Starting phenix.real_space_refine on Sat Sep 12 12:21:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mi9_23843/09_2026/7mi9_23843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mi9_23843/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mi9_23843/09_2026/7mi9_23843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mi9_23843/09_2026/7mi9_23843.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mi9_23843/09_2026/7mi9_23843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mi9_23843/09_2026/7mi9_23843.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 3.05, per 1000 atoms: 0.19 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: 1.23 Conformation dependent library (CDL) restraints added in 629.2 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: 1.85 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: 2.82 Time building geometry restraints manager: 1.70 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=" O3' DT H 27 " pdb=" P DT H 28 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.20e-02 6.94e+03 2.01e+01 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=" 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: 22663 2.58 - 5.16: 501 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: 1.190 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.320 Find NCS groups from input model: 0.270 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.320 ------------------------------------------------------------------------------- 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= 0.442 Angle : 0.944 12.909 23225 Z= 0.651 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 0.94403 / 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: 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: 0.6095 (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: 0.7560 (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: 0.5061 (tpt-90) REVERT: C 472 ILE cc_start: 0.5861 (mp) cc_final: 0.5577 (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: 0.5651 (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: 0.5518 (p90) REVERT: D 410 ARG cc_start: 0.3449 (mmm160) cc_final: 0.3095 (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: 0.1520 time to fit residues: 79.4278 Evaluate side-chains 211 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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: 9.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 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 = 0.4898 r_free = 0.4898 target = 0.176492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.160059 restraints weight = 69722.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.159566 restraints weight = 70143.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.160030 restraints weight = 52392.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.160132 restraints weight = 39903.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.160212 restraints weight = 37909.608| |-----------------------------------------------------------------------------| r_work (final): 0.4625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 16628 Z= 0.232 Angle : 0.906 11.456 23225 Z= 0.492 Chirality : 0.055 0.329 2526 Planarity : 0.008 0.083 2421 Dihedral : 27.672 179.301 3611 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 26.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.99 % Favored : 89.88 % Rotamer: Outliers : 3.24 % Allowed : 14.81 % Favored : 81.94 % 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: -1.51 (0.18), residues: 698 sheet: -2.13 (0.51), residues: 99 loop : -2.73 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 515 TYR 0.030 0.003 TYR B 387 PHE 0.034 0.003 PHE C 292 TRP 0.025 0.003 TRP B 343 HIS 0.022 0.002 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 (16628) covalent geometry : angle 0.90606 / 0.49 (23225) hydrogen bonds : bond 0.06418 / 4.37 ( 631) hydrogen bonds : angle 6.30022 / 4.32 ( 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 266 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.511 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: A 259 GLN cc_start: 0.7481 (mp10) cc_final: 0.7190 (mp10) REVERT: A 364 MET cc_start: 0.7719 (mtp) cc_final: 0.7407 (mtp) REVERT: A 389 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 416 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7679 (ttpt) REVERT: A 417 ASP cc_start: 0.5746 (m-30) cc_final: 0.5308 (m-30) REVERT: A 464 MET cc_start: 0.8743 (ttm) cc_final: 0.8371 (tpp) REVERT: A 508 PHE cc_start: 0.6715 (t80) cc_final: 0.6369 (t80) REVERT: B 293 MET cc_start: 0.6331 (mmt) cc_final: 0.6035 (mmm) REVERT: B 341 ARG cc_start: 0.2596 (OUTLIER) cc_final: 0.1289 (ptp90) REVERT: B 343 TRP cc_start: 0.6189 (t-100) cc_final: 0.5687 (t-100) REVERT: B 403 MET cc_start: 0.3320 (mmm) cc_final: 0.2965 (mmm) REVERT: B 538 GLN cc_start: 0.8840 (tp40) cc_final: 0.8334 (tp40) REVERT: C 391 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6781 (t80) REVERT: C 429 MET cc_start: 0.7737 (tmm) cc_final: 0.7449 (tmm) REVERT: C 454 ARG cc_start: 0.5202 (tmt170) cc_final: 0.4996 (ptt90) REVERT: D 232 TYR cc_start: 0.4263 (t80) cc_final: 0.3836 (t80) REVERT: D 358 MET cc_start: 0.6056 (tpt) cc_final: 0.5267 (tpt) REVERT: D 368 MET cc_start: 0.6098 (ptp) cc_final: 0.5522 (mmt) REVERT: D 479 MET cc_start: 0.6040 (mmm) cc_final: 0.5589 (mtp) outliers start: 42 outliers final: 19 residues processed: 252 average time/residue: 0.1323 time to fit residues: 48.6064 Evaluate side-chains 192 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 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 391 PHE 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 286 LEU Chi-restraints excluded: chain D residue 541 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 163 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 3 optimal weight: 0.2980 chunk 157 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN C 274 HIS C 322 ASN C 334 ASN ** C 390 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.170368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.151929 restraints weight = 67920.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.150558 restraints weight = 68202.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.150916 restraints weight = 54608.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.151053 restraints weight = 44708.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.151286 restraints weight = 41601.950| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5713 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 16628 Z= 0.259 Angle : 0.877 13.181 23225 Z= 0.474 Chirality : 0.052 0.362 2526 Planarity : 0.008 0.069 2421 Dihedral : 27.506 177.420 3599 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 26.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.64 % Favored : 89.23 % Rotamer: Outliers : 3.40 % Allowed : 19.91 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.10 (0.19), residues: 1542 helix: -1.28 (0.19), residues: 691 sheet: -2.44 (0.45), residues: 115 loop : -2.78 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 365 TYR 0.028 0.003 TYR A 527 PHE 0.030 0.003 PHE C 263 TRP 0.040 0.003 TRP A 327 HIS 0.024 0.003 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.26 (16628) covalent geometry : angle 0.87676 / 0.47 (23225) hydrogen bonds : bond 0.06284 / 4.25 ( 631) hydrogen bonds : angle 5.98111 / 4.13 ( 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 233 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.402 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: 0.7381 (mp10) cc_final: 0.6934 (mp10) REVERT: A 416 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7698 (ttpt) REVERT: A 462 LEU cc_start: 0.8909 (tp) cc_final: 0.8522 (tp) REVERT: A 464 MET cc_start: 0.9059 (ttm) cc_final: 0.8254 (tpp) REVERT: A 506 LYS cc_start: 0.8575 (ttmt) cc_final: 0.7932 (tptm) REVERT: A 508 PHE cc_start: 0.6866 (t80) cc_final: 0.6636 (t80) REVERT: A 536 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: B 341 ARG cc_start: 0.3050 (OUTLIER) cc_final: 0.2255 (ptp90) REVERT: B 343 TRP cc_start: 0.6300 (t-100) cc_final: 0.5898 (t-100) REVERT: B 538 GLN cc_start: 0.8896 (tp40) cc_final: 0.8464 (tp40) REVERT: D 332 ILE cc_start: 0.0858 (mm) cc_final: 0.0579 (mm) REVERT: D 358 MET cc_start: 0.5957 (tpt) cc_final: 0.5440 (tpt) REVERT: D 479 MET cc_start: 0.6210 (mmm) cc_final: 0.5580 (mtp) outliers start: 44 outliers final: 26 residues processed: 216 average time/residue: 0.1285 time to fit residues: 40.9321 Evaluate side-chains 185 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 327 TRP 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 536 GLU 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 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 395 LEU 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 D residue 508 PHE Chi-restraints excluded: chain D residue 541 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: 1.9990 chunk 88 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 18 optimal weight: 0.0970 chunk 145 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 162 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 555 ASN ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 555 ASN C 301 HIS C 310 GLN ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.171943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.153703 restraints weight = 66868.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.153616 restraints weight = 50449.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.154359 restraints weight = 39692.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.154185 restraints weight = 34145.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.154250 restraints weight = 31362.694| |-----------------------------------------------------------------------------| r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5632 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16628 Z= 0.174 Angle : 0.774 8.604 23225 Z= 0.421 Chirality : 0.049 0.348 2526 Planarity : 0.007 0.062 2421 Dihedral : 27.439 172.350 3595 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.86 % Favored : 90.01 % Rotamer: Outliers : 3.16 % Allowed : 21.91 % Favored : 74.92 % 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: -1.00 (0.19), residues: 697 sheet: -2.38 (0.48), residues: 105 loop : -2.72 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 454 TYR 0.020 0.002 TYR A 527 PHE 0.017 0.002 PHE D 455 TRP 0.036 0.003 TRP A 327 HIS 0.015 0.002 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (16628) covalent geometry : angle 0.77353 / 0.42 (23225) hydrogen bonds : bond 0.04776 / 3.24 ( 631) hydrogen bonds : angle 5.57699 / 3.85 ( 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 217 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.529 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: A 259 GLN cc_start: 0.7188 (mp10) cc_final: 0.6658 (mp10) REVERT: A 462 LEU cc_start: 0.8822 (tp) cc_final: 0.8471 (tp) REVERT: A 464 MET cc_start: 0.9007 (ttm) cc_final: 0.7226 (tpt) REVERT: B 341 ARG cc_start: 0.2730 (OUTLIER) cc_final: 0.2047 (ptp90) REVERT: B 368 MET cc_start: 0.8054 (tpp) cc_final: 0.7456 (ppp) REVERT: B 538 GLN cc_start: 0.8878 (tp40) cc_final: 0.8464 (tp40) REVERT: C 277 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7537 (mm) REVERT: C 293 MET cc_start: 0.7108 (ptp) cc_final: 0.5045 (tpt) REVERT: C 327 TRP cc_start: 0.3559 (m100) cc_final: 0.3342 (m100) REVERT: C 389 GLN cc_start: 0.7456 (mt0) cc_final: 0.7215 (mp10) REVERT: C 394 MET cc_start: 0.2235 (ppp) cc_final: 0.1946 (ppp) REVERT: C 531 TYR cc_start: 0.7686 (m-80) cc_final: 0.7457 (m-80) REVERT: D 358 MET cc_start: 0.6093 (tpt) cc_final: 0.5511 (tpt) REVERT: D 368 MET cc_start: 0.6736 (mtp) cc_final: 0.6488 (mtm) REVERT: D 465 MET cc_start: 0.1300 (ppp) cc_final: 0.0996 (ptm) REVERT: D 479 MET cc_start: 0.6249 (mmm) cc_final: 0.5661 (mtp) outliers start: 41 outliers final: 22 residues processed: 205 average time/residue: 0.1165 time to fit residues: 36.1089 Evaluate side-chains 180 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 357 LEU Chi-restraints excluded: chain A residue 377 LEU 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 341 ARG Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR 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 286 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 49 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 158 optimal weight: 30.0000 chunk 163 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 154 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 B 361 GLN B 451 HIS ** C 227 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** ** 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 = 0.4763 r_free = 0.4763 target = 0.165956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.146738 restraints weight = 64436.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.146818 restraints weight = 48595.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.146509 restraints weight = 38676.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.146653 restraints weight = 31925.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.146690 restraints weight = 29028.336| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 16628 Z= 0.248 Angle : 0.832 10.061 23225 Z= 0.452 Chirality : 0.051 0.344 2526 Planarity : 0.007 0.076 2421 Dihedral : 27.305 173.007 3595 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.70 % Favored : 89.23 % Rotamer: Outliers : 4.01 % Allowed : 22.84 % Favored : 73.15 % 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 (0.19), residues: 1542 helix: -0.86 (0.19), residues: 698 sheet: -2.65 (0.44), residues: 104 loop : -2.84 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG B 393 TYR 0.030 0.002 TYR D 450 PHE 0.022 0.002 PHE A 508 TRP 0.068 0.003 TRP A 327 HIS 0.012 0.002 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.25 (16628) covalent geometry : angle 0.83221 / 0.45 (23225) hydrogen bonds : bond 0.05967 / 4.03 ( 631) hydrogen bonds : angle 5.64060 / 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 224 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 0.563 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: 0.7013 (mp10) cc_final: 0.6381 (mp10) REVERT: A 389 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7805 (tm-30) REVERT: A 462 LEU cc_start: 0.8879 (tp) cc_final: 0.8608 (tp) REVERT: A 464 MET cc_start: 0.9093 (ttm) cc_final: 0.7460 (tpt) REVERT: A 508 PHE cc_start: 0.6354 (t80) cc_final: 0.6141 (t80) REVERT: A 535 LEU cc_start: 0.8246 (mt) cc_final: 0.7960 (mt) REVERT: B 535 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7856 (tt) REVERT: B 538 GLN cc_start: 0.8978 (tp40) cc_final: 0.8289 (tp40) REVERT: C 277 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7743 (mm) REVERT: C 389 GLN cc_start: 0.7560 (mt0) cc_final: 0.7336 (mp10) REVERT: C 479 MET cc_start: 0.5037 (ppp) cc_final: 0.4254 (tmm) REVERT: C 491 PHE cc_start: 0.6472 (m-80) cc_final: 0.6246 (m-80) REVERT: D 332 ILE cc_start: 0.0922 (mm) cc_final: 0.0715 (mm) REVERT: D 479 MET cc_start: 0.6388 (mmm) cc_final: 0.5944 (mtp) REVERT: E 1 MET cc_start: 0.7221 (tpp) cc_final: 0.6914 (tpt) outliers start: 52 outliers final: 29 residues processed: 210 average time/residue: 0.1369 time to fit residues: 43.1587 Evaluate side-chains 180 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 356 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU 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 B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 535 LEU 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 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 407 PHE Chi-restraints excluded: chain D residue 416 LYS 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 49 GLU 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: 8.9990 chunk 82 optimal weight: 8.9990 chunk 156 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 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 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4621 r_free = 0.4621 target = 0.156568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.136902 restraints weight = 64775.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.136639 restraints weight = 53246.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.137249 restraints weight = 38856.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.137221 restraints weight = 33959.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.137239 restraints weight = 31375.998| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.7530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.138 16628 Z= 0.413 Angle : 1.103 19.474 23225 Z= 0.588 Chirality : 0.062 0.320 2526 Planarity : 0.010 0.092 2421 Dihedral : 27.389 170.585 3595 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 38.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.68 % Favored : 86.25 % Rotamer: Outliers : 5.40 % Allowed : 24.46 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.07 % 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: -3.53 (0.19), residues: 1542 helix: -1.39 (0.18), residues: 685 sheet: -3.27 (0.47), residues: 88 loop : -3.20 (0.18), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 39 TYR 0.046 0.004 TYR D 450 PHE 0.032 0.004 PHE D 455 TRP 0.084 0.005 TRP A 327 HIS 0.014 0.004 HIS F 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00878 / 0.41 (16628) covalent geometry : angle 1.10265 / 0.59 (23225) hydrogen bonds : bond 0.08878 / 6.02 ( 631) hydrogen bonds : angle 6.42576 / 4.47 ( 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 234 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 164 time to evaluate : 0.550 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: 0.7149 (mp10) cc_final: 0.6437 (mp10) REVERT: A 464 MET cc_start: 0.8895 (ttm) cc_final: 0.7533 (tpt) REVERT: A 508 PHE cc_start: 0.6860 (t80) cc_final: 0.6547 (t80) REVERT: A 535 LEU cc_start: 0.8424 (mt) cc_final: 0.8159 (mt) REVERT: B 450 TYR cc_start: 0.7580 (t80) cc_final: 0.7192 (t80) REVERT: B 538 GLN cc_start: 0.9136 (tp40) cc_final: 0.8629 (tp40) REVERT: C 277 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8122 (mm) REVERT: C 285 TRP cc_start: 0.8246 (m-90) cc_final: 0.7535 (m-10) REVERT: C 403 MET cc_start: 0.1904 (mmm) cc_final: 0.0632 (mmm) REVERT: C 464 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8301 (tpp) REVERT: C 479 MET cc_start: 0.5232 (ppp) cc_final: 0.4247 (tmm) REVERT: C 491 PHE cc_start: 0.7009 (m-80) cc_final: 0.6705 (m-80) REVERT: D 286 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6425 (mm) REVERT: D 368 MET cc_start: 0.5731 (OUTLIER) cc_final: 0.4525 (tpt) REVERT: D 465 MET cc_start: 0.2313 (ppp) cc_final: 0.2109 (ppp) REVERT: D 479 MET cc_start: 0.7470 (mmm) cc_final: 0.6096 (mtp) REVERT: E 79 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7700 (m) REVERT: F 48 MET cc_start: 0.8587 (mmt) cc_final: 0.8231 (mmt) outliers start: 70 outliers final: 35 residues processed: 213 average time/residue: 0.1434 time to fit residues: 44.9475 Evaluate side-chains 179 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 241 VAL 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 296 THR 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 518 GLN Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 ARG 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 351 LYS 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 464 MET Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 529 ILE 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 358 MET Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 407 PHE 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 79 SER Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 46 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 164 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN C 420 ASN ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 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 = 0.4715 r_free = 0.4715 target = 0.163265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.143438 restraints weight = 63927.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.143165 restraints weight = 44843.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.143479 restraints weight = 33472.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.143449 restraints weight = 30535.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.143538 restraints weight = 27667.956| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.7636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 16628 Z= 0.189 Angle : 0.843 9.892 23225 Z= 0.456 Chirality : 0.052 0.311 2526 Planarity : 0.007 0.073 2421 Dihedral : 27.363 169.606 3595 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.34 % Favored : 90.60 % Rotamer: Outliers : 3.78 % Allowed : 26.23 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % 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: -3.06 (0.19), residues: 1542 helix: -1.03 (0.19), residues: 684 sheet: -3.02 (0.42), residues: 101 loop : -2.91 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 515 TYR 0.026 0.002 TYR B 387 PHE 0.026 0.002 PHE C 468 TRP 0.092 0.003 TRP A 327 HIS 0.010 0.002 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (16628) covalent geometry : angle 0.84290 / 0.46 (23225) hydrogen bonds : bond 0.05142 / 3.52 ( 631) hydrogen bonds : angle 5.79030 / 4.05 ( 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 214 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8566 (p) REVERT: A 259 GLN cc_start: 0.6623 (mp10) cc_final: 0.6108 (mp10) REVERT: A 274 HIS cc_start: 0.7468 (m-70) cc_final: 0.7105 (m-70) REVERT: A 374 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 508 PHE cc_start: 0.6778 (t80) cc_final: 0.6513 (t80) REVERT: B 296 THR cc_start: 0.7974 (m) cc_final: 0.7773 (m) REVERT: B 450 TYR cc_start: 0.6983 (t80) cc_final: 0.6677 (t80) REVERT: B 538 GLN cc_start: 0.9103 (tp40) cc_final: 0.8544 (tp40) REVERT: C 265 ASN cc_start: 0.7233 (m110) cc_final: 0.6878 (m110) REVERT: C 277 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7996 (mm) REVERT: C 285 TRP cc_start: 0.8054 (m-90) cc_final: 0.7380 (m-90) REVERT: C 362 ASP cc_start: 0.5900 (OUTLIER) cc_final: 0.5580 (m-30) REVERT: C 403 MET cc_start: 0.1664 (mmm) cc_final: 0.1022 (mmm) REVERT: C 464 MET cc_start: 0.8528 (tpp) cc_final: 0.8011 (tpt) REVERT: C 479 MET cc_start: 0.5163 (ppp) cc_final: 0.4168 (tmm) REVERT: C 491 PHE cc_start: 0.6973 (m-80) cc_final: 0.6729 (m-80) REVERT: D 296 THR cc_start: 0.7682 (m) cc_final: 0.6154 (m) REVERT: D 368 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.3903 (tpt) REVERT: D 479 MET cc_start: 0.7498 (mmm) cc_final: 0.6341 (mtp) REVERT: E 79 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7541 (m) outliers start: 49 outliers final: 28 residues processed: 204 average time/residue: 0.1425 time to fit residues: 42.9110 Evaluate side-chains 184 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 335 CYS Chi-restraints excluded: chain A residue 356 LEU 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 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 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 407 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 107 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 30.0000 chunk 126 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.159657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.139366 restraints weight = 64267.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.138910 restraints weight = 47420.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.139118 restraints weight = 34934.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.139236 restraints weight = 30628.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.139277 restraints weight = 29360.587| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.8073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 16628 Z= 0.243 Angle : 0.867 11.126 23225 Z= 0.466 Chirality : 0.052 0.320 2526 Planarity : 0.007 0.093 2421 Dihedral : 27.234 168.898 3595 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 28.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.61 % Favored : 88.33 % Rotamer: Outliers : 3.70 % Allowed : 26.93 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % 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: -0.89 (0.19), residues: 674 sheet: -3.25 (0.43), residues: 95 loop : -2.86 (0.19), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG D 515 TYR 0.017 0.002 TYR A 527 PHE 0.022 0.003 PHE C 512 TRP 0.100 0.004 TRP A 327 HIS 0.011 0.002 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 (16628) covalent geometry : angle 0.86682 / 0.47 (23225) hydrogen bonds : bond 0.06018 / 4.12 ( 631) hydrogen bonds : angle 5.90587 / 4.12 ( 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 201 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8698 (p) REVERT: A 259 GLN cc_start: 0.6556 (mp10) cc_final: 0.6062 (mp10) REVERT: A 358 MET cc_start: 0.7679 (tpp) cc_final: 0.7340 (mpp) REVERT: A 374 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7367 (mm-30) REVERT: B 450 TYR cc_start: 0.7321 (t80) cc_final: 0.6917 (t80) REVERT: B 463 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8229 (t0) REVERT: B 538 GLN cc_start: 0.9162 (tp40) cc_final: 0.8800 (tp40) REVERT: C 277 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8207 (mm) REVERT: C 285 TRP cc_start: 0.8175 (m-90) cc_final: 0.7480 (m-90) REVERT: C 389 GLN cc_start: 0.7553 (pm20) cc_final: 0.7183 (pm20) REVERT: C 403 MET cc_start: 0.1504 (mmm) cc_final: 0.0612 (mtt) REVERT: C 464 MET cc_start: 0.8646 (tpp) cc_final: 0.8294 (tpt) REVERT: C 479 MET cc_start: 0.5208 (ppp) cc_final: 0.4232 (tmm) REVERT: C 491 PHE cc_start: 0.7068 (m-80) cc_final: 0.6812 (m-80) REVERT: C 525 PHE cc_start: 0.4602 (OUTLIER) cc_final: 0.3969 (m-10) REVERT: D 368 MET cc_start: 0.6241 (pmm) cc_final: 0.3917 (tpt) REVERT: D 479 MET cc_start: 0.7609 (mmm) cc_final: 0.6395 (mtp) REVERT: E 79 SER cc_start: 0.7869 (OUTLIER) cc_final: 0.7344 (m) outliers start: 48 outliers final: 36 residues processed: 186 average time/residue: 0.1282 time to fit residues: 35.7626 Evaluate side-chains 178 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU 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 293 MET Chi-restraints excluded: chain A residue 335 CYS 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 520 VAL Chi-restraints excluded: chain A residue 535 LEU 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 463 ASP 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 407 PHE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 525 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain E residue 6 ILE 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 E residue 79 SER Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 164 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN ** D 420 ASN ** 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 = 0.4664 r_free = 0.4664 target = 0.159634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.140124 restraints weight = 63594.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.139330 restraints weight = 48565.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.139541 restraints weight = 37979.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.139898 restraints weight = 32187.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.139863 restraints weight = 30825.167| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.8461 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= 0.223 Angle : 0.857 10.858 23225 Z= 0.462 Chirality : 0.051 0.287 2526 Planarity : 0.007 0.078 2421 Dihedral : 27.236 167.995 3595 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.77 % Favored : 89.17 % Rotamer: Outliers : 4.32 % Allowed : 26.54 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % 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: -2.91 (0.20), residues: 1542 helix: -0.85 (0.19), residues: 678 sheet: -3.24 (0.40), residues: 106 loop : -2.81 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 515 TYR 0.026 0.002 TYR D 450 PHE 0.045 0.002 PHE A 508 TRP 0.109 0.004 TRP A 327 HIS 0.011 0.002 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (16628) covalent geometry : angle 0.85719 / 0.46 (23225) hydrogen bonds : bond 0.05280 / 3.61 ( 631) hydrogen bonds : angle 5.82776 / 4.06 ( 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 210 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.6336 (mp10) cc_final: 0.5854 (mp10) REVERT: A 331 LYS cc_start: 0.8177 (ttpt) cc_final: 0.7876 (ttpt) REVERT: A 358 MET cc_start: 0.7696 (tpp) cc_final: 0.7350 (mpp) REVERT: A 374 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7475 (mm-30) REVERT: A 389 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 390 HIS cc_start: 0.7218 (m170) cc_final: 0.6262 (m-70) REVERT: A 465 MET cc_start: 0.8786 (tpp) cc_final: 0.8509 (tpp) REVERT: A 506 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8244 (mttt) REVERT: B 450 TYR cc_start: 0.7269 (t80) cc_final: 0.6971 (t80) REVERT: B 463 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8158 (t0) REVERT: B 538 GLN cc_start: 0.9173 (tp40) cc_final: 0.8727 (tp40) REVERT: C 277 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8199 (mm) REVERT: C 285 TRP cc_start: 0.8109 (m-90) cc_final: 0.7474 (m-90) REVERT: C 293 MET cc_start: 0.7277 (ptp) cc_final: 0.6777 (ppp) REVERT: C 358 MET cc_start: 0.7455 (pmm) cc_final: 0.7036 (pmm) REVERT: C 362 ASP cc_start: 0.6290 (OUTLIER) cc_final: 0.5933 (m-30) REVERT: C 389 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7138 (pm20) REVERT: C 403 MET cc_start: 0.1429 (mmm) cc_final: 0.0649 (mtt) REVERT: C 464 MET cc_start: 0.8618 (tpp) cc_final: 0.8195 (tpt) REVERT: C 479 MET cc_start: 0.5248 (ppp) cc_final: 0.4279 (tmm) REVERT: C 491 PHE cc_start: 0.7166 (m-80) cc_final: 0.6945 (m-80) REVERT: D 227 GLN cc_start: 0.5130 (tm-30) cc_final: 0.4691 (mp10) REVERT: D 368 MET cc_start: 0.6376 (pmm) cc_final: 0.3803 (tpt) REVERT: D 479 MET cc_start: 0.7756 (mmm) cc_final: 0.6765 (mtp) REVERT: E 79 SER cc_start: 0.7824 (OUTLIER) cc_final: 0.7251 (m) outliers start: 56 outliers final: 35 residues processed: 191 average time/residue: 0.1231 time to fit residues: 36.0058 Evaluate side-chains 190 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 335 CYS 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 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 357 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 463 ASP 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 389 GLN Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 49 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN C 451 HIS ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4657 r_free = 0.4657 target = 0.159087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.139238 restraints weight = 63795.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.138645 restraints weight = 48801.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.138881 restraints weight = 38538.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.139019 restraints weight = 32700.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.139072 restraints weight = 31684.181| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.8749 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= 0.211 Angle : 0.848 17.728 23225 Z= 0.454 Chirality : 0.051 0.289 2526 Planarity : 0.007 0.075 2421 Dihedral : 27.193 166.881 3595 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.74 % Favored : 88.20 % Rotamer: Outliers : 3.40 % Allowed : 27.78 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % 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: -2.90 (0.20), residues: 1542 helix: -0.89 (0.19), residues: 678 sheet: -3.18 (0.42), residues: 96 loop : -2.78 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 515 TYR 0.019 0.002 TYR D 427 PHE 0.034 0.002 PHE A 508 TRP 0.122 0.004 TRP A 327 HIS 0.011 0.002 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (16628) covalent geometry : angle 0.84777 / 0.45 (23225) hydrogen bonds : bond 0.05263 / 3.61 ( 631) hydrogen bonds : angle 5.81981 / 4.07 ( 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 199 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.6201 (mp10) cc_final: 0.5643 (mp10) REVERT: A 369 ARG cc_start: 0.8435 (mpt-90) cc_final: 0.7906 (mpt180) REVERT: A 374 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 506 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8249 (mttt) REVERT: B 463 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8076 (t0) REVERT: B 538 GLN cc_start: 0.9131 (tp40) cc_final: 0.8681 (tp40) REVERT: C 277 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8211 (mm) REVERT: C 285 TRP cc_start: 0.8146 (m-90) cc_final: 0.7574 (m-90) REVERT: C 341 ARG cc_start: 0.6827 (ptp90) cc_final: 0.6531 (ptp-170) REVERT: C 358 MET cc_start: 0.7466 (pmm) cc_final: 0.7122 (pmm) REVERT: C 389 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: C 403 MET cc_start: 0.1350 (mmm) cc_final: 0.0566 (mtt) REVERT: C 452 GLN cc_start: 0.7644 (tp40) cc_final: 0.6912 (pp30) REVERT: C 464 MET cc_start: 0.8605 (tpp) cc_final: 0.8165 (tpt) REVERT: C 479 MET cc_start: 0.5131 (ppp) cc_final: 0.4118 (tmm) REVERT: C 491 PHE cc_start: 0.7194 (m-80) cc_final: 0.6992 (m-80) REVERT: C 525 PHE cc_start: 0.4560 (OUTLIER) cc_final: 0.3983 (m-10) REVERT: D 368 MET cc_start: 0.6454 (pmm) cc_final: 0.3854 (tpt) REVERT: D 394 MET cc_start: 0.4785 (mmt) cc_final: 0.4396 (mmt) REVERT: D 479 MET cc_start: 0.7867 (mmm) cc_final: 0.6910 (mtp) REVERT: E 79 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7380 (m) outliers start: 44 outliers final: 33 residues processed: 187 average time/residue: 0.1237 time to fit residues: 34.9034 Evaluate side-chains 181 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 335 CYS 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 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 357 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 463 ASP 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 389 GLN 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 525 PHE Chi-restraints excluded: chain C residue 528 THR 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 332 ILE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain D residue 407 PHE Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 79 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 0.0000 chunk 135 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 157 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS C 322 ASN ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4690 r_free = 0.4690 target = 0.161484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.142047 restraints weight = 64502.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.142409 restraints weight = 46268.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.142599 restraints weight = 34095.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.142613 restraints weight = 30526.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.142697 restraints weight = 27744.531| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.8937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16628 Z= 0.173 Angle : 0.825 12.042 23225 Z= 0.438 Chirality : 0.050 0.268 2526 Planarity : 0.006 0.069 2421 Dihedral : 27.140 167.221 3595 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 2.78 % Allowed : 28.32 % 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: -2.82 (0.20), residues: 1542 helix: -0.79 (0.20), residues: 681 sheet: -3.45 (0.41), residues: 102 loop : -2.70 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 515 TYR 0.023 0.002 TYR D 450 PHE 0.030 0.002 PHE A 508 TRP 0.128 0.004 TRP A 327 HIS 0.011 0.002 HIS D 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (16628) covalent geometry : angle 0.82527 / 0.44 (23225) hydrogen bonds : bond 0.04698 / 3.18 ( 631) hydrogen bonds : angle 5.64979 / 3.95 ( 1685) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.69 seconds wall clock time: 45 minutes 1.33 seconds (2701.33 seconds total)