348 ( 1926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 266 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: A 332 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.6486 (t80) REVERT: A 367 LYS cc_start: 0.6730 (ptmt) cc_final: 0.6376 (pttp) REVERT: A 372 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7944 (tm-30) REVERT: C 387 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.8927 (mp) REVERT: C 408 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8104 (tm-30) REVERT: D 140 GLU cc_start: 0.4744 (OUTLIER) cc_final: 0.4211 (mt-10) REVERT: D 359 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8004 (pp20) REVERT: D 520 MET cc_start: 0.7353 (mmt) cc_final: 0.6866 (mmt) REVERT: K 261 LYS cc_start: 0.9436 (mtpt) cc_final: 0.8810 (mmtt) REVERT: K 265 ARG cc_start: 0.4469 (OUTLIER) cc_final: 0.4207 (ppt170) outliers start: 56 outliers final: 37 residues processed: 227 average time/residue: 0.0987 time to fit residues: 35.0632 Evaluate side-chains 215 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain K residue 265 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 165 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 67 optimal weight: 0.0020 chunk 124 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 ASN B 474 ASN D 69 HIS ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091617 restraints weight = 32978.479| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.70 r_work: 0.3093 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15636 Z= 0.134 Angle : 0.579 8.484 21200 Z= 0.292 Chirality : 0.044 0.187 2535 Planarity : 0.004 0.041 2642 Dihedral : 4.741 48.544 2029 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.11 % Allowed : 18.94 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.19), residues: 1878 helix: 1.38 (0.19), residues: 767 sheet: -0.69 (0.28), residues: 305 loop : -1.28 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 244 TYR 0.013 0.001 TYR A 224 PHE 0.013 0.001 PHE B 7 TRP 0.011 0.001 TRP C 65 HIS 0.003 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00316 (15636) covalent geometry : angle 0.57888 (21200) hydrogen bonds : bond 0.03626 ( 673) hydrogen bonds : angle 4.34429 ( 1926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.636 Fit side-chains REVERT: A 266 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8187 (m-30) REVERT: A 332 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.6486 (t80) REVERT: A 367 LYS cc_start: 0.6750 (ptmt) cc_final: 0.6379 (pttp) REVERT: A 372 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7920 (tm-30) REVERT: C 387 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8882 (mp) REVERT: C 408 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8121 (tm-30) REVERT: D 140 GLU cc_start: 0.4805 (OUTLIER) cc_final: 0.4235 (mt-10) REVERT: D 359 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8008 (pp20) REVERT: D 520 MET cc_start: 0.7369 (mmt) cc_final: 0.6799 (mmt) REVERT: K 261 LYS cc_start: 0.9438 (mtpt) cc_final: 0.8807 (mmtt) REVERT: K 265 ARG cc_start: 0.4457 (OUTLIER) cc_final: 0.4188 (ppt170) outliers start: 55 outliers final: 45 residues processed: 223 average time/residue: 0.1037 time to fit residues: 35.8381 Evaluate side-chains 218 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain K residue 265 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 105 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 304 ASN B 474 ASN D 69 HIS ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.092931 restraints weight = 32579.246| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.68 r_work: 0.3115 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15636 Z= 0.112 Angle : 0.567 9.333 21200 Z= 0.285 Chirality : 0.044 0.175 2535 Planarity : 0.003 0.041 2642 Dihedral : 4.603 48.289 2029 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.94 % Allowed : 19.22 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.20), residues: 1878 helix: 1.51 (0.19), residues: 762 sheet: -0.60 (0.28), residues: 317 loop : -1.22 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 244 TYR 0.012 0.001 TYR A 224 PHE 0.017 0.001 PHE D 431 TRP 0.012 0.001 TRP C 65 HIS 0.003 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00261 (15636) covalent geometry : angle 0.56723 (21200) hydrogen bonds : bond 0.03399 ( 673) hydrogen bonds : angle 4.26839 ( 1926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 266 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: A 332 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.6461 (t80) REVERT: A 367 LYS cc_start: 0.6725 (ptmt) cc_final: 0.6357 (pttp) REVERT: C 387 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8855 (mp) REVERT: C 408 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8086 (tm-30) REVERT: D 140 GLU cc_start: 0.4778 (OUTLIER) cc_final: 0.4146 (mt-10) REVERT: D 359 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8010 (pp20) REVERT: D 388 MET cc_start: 0.8605 (tmm) cc_final: 0.8300 (tmm) REVERT: D 403 ILE cc_start: 0.9065 (pt) cc_final: 0.8790 (pt) REVERT: D 520 MET cc_start: 0.7429 (mmt) cc_final: 0.6974 (mmt) REVERT: K 252 ASP cc_start: 0.8781 (p0) cc_final: 0.8452 (p0) REVERT: K 261 LYS cc_start: 0.9437 (mtpt) cc_final: 0.8810 (mmtt) REVERT: K 265 ARG cc_start: 0.4440 (OUTLIER) cc_final: 0.4188 (ppt170) outliers start: 52 outliers final: 38 residues processed: 224 average time/residue: 0.1042 time to fit residues: 36.8982 Evaluate side-chains 215 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain K residue 265 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 163 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 ASN B 474 ASN D 69 HIS ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.091039 restraints weight = 33133.271| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.69 r_work: 0.3084 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15636 Z= 0.156 Angle : 0.597 9.699 21200 Z= 0.301 Chirality : 0.045 0.181 2535 Planarity : 0.004 0.041 2642 Dihedral : 4.704 48.603 2029 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.71 % Allowed : 20.29 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1878 helix: 1.39 (0.19), residues: 774 sheet: -0.54 (0.28), residues: 305 loop : -1.22 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 244 TYR 0.014 0.001 TYR A 224 PHE 0.015 0.001 PHE B 7 TRP 0.010 0.001 TRP C 65 HIS 0.004 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00377 (15636) covalent geometry : angle 0.59733 (21200) hydrogen bonds : bond 0.03698 ( 673) hydrogen bonds : angle 4.31806 ( 1926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.646 Fit side-chains REVERT: A 332 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.6559 (t80) REVERT: A 367 LYS cc_start: 0.6795 (ptmt) cc_final: 0.6416 (pttp) REVERT: C 387 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8895 (mp) REVERT: C 408 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8115 (tm-30) REVERT: C 604 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8968 (tm-30) REVERT: D 140 GLU cc_start: 0.4780 (OUTLIER) cc_final: 0.4233 (mt-10) REVERT: D 359 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8024 (pp20) REVERT: D 403 ILE cc_start: 0.9081 (pt) cc_final: 0.8820 (pt) REVERT: K 252 ASP cc_start: 0.8844 (p0) cc_final: 0.8492 (p0) REVERT: K 261 LYS cc_start: 0.9438 (mtpt) cc_final: 0.8807 (mmtt) REVERT: K 265 ARG cc_start: 0.4462 (OUTLIER) cc_final: 0.4200 (ppt170) outliers start: 48 outliers final: 39 residues processed: 209 average time/residue: 0.1005 time to fit residues: 33.4247 Evaluate side-chains 208 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 362 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 585 VAL Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain K residue 265 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 100 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 ASN B 474 ASN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.092474 restraints weight = 32551.090| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.68 r_work: 0.3109 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15636 Z= 0.122 Angle : 0.574 9.874 21200 Z= 0.289 Chirality : 0.044 0.178 2535 Planarity : 0.004 0.041 2642 Dihedral : 4.598 48.430 2029 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.71 % Allowed : 20.58 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.20), residues: 1878 helix: 1.51 (0.19), residues: 766 sheet: -0.47 (0.28), residues: 317 loop : -1.18 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 244 TYR 0.013 0.001 TYR A 224 PHE 0.016 0.001 PHE D 431 TRP 0.011 0.001 TRP C 65 HIS 0.004 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00291 (15636) covalent geometry : angle 0.57412 (21200) hydrogen bonds : bond 0.03463 ( 673) hydrogen bonds : angle 4.26119 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2532.19 seconds wall clock time: 44 minutes 41.65 seconds (2681.65 seconds total)