Starting phenix.real_space_refine on Fri Jul 3 19:22:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mi9_23843/07_2026/7mi9_23843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mi9_23843/07_2026/7mi9_23843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mi9_23843/07_2026/7mi9_23843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mi9_23843/07_2026/7mi9_23843.map" model { file = "/net/cci-nas-00/data/ceres_data/7mi9_23843/07_2026/7mi9_23843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mi9_23843/07_2026/7mi9_23843.cif" } resolution = 3.89 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 170 5.49 5 S 74 5.16 5 C 9521 2.51 5 N 2935 2.21 5 O 3224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15924 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2772 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 20, 'TRANS': 327} Chain: "B" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2696 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 18, 'TRANS': 319} Chain: "C" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2707 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 18, 'TRANS': 320} Chain: "D" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2696 Classifications: {'peptide': 339} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 320} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1639 Classifications: {'DNA': 80} Link IDs: {'rna3p': 79} Chain: "H" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1468 Classifications: {'DNA': 72} Link IDs: {'rna3p': 71} Chain: "I" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "J" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 2.78, per 1000 atoms: 0.17 Number of scatterers: 15924 At special positions: 0 Unit cell: (119.574, 103.806, 185.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 170 15.00 O 3224 8.00 N 2935 7.00 C 9521 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: 1.32 Conformation dependent library (CDL) restraints added in 590.8 milliseconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 15 sheets defined 45.9% alpha, 9.2% beta 47 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 269 through 278 removed outlier: 3.604A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 316 through 343 removed outlier: 3.914A pdb=" N CYS A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS A 331 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 419 through 438 removed outlier: 4.467A pdb=" N PHE A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.798A pdb=" N PHE A 491 " --> pdb=" O THR A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 removed outlier: 3.591A pdb=" N LYS A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.931A pdb=" N THR B 257 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.671A pdb=" N THR B 306 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 336 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 353 through 368 Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 424 through 437 removed outlier: 3.694A pdb=" N ARG B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 501 through 518 Processing helix chain 'B' and resid 531 through 546 removed outlier: 4.477A pdb=" N ALA B 539 " --> pdb=" O LEU B 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 277 Processing helix chain 'C' and resid 303 through 315 removed outlier: 3.574A pdb=" N ARG C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 333 removed outlier: 3.617A pdb=" N CYS C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 353 through 358 removed outlier: 3.880A pdb=" N MET C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 366 removed outlier: 3.689A pdb=" N MET C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 390 removed outlier: 3.717A pdb=" N GLY C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 394 removed outlier: 3.729A pdb=" N MET C 394 " --> pdb=" O PHE C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 417 through 441 removed outlier: 3.938A pdb=" N LEU C 422 " --> pdb=" O PRO C 418 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 467 through 472 removed outlier: 4.395A pdb=" N LEU C 471 " --> pdb=" O PRO C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.973A pdb=" N VAL C 477 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 518 removed outlier: 3.748A pdb=" N ALA C 510 " --> pdb=" O LYS C 506 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN C 518 " --> pdb=" O ARG C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 548 Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 269 through 279 removed outlier: 4.156A pdb=" N ARG D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 316 through 342 removed outlier: 3.908A pdb=" N CYS D 320 " --> pdb=" O ASP D 316 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG D 326 " --> pdb=" O ASN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 368 Processing helix chain 'D' and resid 375 through 392 removed outlier: 3.633A pdb=" N SER D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 441 removed outlier: 3.623A pdb=" N ARG D 432 " --> pdb=" O ALA D 428 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 433 " --> pdb=" O MET D 429 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 467 through 472 removed outlier: 3.681A pdb=" N LEU D 471 " --> pdb=" O PRO D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.679A pdb=" N ASN D 483 " --> pdb=" O MET D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 518 removed outlier: 3.577A pdb=" N MET D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 547 Processing helix chain 'E' and resid 13 through 26 removed outlier: 4.611A pdb=" N ARG E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 52 Processing helix chain 'F' and resid 13 through 26 removed outlier: 4.611A pdb=" N ARG F 19 " --> pdb=" O ARG F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 52 Processing sheet with id=AA1, first strand: chain 'A' and resid 222 through 226 removed outlier: 6.832A pdb=" N LEU A 222 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ALA A 261 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 224 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE A 263 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 226 " --> pdb=" O PHE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 253 removed outlier: 7.087A pdb=" N ILE A 242 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU A 251 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU A 240 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 233 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA4, first strand: chain 'A' and resid 519 through 521 Processing sheet with id=AA5, first strand: chain 'B' and resid 225 through 226 removed outlier: 6.132A pdb=" N VAL B 260 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 286 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU B 262 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP B 285 " --> pdb=" O MET B 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.759A pdb=" N ILE B 242 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AA8, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AA9, first strand: chain 'D' and resid 224 through 225 removed outlier: 7.982A pdb=" N LEU D 224 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL D 260 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL D 283 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 296 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS D 295 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL C 283 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 222 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 260 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU C 224 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU C 262 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 226 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 248 through 253 removed outlier: 4.881A pdb=" N ALA C 250 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 491 through 493 Processing sheet with id=AB3, first strand: chain 'C' and resid 519 through 521 Processing sheet with id=AB4, first strand: chain 'D' and resid 231 through 236 Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 32 removed outlier: 5.515A pdb=" N TRP E 30 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLN E 37 " --> pdb=" O TRP E 30 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER F 79 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 78 through 80 removed outlier: 3.879A pdb=" N SER E 79 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN F 37 " --> pdb=" O TRP F 30 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TRP F 30 " --> pdb=" O GLN F 37 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3916 1.33 - 1.45: 4233 1.45 - 1.57: 8019 1.57 - 1.69: 336 1.69 - 1.82: 124 Bond restraints: 16628 Sorted by residual: bond pdb=" N GLY C 345 " pdb=" CA GLY C 345 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.98e+01 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.44e+01 bond pdb=" N ILE A 328 " pdb=" CA ILE A 328 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.40e+01 bond pdb=" O3' DT H 27 " pdb=" P DT H 28 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.29e+01 bond pdb=" C3' DG H 42 " pdb=" C2' DG H 42 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 ... (remaining 16623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 22664 2.58 - 5.16: 500 5.16 - 7.75: 49 7.75 - 10.33: 10 10.33 - 12.91: 2 Bond angle restraints: 23225 Sorted by residual: angle pdb=" N ILE B 524 " pdb=" CA ILE B 524 " pdb=" C ILE B 524 " ideal model delta sigma weight residual 113.71 107.60 6.11 9.50e-01 1.11e+00 4.13e+01 angle pdb=" C ARG B 412 " pdb=" N ARG B 413 " pdb=" CA ARG B 413 " ideal model delta sigma weight residual 121.80 108.89 12.91 2.44e+00 1.68e-01 2.80e+01 angle pdb=" O4' DG H 70 " pdb=" C4' DG H 70 " pdb=" C3' DG H 70 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.78e+01 angle pdb=" N PHE B 388 " pdb=" CA PHE B 388 " pdb=" C PHE B 388 " ideal model delta sigma weight residual 113.17 106.74 6.43 1.26e+00 6.30e-01 2.60e+01 angle pdb=" N SER B 424 " pdb=" CA SER B 424 " pdb=" C SER B 424 " ideal model delta sigma weight residual 114.75 108.89 5.86 1.26e+00 6.30e-01 2.16e+01 ... (remaining 23220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 8490 34.99 - 69.97: 925 69.97 - 104.96: 41 104.96 - 139.94: 8 139.94 - 174.93: 5 Dihedral angle restraints: 9469 sinusoidal: 5001 harmonic: 4468 Sorted by residual: dihedral pdb=" CA ILE A 215 " pdb=" C ILE A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU A 478 " pdb=" C LEU A 478 " pdb=" N MET A 479 " pdb=" CA MET A 479 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLU B 243 " pdb=" C GLU B 243 " pdb=" N GLU B 244 " pdb=" CA GLU B 244 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 9466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2240 0.088 - 0.177: 273 0.177 - 0.265: 6 0.265 - 0.354: 2 0.354 - 0.442: 5 Chirality restraints: 2526 Sorted by residual: chirality pdb=" C3' DT H 6 " pdb=" C4' DT H 6 " pdb=" O3' DT H 6 " pdb=" C2' DT H 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.29 -0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" C3' DT G 10 " pdb=" C4' DT G 10 " pdb=" O3' DT G 10 " pdb=" C2' DT G 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.29 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C3' DG H 10 " pdb=" C4' DG H 10 " pdb=" O3' DG H 10 " pdb=" C2' DG H 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.31 -0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 2523 not shown) Planarity restraints: 2421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 466 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO A 467 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 370 " -0.062 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO D 371 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 371 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 371 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 550 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO C 551 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 551 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 551 " 0.039 5.00e-02 4.00e+02 ... (remaining 2418 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 337 2.59 - 3.16: 14547 3.16 - 3.74: 29004 3.74 - 4.32: 38425 4.32 - 4.90: 58256 Nonbonded interactions: 140569 Sorted by model distance: nonbonded pdb=" O ARG B 413 " pdb=" OP2 DT H 30 " model vdw 2.008 3.040 nonbonded pdb=" O GLN C 361 " pdb=" NE2 GLN C 361 " model vdw 2.117 3.120 nonbonded pdb=" O LEU A 323 " pdb=" CB TRP A 327 " model vdw 2.176 2.752 nonbonded pdb=" OD2 ASP A 490 " pdb=" NH2 ARG A 507 " model vdw 2.197 3.120 nonbonded pdb=" O PRO B 353 " pdb=" CD2 LEU B 357 " model vdw 2.202 3.460 ... (remaining 140564 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 221 through 379 or (resid 380 through 381 and (name N or n \ ame CA or name C or name O )) or resid 382 through 558)) selection = (chain 'B' and (resid 221 through 379 or (resid 380 through 381 and (name N or n \ ame CA or name C or name O )) or resid 382 through 558)) selection = (chain 'C' and (resid 221 through 379 or (resid 380 through 381 and (name N or n \ ame CA or name C or name O )) or resid 382 through 558)) selection = (chain 'D' and resid 221 through 558) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.030 Find NCS groups from input model: 0.290 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4839 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 : 0.006 0.054 16628 Z= 0.441 Angle : 0.942 12.909 23225 Z= 0.647 Chirality : 0.057 0.442 2526 Planarity : 0.007 0.113 2421 Dihedral : 24.159 174.930 6605 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 38.66 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.16 % Favored : 86.25 % Rotamer: Outliers : 2.08 % Allowed : 1.85 % Favored : 96.06 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.37 (0.20), residues: 1542 helix: -1.59 (0.19), residues: 677 sheet: -2.83 (0.46), residues: 111 loop : -2.78 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 514 TYR 0.037 0.003 TYR B 387 PHE 0.018 0.002 PHE B 556 TRP 0.033 0.003 TRP B 434 HIS 0.009 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.44 (16628) covalent geometry : angle 0.94161 / 0.65 (23225) hydrogen bonds : bond 0.18546 / 12.52 ( 631) hydrogen bonds : angle 8.11234 / 5.58 ( 1685) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 357 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 MET cc_start: 0.7780 (ttm) cc_final: 0.6765 (tpt) REVERT: A 508 PHE cc_start: 0.6403 (t80) cc_final: 0.6129 (t80) REVERT: B 293 MET cc_start: 0.6330 (mmt) cc_final: 0.6096 (mmm) REVERT: B 343 TRP cc_start: 0.5166 (OUTLIER) cc_final: 0.4940 (t-100) REVERT: B 429 MET cc_start: 0.7922 (mtm) cc_final: 0.7559 (mtp) REVERT: B 538 GLN cc_start: 0.8540 (tp40) cc_final: 0.8326 (tp40) REVERT: C 322 ASN cc_start: 0.6431 (m-40) cc_final: 0.5644 (m-40) REVERT: C 356 LEU cc_start: 0.5828 (tp) cc_final: 0.5627 (tp) REVERT: C 454 ARG cc_start: 0.5319 (tmt170) cc_final: 0.5060 (tpt-90) REVERT: C 472 ILE cc_start: 0.5861 (mp) cc_final: 0.5576 (mm) REVERT: D 236 ASP cc_start: 0.6354 (p0) cc_final: 0.6026 (p0) REVERT: D 358 MET cc_start: 0.6249 (tpt) cc_final: 0.5650 (tpt) REVERT: D 368 MET cc_start: 0.6404 (ptp) cc_final: 0.5783 (mmt) REVERT: D 407 PHE cc_start: 0.5802 (p90) cc_final: 0.5531 (p90) REVERT: D 410 ARG cc_start: 0.3449 (mmm160) cc_final: 0.3094 (tmt170) REVERT: D 479 MET cc_start: 0.5382 (mmm) cc_final: 0.4807 (mtp) REVERT: E 1 MET cc_start: 0.6882 (tpt) cc_final: 0.6670 (tpp) REVERT: F 74 VAL cc_start: 0.7423 (p) cc_final: 0.7109 (t) outliers start: 27 outliers final: 7 residues processed: 376 average time/residue: 0.1404 time to fit residues: 73.7810 Evaluate side-chains 212 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 343 TRP Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 11 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 ASN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 ASN E 32 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.177355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.161123 restraints weight = 70282.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.160696 restraints weight = 65933.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.161247 restraints weight = 48170.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.161277 restraints weight = 37208.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.161352 restraints weight = 35622.636| |-----------------------------------------------------------------------------| r_work (final): 0.4641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5348 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16628 Z= 0.222 Angle : 0.882 10.564 23225 Z= 0.481 Chirality : 0.054 0.292 2526 Planarity : 0.008 0.090 2421 Dihedral : 27.693 179.363 3611 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 26.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.18 % Favored : 89.69 % Rotamer: Outliers : 3.16 % Allowed : 14.58 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.19 (0.19), residues: 1542 helix: -1.52 (0.18), residues: 698 sheet: -2.14 (0.51), residues: 99 loop : -2.72 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 515 TYR 0.033 0.003 TYR B 387 PHE 0.032 0.003 PHE C 292 TRP 0.032 0.003 TRP D 285 HIS 0.028 0.002 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 (16628) covalent geometry : angle 0.88239 / 0.48 (23225) hydrogen bonds : bond 0.06339 / 4.31 ( 631) hydrogen bonds : angle 6.32808 / 4.33 ( 1685) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.7420 (mp10) cc_final: 0.7076 (mp10) REVERT: A 364 MET cc_start: 0.7725 (mtp) cc_final: 0.7403 (mtp) REVERT: A 389 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7352 (tm-30) REVERT: A 416 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7756 (ttpt) REVERT: A 464 MET cc_start: 0.8742 (ttm) cc_final: 0.8462 (tpp) REVERT: A 508 PHE cc_start: 0.6598 (t80) cc_final: 0.6300 (t80) REVERT: B 293 MET cc_start: 0.6299 (mmt) cc_final: 0.6034 (mmm) REVERT: B 343 TRP cc_start: 0.6144 (t-100) cc_final: 0.5565 (t-100) REVERT: B 403 MET cc_start: 0.3494 (mmm) cc_final: 0.3161 (mmm) REVERT: B 538 GLN cc_start: 0.8884 (tp40) cc_final: 0.8400 (tp40) REVERT: C 454 ARG cc_start: 0.5321 (tmt170) cc_final: 0.5052 (ptt90) REVERT: C 464 MET cc_start: 0.6023 (mpp) cc_final: 0.5757 (mmm) REVERT: D 232 TYR cc_start: 0.4233 (t80) cc_final: 0.3820 (t80) REVERT: D 358 MET cc_start: 0.6048 (tpt) cc_final: 0.5280 (tpt) REVERT: D 368 MET cc_start: 0.6109 (ptp) cc_final: 0.5528 (mmt) REVERT: D 479 MET cc_start: 0.5894 (mmm) cc_final: 0.5265 (mtp) outliers start: 41 outliers final: 19 residues processed: 255 average time/residue: 0.1228 time to fit residues: 45.9909 Evaluate side-chains 195 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 527 TYR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain F residue 43 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 163 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 3 optimal weight: 0.0980 chunk 157 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN A 390 HIS A 522 HIS A 555 ASN ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 ASN C 265 ASN C 274 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.173525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.155796 restraints weight = 67413.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.154153 restraints weight = 55719.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.154376 restraints weight = 47115.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.154562 restraints weight = 38393.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.154757 restraints weight = 35772.393| |-----------------------------------------------------------------------------| r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16628 Z= 0.206 Angle : 0.811 12.081 23225 Z= 0.443 Chirality : 0.051 0.331 2526 Planarity : 0.007 0.065 2421 Dihedral : 27.509 173.213 3599 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.79 % Favored : 90.08 % Rotamer: Outliers : 3.32 % Allowed : 18.13 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.96 (0.19), residues: 1542 helix: -1.24 (0.19), residues: 693 sheet: -2.07 (0.52), residues: 94 loop : -2.68 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 393 TYR 0.026 0.002 TYR A 527 PHE 0.025 0.003 PHE C 263 TRP 0.048 0.003 TRP A 327 HIS 0.021 0.002 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 (16628) covalent geometry : angle 0.81148 / 0.44 (23225) hydrogen bonds : bond 0.05345 / 3.63 ( 631) hydrogen bonds : angle 5.85557 / 4.04 ( 1685) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.7217 (mp10) cc_final: 0.6878 (mp10) REVERT: A 299 THR cc_start: 0.5196 (OUTLIER) cc_final: 0.4977 (p) REVERT: A 462 LEU cc_start: 0.8807 (tp) cc_final: 0.8544 (tp) REVERT: A 508 PHE cc_start: 0.6803 (t80) cc_final: 0.6525 (t80) REVERT: B 328 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.6776 (tt) REVERT: B 341 ARG cc_start: 0.2736 (OUTLIER) cc_final: 0.2010 (ptp90) REVERT: B 343 TRP cc_start: 0.6087 (t-100) cc_final: 0.5460 (t-100) REVERT: B 538 GLN cc_start: 0.8835 (tp40) cc_final: 0.8381 (tp40) REVERT: C 389 GLN cc_start: 0.7542 (mt0) cc_final: 0.7213 (mp10) REVERT: C 391 PHE cc_start: 0.7799 (t80) cc_final: 0.7128 (t80) REVERT: C 454 ARG cc_start: 0.5672 (tmt170) cc_final: 0.5414 (ptt90) REVERT: D 358 MET cc_start: 0.6022 (tpt) cc_final: 0.5290 (tpt) REVERT: D 479 MET cc_start: 0.6004 (mmm) cc_final: 0.5491 (mtp) REVERT: E 1 MET cc_start: 0.7232 (tpp) cc_final: 0.6971 (tpp) outliers start: 43 outliers final: 22 residues processed: 226 average time/residue: 0.1115 time to fit residues: 37.3251 Evaluate side-chains 191 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 527 TYR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 42 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 18 optimal weight: 0.0980 chunk 145 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 31 optimal weight: 0.0870 overall best weight: 2.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS C 310 GLN C 334 ASN ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.170080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.151696 restraints weight = 66236.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.150811 restraints weight = 48057.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.151187 restraints weight = 41808.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.151240 restraints weight = 32368.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.151517 restraints weight = 31118.608| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 16628 Z= 0.215 Angle : 0.794 8.608 23225 Z= 0.435 Chirality : 0.050 0.310 2526 Planarity : 0.007 0.063 2421 Dihedral : 27.387 171.060 3595 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.12 % Favored : 89.75 % Rotamer: Outliers : 3.86 % Allowed : 21.53 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.84 (0.20), residues: 1542 helix: -1.01 (0.19), residues: 704 sheet: -2.45 (0.45), residues: 110 loop : -2.71 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 42 TYR 0.023 0.002 TYR A 527 PHE 0.016 0.002 PHE D 455 TRP 0.029 0.003 TRP A 327 HIS 0.016 0.002 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 (16628) covalent geometry : angle 0.79449 / 0.44 (23225) hydrogen bonds : bond 0.05339 / 3.62 ( 631) hydrogen bonds : angle 5.55467 / 3.84 ( 1685) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.7235 (mp10) cc_final: 0.6730 (mp10) REVERT: A 339 LEU cc_start: 0.8035 (mt) cc_final: 0.7708 (mt) REVERT: A 389 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: A 390 HIS cc_start: 0.6606 (m170) cc_final: 0.6211 (m170) REVERT: A 416 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7709 (ttpt) REVERT: A 462 LEU cc_start: 0.8840 (tp) cc_final: 0.8479 (tp) REVERT: B 341 ARG cc_start: 0.2818 (OUTLIER) cc_final: 0.2321 (ptp90) REVERT: B 519 GLU cc_start: 0.7623 (tp30) cc_final: 0.7419 (tp30) REVERT: B 538 GLN cc_start: 0.8973 (tp40) cc_final: 0.8476 (tp40) REVERT: C 277 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7648 (mm) REVERT: C 322 ASN cc_start: 0.7627 (m-40) cc_final: 0.7353 (m110) REVERT: C 389 GLN cc_start: 0.7522 (mt0) cc_final: 0.7238 (mp10) REVERT: C 474 ASP cc_start: 0.8051 (m-30) cc_final: 0.7609 (m-30) REVERT: D 368 MET cc_start: 0.6809 (mtp) cc_final: 0.6553 (mtm) REVERT: D 465 MET cc_start: 0.1806 (ppp) cc_final: 0.1588 (ptm) REVERT: D 479 MET cc_start: 0.6261 (mmm) cc_final: 0.5790 (mtp) outliers start: 50 outliers final: 27 residues processed: 213 average time/residue: 0.1212 time to fit residues: 37.8933 Evaluate side-chains 191 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 508 PHE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain F residue 43 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 555 ASN B 366 HIS B 451 HIS ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.166115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.147303 restraints weight = 65011.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.146916 restraints weight = 47990.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.147197 restraints weight = 38651.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.147217 restraints weight = 31464.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.147328 restraints weight = 29794.636| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 16628 Z= 0.245 Angle : 0.835 10.459 23225 Z= 0.454 Chirality : 0.051 0.298 2526 Planarity : 0.007 0.061 2421 Dihedral : 27.307 171.596 3595 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.05 % Favored : 89.88 % Rotamer: Outliers : 4.78 % Allowed : 22.84 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.94 (0.19), residues: 1542 helix: -1.01 (0.19), residues: 697 sheet: -2.74 (0.43), residues: 104 loop : -2.79 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 393 TYR 0.023 0.002 TYR A 527 PHE 0.024 0.002 PHE D 491 TRP 0.086 0.004 TRP A 327 HIS 0.023 0.002 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.25 (16628) covalent geometry : angle 0.83482 / 0.45 (23225) hydrogen bonds : bond 0.05636 / 3.81 ( 631) hydrogen bonds : angle 5.61081 / 3.91 ( 1685) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 171 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.2525 (OUTLIER) cc_final: 0.2323 (tpt90) REVERT: A 259 GLN cc_start: 0.6893 (mp10) cc_final: 0.6291 (mp10) REVERT: A 299 THR cc_start: 0.5437 (OUTLIER) cc_final: 0.5174 (p) REVERT: A 389 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.6997 (tm-30) REVERT: A 390 HIS cc_start: 0.6527 (OUTLIER) cc_final: 0.6111 (m170) REVERT: A 462 LEU cc_start: 0.8760 (tp) cc_final: 0.8520 (tp) REVERT: A 508 PHE cc_start: 0.6481 (t80) cc_final: 0.6276 (t80) REVERT: B 368 MET cc_start: 0.8331 (tpp) cc_final: 0.7831 (mpp) REVERT: B 519 GLU cc_start: 0.7684 (tp30) cc_final: 0.7421 (tp30) REVERT: B 538 GLN cc_start: 0.8988 (tp40) cc_final: 0.8474 (tp40) REVERT: C 277 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7766 (mm) REVERT: C 389 GLN cc_start: 0.7471 (mt0) cc_final: 0.7256 (mp10) REVERT: C 479 MET cc_start: 0.5086 (ppp) cc_final: 0.4106 (tmm) REVERT: C 491 PHE cc_start: 0.6680 (m-80) cc_final: 0.6420 (m-80) REVERT: C 512 PHE cc_start: 0.7179 (t80) cc_final: 0.6966 (t80) REVERT: D 227 GLN cc_start: 0.5016 (tp40) cc_final: 0.4189 (mp10) REVERT: D 479 MET cc_start: 0.6444 (mmm) cc_final: 0.5929 (mtp) REVERT: E 1 MET cc_start: 0.7080 (tpp) cc_final: 0.6771 (tpt) REVERT: F 1 MET cc_start: 0.6374 (mpp) cc_final: 0.6014 (mpp) outliers start: 62 outliers final: 33 residues processed: 209 average time/residue: 0.1103 time to fit residues: 34.4929 Evaluate side-chains 182 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 390 HIS Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 508 PHE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 43 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 117 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 70 optimal weight: 0.0570 chunk 40 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS B 451 HIS B 555 ASN C 322 ASN ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** 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 = 0.4778 r_free = 0.4778 target = 0.167252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.147871 restraints weight = 64272.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.147929 restraints weight = 45854.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.148194 restraints weight = 33895.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.148271 restraints weight = 28392.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.148301 restraints weight = 27134.512| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16628 Z= 0.180 Angle : 0.766 11.803 23225 Z= 0.418 Chirality : 0.048 0.286 2526 Planarity : 0.006 0.059 2421 Dihedral : 27.245 171.205 3595 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.86 % Favored : 90.08 % Rotamer: Outliers : 4.01 % Allowed : 24.69 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.74 (0.20), residues: 1542 helix: -0.78 (0.19), residues: 696 sheet: -2.64 (0.43), residues: 104 loop : -2.77 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 302 TYR 0.018 0.002 TYR A 527 PHE 0.020 0.002 PHE D 455 TRP 0.061 0.003 TRP A 327 HIS 0.010 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (16628) covalent geometry : angle 0.76625 / 0.42 (23225) hydrogen bonds : bond 0.04843 / 3.29 ( 631) hydrogen bonds : angle 5.44850 / 3.78 ( 1685) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.6683 (mp10) cc_final: 0.6063 (mp10) REVERT: A 299 THR cc_start: 0.5151 (OUTLIER) cc_final: 0.4857 (p) REVERT: A 389 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: A 390 HIS cc_start: 0.7013 (OUTLIER) cc_final: 0.6582 (m170) REVERT: A 462 LEU cc_start: 0.8886 (tp) cc_final: 0.8678 (tp) REVERT: A 465 MET cc_start: 0.8505 (ttm) cc_final: 0.8070 (tpp) REVERT: B 343 TRP cc_start: 0.4543 (t-100) cc_final: 0.3898 (t-100) REVERT: B 368 MET cc_start: 0.8277 (tpp) cc_final: 0.7793 (mpp) REVERT: B 519 GLU cc_start: 0.7431 (tp30) cc_final: 0.7038 (mm-30) REVERT: B 538 GLN cc_start: 0.8999 (tp40) cc_final: 0.8474 (tp40) REVERT: C 277 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7777 (mm) REVERT: C 285 TRP cc_start: 0.7916 (m-90) cc_final: 0.7265 (m-90) REVERT: C 318 GLU cc_start: 0.7357 (tp30) cc_final: 0.7118 (tp30) REVERT: C 389 GLN cc_start: 0.7665 (mt0) cc_final: 0.7422 (mp10) REVERT: C 391 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: C 403 MET cc_start: 0.1154 (mmm) cc_final: 0.0476 (mmt) REVERT: C 479 MET cc_start: 0.5132 (ppp) cc_final: 0.4158 (tmm) REVERT: C 491 PHE cc_start: 0.6419 (m-80) cc_final: 0.6138 (m-80) REVERT: C 524 ILE cc_start: 0.8592 (mp) cc_final: 0.8314 (tt) REVERT: D 227 GLN cc_start: 0.4705 (tp40) cc_final: 0.3856 (mp10) REVERT: D 286 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6745 (mm) REVERT: D 296 THR cc_start: 0.6585 (OUTLIER) cc_final: 0.5663 (m) REVERT: D 368 MET cc_start: 0.6318 (OUTLIER) cc_final: 0.4033 (tpt) REVERT: D 479 MET cc_start: 0.6369 (mmm) cc_final: 0.6156 (mtp) outliers start: 52 outliers final: 32 residues processed: 195 average time/residue: 0.0978 time to fit residues: 30.1185 Evaluate side-chains 191 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 390 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 391 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 508 PHE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 46 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 164 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 538 GLN A 555 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** 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 = 0.4718 r_free = 0.4718 target = 0.163226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.143790 restraints weight = 63880.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.143243 restraints weight = 52897.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.143811 restraints weight = 39817.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.143848 restraints weight = 31846.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.143943 restraints weight = 30896.695| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 16628 Z= 0.235 Angle : 0.825 10.784 23225 Z= 0.448 Chirality : 0.050 0.295 2526 Planarity : 0.007 0.059 2421 Dihedral : 27.104 170.312 3595 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.83 % Favored : 89.11 % Rotamer: Outliers : 5.17 % Allowed : 24.38 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.78 (0.19), residues: 1542 helix: -0.77 (0.19), residues: 688 sheet: -3.02 (0.43), residues: 100 loop : -2.77 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 336 TYR 0.022 0.003 TYR D 450 PHE 0.039 0.003 PHE A 508 TRP 0.058 0.003 TRP A 327 HIS 0.010 0.002 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.24 (16628) covalent geometry : angle 0.82512 / 0.45 (23225) hydrogen bonds : bond 0.05877 / 3.94 ( 631) hydrogen bonds : angle 5.54517 / 3.83 ( 1685) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 161 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.6623 (mp10) cc_final: 0.6045 (mp10) REVERT: A 299 THR cc_start: 0.5408 (OUTLIER) cc_final: 0.5099 (p) REVERT: A 389 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: A 390 HIS cc_start: 0.6852 (m170) cc_final: 0.6395 (m170) REVERT: A 464 MET cc_start: 0.8953 (tpp) cc_final: 0.8677 (tpp) REVERT: A 508 PHE cc_start: 0.7220 (t80) cc_final: 0.6992 (t80) REVERT: B 343 TRP cc_start: 0.5361 (t-100) cc_final: 0.4663 (t-100) REVERT: B 368 MET cc_start: 0.8436 (tpp) cc_final: 0.8185 (mtt) REVERT: B 538 GLN cc_start: 0.9038 (tp40) cc_final: 0.8579 (tp40) REVERT: C 277 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7855 (mm) REVERT: C 285 TRP cc_start: 0.8070 (m-90) cc_final: 0.7406 (m-90) REVERT: C 318 GLU cc_start: 0.7388 (tp30) cc_final: 0.7097 (tp30) REVERT: C 362 ASP cc_start: 0.6014 (OUTLIER) cc_final: 0.5660 (m-30) REVERT: C 391 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: C 403 MET cc_start: 0.1224 (mmm) cc_final: 0.0267 (mmm) REVERT: C 479 MET cc_start: 0.5397 (ppp) cc_final: 0.4484 (tmm) REVERT: C 491 PHE cc_start: 0.6768 (m-80) cc_final: 0.6500 (m-80) REVERT: D 226 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7257 (p) REVERT: D 227 GLN cc_start: 0.5433 (tp40) cc_final: 0.4627 (mp10) REVERT: D 286 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6435 (mm) REVERT: D 296 THR cc_start: 0.6882 (OUTLIER) cc_final: 0.6175 (m) REVERT: D 368 MET cc_start: 0.6434 (pmm) cc_final: 0.4144 (tpt) REVERT: D 479 MET cc_start: 0.6734 (mmm) cc_final: 0.5938 (mtp) outliers start: 67 outliers final: 38 residues processed: 203 average time/residue: 0.1210 time to fit residues: 36.6009 Evaluate side-chains 186 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 391 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 508 PHE Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 107 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 130 optimal weight: 30.0000 chunk 126 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN B 361 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN C 390 HIS ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.163715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.144281 restraints weight = 64437.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.144615 restraints weight = 51033.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.144984 restraints weight = 37708.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.144988 restraints weight = 30996.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.145189 restraints weight = 29377.253| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.7370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16628 Z= 0.189 Angle : 0.784 10.752 23225 Z= 0.427 Chirality : 0.049 0.265 2526 Planarity : 0.006 0.058 2421 Dihedral : 27.084 169.900 3595 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 23.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.99 % Favored : 89.95 % Rotamer: Outliers : 4.09 % Allowed : 26.16 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.68 (0.20), residues: 1542 helix: -0.66 (0.19), residues: 683 sheet: -3.03 (0.41), residues: 103 loop : -2.70 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 469 TYR 0.018 0.002 TYR A 527 PHE 0.021 0.002 PHE A 508 TRP 0.038 0.003 TRP A 327 HIS 0.009 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (16628) covalent geometry : angle 0.78435 / 0.43 (23225) hydrogen bonds : bond 0.04799 / 3.25 ( 631) hydrogen bonds : angle 5.53500 / 3.85 ( 1685) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8416 (p) REVERT: A 259 GLN cc_start: 0.6584 (mp10) cc_final: 0.6051 (mp10) REVERT: A 299 THR cc_start: 0.5316 (OUTLIER) cc_final: 0.4986 (p) REVERT: A 389 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: A 390 HIS cc_start: 0.6812 (m170) cc_final: 0.6407 (m170) REVERT: A 464 MET cc_start: 0.8980 (tpp) cc_final: 0.8688 (tpp) REVERT: A 476 THR cc_start: 0.8628 (t) cc_final: 0.8387 (m) REVERT: B 368 MET cc_start: 0.8485 (tpp) cc_final: 0.8251 (mtt) REVERT: B 538 GLN cc_start: 0.9102 (tp40) cc_final: 0.8609 (tp40) REVERT: C 277 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7955 (mm) REVERT: C 285 TRP cc_start: 0.8010 (m-90) cc_final: 0.7408 (m-90) REVERT: C 318 GLU cc_start: 0.7344 (tp30) cc_final: 0.7029 (tp30) REVERT: C 322 ASN cc_start: 0.8258 (m-40) cc_final: 0.8055 (m110) REVERT: C 362 ASP cc_start: 0.6006 (OUTLIER) cc_final: 0.5777 (m-30) REVERT: C 391 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: C 403 MET cc_start: 0.1376 (mmm) cc_final: 0.1152 (mmm) REVERT: C 479 MET cc_start: 0.5370 (ppp) cc_final: 0.4457 (tmm) REVERT: C 491 PHE cc_start: 0.6954 (m-80) cc_final: 0.6724 (m-80) REVERT: C 524 ILE cc_start: 0.8369 (mp) cc_final: 0.8084 (tt) REVERT: D 226 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7145 (p) REVERT: D 227 GLN cc_start: 0.5465 (tp40) cc_final: 0.4753 (mp10) REVERT: D 296 THR cc_start: 0.6882 (OUTLIER) cc_final: 0.6124 (m) REVERT: D 368 MET cc_start: 0.6123 (pmm) cc_final: 0.3934 (tpt) REVERT: D 479 MET cc_start: 0.7158 (mmm) cc_final: 0.6042 (mtp) REVERT: E 79 SER cc_start: 0.7823 (OUTLIER) cc_final: 0.7406 (m) outliers start: 53 outliers final: 31 residues processed: 198 average time/residue: 0.1142 time to fit residues: 34.0458 Evaluate side-chains 188 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 391 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 508 PHE Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 24 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 164 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 140 optimal weight: 0.0060 chunk 39 optimal weight: 5.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.163448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.143468 restraints weight = 63362.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.143146 restraints weight = 44257.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.143474 restraints weight = 34555.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.143504 restraints weight = 29694.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.143576 restraints weight = 27898.100| |-----------------------------------------------------------------------------| r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.7672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 16628 Z= 0.183 Angle : 0.784 11.424 23225 Z= 0.424 Chirality : 0.048 0.266 2526 Planarity : 0.006 0.056 2421 Dihedral : 27.028 169.380 3595 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.99 % Favored : 89.95 % Rotamer: Outliers : 4.09 % Allowed : 26.54 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.59 (0.20), residues: 1542 helix: -0.57 (0.20), residues: 679 sheet: -3.01 (0.41), residues: 103 loop : -2.67 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 515 TYR 0.017 0.002 TYR A 527 PHE 0.032 0.002 PHE A 508 TRP 0.036 0.003 TRP A 327 HIS 0.010 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (16628) covalent geometry : angle 0.78431 / 0.42 (23225) hydrogen bonds : bond 0.04727 / 3.18 ( 631) hydrogen bonds : angle 5.47803 / 3.80 ( 1685) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8472 (p) REVERT: A 259 GLN cc_start: 0.6105 (mp10) cc_final: 0.5640 (mp10) REVERT: A 299 THR cc_start: 0.5283 (OUTLIER) cc_final: 0.4958 (p) REVERT: A 358 MET cc_start: 0.7107 (mmp) cc_final: 0.6762 (tpp) REVERT: A 389 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: A 390 HIS cc_start: 0.7043 (m170) cc_final: 0.6782 (m170) REVERT: A 464 MET cc_start: 0.8946 (tpp) cc_final: 0.8642 (tpp) REVERT: A 476 THR cc_start: 0.8725 (t) cc_final: 0.8523 (m) REVERT: B 429 MET cc_start: 0.7767 (mtm) cc_final: 0.7266 (ptp) REVERT: B 538 GLN cc_start: 0.9104 (tp40) cc_final: 0.8617 (tp40) REVERT: C 277 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7968 (mm) REVERT: C 285 TRP cc_start: 0.8026 (m-90) cc_final: 0.7441 (m-90) REVERT: C 293 MET cc_start: 0.7523 (ptp) cc_final: 0.6768 (ppp) REVERT: C 318 GLU cc_start: 0.7389 (tp30) cc_final: 0.7067 (tp30) REVERT: C 362 ASP cc_start: 0.6033 (OUTLIER) cc_final: 0.5777 (m-30) REVERT: C 386 ARG cc_start: 0.8429 (ptt-90) cc_final: 0.7902 (ptt90) REVERT: C 391 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7753 (m-80) REVERT: C 479 MET cc_start: 0.5184 (ppp) cc_final: 0.4258 (tmm) REVERT: C 491 PHE cc_start: 0.7003 (m-80) cc_final: 0.6764 (m-80) REVERT: D 226 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7241 (p) REVERT: D 227 GLN cc_start: 0.5452 (tp40) cc_final: 0.4774 (mp10) REVERT: D 296 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6432 (m) REVERT: D 368 MET cc_start: 0.6070 (pmm) cc_final: 0.3919 (tpt) REVERT: D 479 MET cc_start: 0.7085 (mmm) cc_final: 0.6199 (mtp) REVERT: E 79 SER cc_start: 0.7628 (OUTLIER) cc_final: 0.7257 (m) REVERT: F 48 MET cc_start: 0.8045 (mmm) cc_final: 0.7649 (tpp) outliers start: 53 outliers final: 32 residues processed: 186 average time/residue: 0.1236 time to fit residues: 34.6462 Evaluate side-chains 187 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 391 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 508 PHE Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 49 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.161948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.142282 restraints weight = 63720.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.142633 restraints weight = 50570.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.142962 restraints weight = 33993.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.143151 restraints weight = 28994.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.143143 restraints weight = 28787.927| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.8076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16628 Z= 0.190 Angle : 0.790 12.080 23225 Z= 0.428 Chirality : 0.048 0.257 2526 Planarity : 0.007 0.057 2421 Dihedral : 26.967 168.238 3595 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.60 % Favored : 90.34 % Rotamer: Outliers : 3.32 % Allowed : 27.39 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.52 (0.20), residues: 1542 helix: -0.48 (0.20), residues: 679 sheet: -3.11 (0.39), residues: 107 loop : -2.63 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG C 412 TYR 0.016 0.002 TYR A 527 PHE 0.036 0.002 PHE A 508 TRP 0.044 0.003 TRP E 17 HIS 0.010 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (16628) covalent geometry : angle 0.79021 / 0.43 (23225) hydrogen bonds : bond 0.04802 / 3.25 ( 631) hydrogen bonds : angle 5.44833 / 3.78 ( 1685) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.6016 (mp10) cc_final: 0.5522 (mp10) REVERT: A 299 THR cc_start: 0.5330 (OUTLIER) cc_final: 0.5033 (p) REVERT: A 358 MET cc_start: 0.7167 (mmp) cc_final: 0.6864 (tpp) REVERT: A 389 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: A 390 HIS cc_start: 0.7005 (OUTLIER) cc_final: 0.6728 (m170) REVERT: A 464 MET cc_start: 0.8951 (tpp) cc_final: 0.8656 (tpp) REVERT: A 476 THR cc_start: 0.8622 (t) cc_final: 0.8374 (m) REVERT: B 538 GLN cc_start: 0.9039 (tp40) cc_final: 0.8537 (tp40) REVERT: C 277 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7995 (mm) REVERT: C 285 TRP cc_start: 0.7986 (m-90) cc_final: 0.7486 (m-90) REVERT: C 293 MET cc_start: 0.7327 (ptp) cc_final: 0.6792 (ppp) REVERT: C 391 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: C 403 MET cc_start: 0.2071 (mmt) cc_final: 0.1771 (mmt) REVERT: C 479 MET cc_start: 0.5087 (ppp) cc_final: 0.4166 (tmm) REVERT: D 226 VAL cc_start: 0.7477 (OUTLIER) cc_final: 0.7138 (p) REVERT: D 227 GLN cc_start: 0.5398 (tp40) cc_final: 0.4854 (mp10) REVERT: D 296 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.6512 (m) REVERT: D 368 MET cc_start: 0.6192 (pmm) cc_final: 0.3832 (tpt) REVERT: D 479 MET cc_start: 0.7563 (mmm) cc_final: 0.6374 (mtp) REVERT: E 79 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7265 (m) REVERT: F 48 MET cc_start: 0.8125 (mmm) cc_final: 0.7779 (tpp) outliers start: 43 outliers final: 32 residues processed: 175 average time/residue: 0.1145 time to fit residues: 30.1264 Evaluate side-chains 178 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 390 HIS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 434 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 391 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 508 PHE Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 58 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 135 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 157 optimal weight: 30.0000 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 57 ASN ** 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 = 0.4725 r_free = 0.4725 target = 0.163240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.143351 restraints weight = 63248.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.143398 restraints weight = 47973.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.143544 restraints weight = 33444.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.143836 restraints weight = 29472.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.143827 restraints weight = 27691.368| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.8240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16628 Z= 0.160 Angle : 0.765 12.360 23225 Z= 0.411 Chirality : 0.047 0.245 2526 Planarity : 0.006 0.062 2421 Dihedral : 26.943 167.549 3595 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 3.09 % Allowed : 28.01 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.43 (0.20), residues: 1542 helix: -0.42 (0.20), residues: 680 sheet: -3.21 (0.38), residues: 107 loop : -2.54 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 344 TYR 0.017 0.001 TYR E 5 PHE 0.027 0.002 PHE A 508 TRP 0.032 0.003 TRP E 17 HIS 0.010 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (16628) covalent geometry : angle 0.76533 / 0.41 (23225) hydrogen bonds : bond 0.04340 / 2.94 ( 631) hydrogen bonds : angle 5.36503 / 3.74 ( 1685) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2287.58 seconds wall clock time: 40 minutes 18.70 seconds (2418.70 seconds total)