Starting phenix.real_space_refine on Sun May 3 06:15:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zwo_74914/05_2026/9zwo_74914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zwo_74914/05_2026/9zwo_74914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zwo_74914/05_2026/9zwo_74914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zwo_74914/05_2026/9zwo_74914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zwo_74914/05_2026/9zwo_74914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zwo_74914/05_2026/9zwo_74914.map" } resolution = 2.72 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= 0.026 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 2 5.49 5 S 62 5.16 5 C 7031 2.51 5 N 1821 2.21 5 O 2033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10951 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4156 Classifications: {'peptide': 557} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 4994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 4994 Classifications: {'peptide': 673} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 646} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'9Y0': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.83, per 1000 atoms: 0.26 Number of scatterers: 10951 At special positions: 0 Unit cell: (132.06, 105.09, 135.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 62 16.00 P 2 15.00 O 2033 8.00 N 1821 7.00 C 7031 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: 0.95 Conformation dependent library (CDL) restraints added in 500.4 milliseconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 9 sheets defined 64.4% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix removed outlier: 3.706A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 50 removed outlier: 3.604A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.792A pdb=" N GLN A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.589A pdb=" N LEU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.696A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 248 through 275 removed outlier: 3.708A pdb=" N PHE A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.669A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 3.903A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.852A pdb=" N LEU A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 4.120A pdb=" N VAL A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 359 through 368 removed outlier: 3.656A pdb=" N MET A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 399 removed outlier: 3.640A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 437 removed outlier: 3.588A pdb=" N MET A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.679A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 510 removed outlier: 4.651A pdb=" N VAL A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 4.069A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 549 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 11 through 24 removed outlier: 3.543A pdb=" N VAL B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 33 through 55 removed outlier: 3.512A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 87 removed outlier: 3.623A pdb=" N TRP B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.564A pdb=" N THR B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 208 removed outlier: 3.534A pdb=" N MET B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 238 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.796A pdb=" N ALA B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 269 through 282 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.570A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.665A pdb=" N LEU B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.605A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 397 through 408 Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.743A pdb=" N ASP B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.903A pdb=" N ALA B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 460 " --> pdb=" O ARG B 456 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.515A pdb=" N ALA B 478 " --> pdb=" O ASN B 474 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.946A pdb=" N ILE B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 529 removed outlier: 3.768A pdb=" N GLN B 528 " --> pdb=" O PRO B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 545 Processing helix chain 'B' and resid 556 through 595 removed outlier: 4.343A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 590 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Proline residue: B 592 - end of helix removed outlier: 4.040A pdb=" N PHE B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 removed outlier: 3.626A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 632 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Proline residue: B 633 - end of helix removed outlier: 3.805A pdb=" N GLY B 638 " --> pdb=" O LEU B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 657 removed outlier: 3.530A pdb=" N LEU B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 679 removed outlier: 3.566A pdb=" N VAL B 664 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 20 through 34 removed outlier: 3.689A pdb=" N LEU C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.975A pdb=" N SER C 82 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.723A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.831A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.609A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 148 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.692A pdb=" N ILE C 171 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY C 172 " --> pdb=" O LYS C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 172' Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 2 through 25 removed outlier: 4.027A pdb=" N GLY D 8 " --> pdb=" O GLY D 4 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 122 removed outlier: 4.203A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 165 through 167 Processing sheet with id=AA5, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.133A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 322 through 323 removed outlier: 6.020A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 396 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER B 384 " --> pdb=" O LYS B 395 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN B 387 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 428 through 429 removed outlier: 3.733A pdb=" N THR B 429 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 445 " --> pdb=" O THR B 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.496A pdb=" N ILE C 43 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.557A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1848 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.26 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: 1951 1.33 - 1.45: 2579 1.45 - 1.57: 6445 1.57 - 1.69: 4 1.69 - 1.81: 112 Bond restraints: 11091 Sorted by residual: bond pdb=" CB GLU C 45 " pdb=" CG GLU C 45 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" CG GLU C 45 " pdb=" CD GLU C 45 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.16e-01 bond pdb=" C ILE B 591 " pdb=" N PRO B 592 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.28e-02 6.10e+03 8.67e-01 bond pdb=" CB PRO A 180 " pdb=" CG PRO A 180 " ideal model delta sigma weight residual 1.492 1.449 0.043 5.00e-02 4.00e+02 7.31e-01 bond pdb=" CG ARG A 44 " pdb=" CD ARG A 44 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.67e-01 ... (remaining 11086 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 14794 1.35 - 2.70: 194 2.70 - 4.05: 60 4.05 - 5.40: 24 5.40 - 6.75: 1 Bond angle restraints: 15073 Sorted by residual: angle pdb=" N ALA C 73 " pdb=" CA ALA C 73 " pdb=" C ALA C 73 " ideal model delta sigma weight residual 110.97 114.39 -3.42 1.09e+00 8.42e-01 9.82e+00 angle pdb=" CB GLU C 45 " pdb=" CG GLU C 45 " pdb=" CD GLU C 45 " ideal model delta sigma weight residual 112.60 117.38 -4.78 1.70e+00 3.46e-01 7.91e+00 angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 118.64 -4.74 1.80e+00 3.09e-01 6.95e+00 angle pdb=" N THR A 522 " pdb=" CA THR A 522 " pdb=" CB THR A 522 " ideal model delta sigma weight residual 113.65 109.88 3.77 1.47e+00 4.63e-01 6.57e+00 angle pdb=" N ASP B 302 " pdb=" CA ASP B 302 " pdb=" C ASP B 302 " ideal model delta sigma weight residual 114.04 110.97 3.07 1.24e+00 6.50e-01 6.13e+00 ... (remaining 15068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 5570 15.69 - 31.38: 735 31.38 - 47.08: 233 47.08 - 62.77: 68 62.77 - 78.46: 18 Dihedral angle restraints: 6624 sinusoidal: 2521 harmonic: 4103 Sorted by residual: dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLN A 61 " pdb=" C GLN A 61 " pdb=" N TYR A 62 " pdb=" CA TYR A 62 " ideal model delta harmonic sigma weight residual 180.00 163.34 16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASP A 33 " pdb=" CB ASP A 33 " pdb=" CG ASP A 33 " pdb=" OD1 ASP A 33 " ideal model delta sinusoidal sigma weight residual -30.00 -87.48 57.48 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 6621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1127 0.028 - 0.056: 453 0.056 - 0.084: 123 0.084 - 0.112: 89 0.112 - 0.140: 15 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CG LEU A 184 " pdb=" CB LEU A 184 " pdb=" CD1 LEU A 184 " pdb=" CD2 LEU A 184 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE B 140 " pdb=" N ILE B 140 " pdb=" C ILE B 140 " pdb=" CB ILE B 140 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE A 34 " pdb=" N ILE A 34 " pdb=" C ILE A 34 " pdb=" CB ILE A 34 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1804 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 26 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 27 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 429 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 430 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 430 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 430 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 612 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO B 613 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 613 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 613 " 0.019 5.00e-02 4.00e+02 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.76: 1891 2.76 - 3.35: 12292 3.35 - 3.95: 21687 3.95 - 4.54: 30474 4.54 - 5.14: 44547 Nonbonded interactions: 110891 Sorted by model distance: nonbonded pdb=" O ASN A 104 " pdb=" OG SER A 108 " model vdw 2.164 3.040 nonbonded pdb=" O SER C 115 " pdb=" OG SER C 115 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASP B 329 " pdb=" OG1 THR B 332 " model vdw 2.223 3.040 nonbonded pdb=" O LEU A 228 " pdb=" O HOH A 701 " model vdw 2.230 3.040 nonbonded pdb=" OG SER C 70 " pdb=" O GLY C 127 " model vdw 2.237 3.040 ... (remaining 110886 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.050 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.002 0.043 11091 Z= 0.098 Angle : 0.466 6.754 15073 Z= 0.236 Chirality : 0.038 0.140 1807 Planarity : 0.003 0.044 1909 Dihedral : 16.650 78.460 3988 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.06 % Allowed : 23.35 % Favored : 75.59 % 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: -0.44 (0.21), residues: 1441 helix: 0.26 (0.17), residues: 833 sheet: -0.14 (0.52), residues: 106 loop : -1.12 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 44 TYR 0.020 0.001 TYR A 381 PHE 0.011 0.001 PHE A 392 TRP 0.006 0.001 TRP C 32 HIS 0.001 0.000 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00234 (11091) covalent geometry : angle 0.46599 (15073) hydrogen bonds : bond 0.25120 ( 639) hydrogen bonds : angle 7.76527 ( 1848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.396 Fit side-chains REVERT: C 75 MET cc_start: 0.8098 (pmt) cc_final: 0.7793 (pmm) outliers start: 12 outliers final: 9 residues processed: 109 average time/residue: 0.6022 time to fit residues: 71.1254 Evaluate side-chains 110 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 48 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 30.0000 chunk 55 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.177986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104355 restraints weight = 12597.651| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.51 r_work: 0.3003 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11091 Z= 0.233 Angle : 0.618 6.630 15073 Z= 0.319 Chirality : 0.044 0.175 1807 Planarity : 0.004 0.045 1909 Dihedral : 8.425 82.624 1618 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.79 % Allowed : 18.15 % Favored : 78.06 % 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: 0.24 (0.22), residues: 1441 helix: 0.91 (0.18), residues: 842 sheet: -0.13 (0.53), residues: 107 loop : -1.00 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 44 TYR 0.028 0.002 TYR A 381 PHE 0.021 0.002 PHE A 373 TRP 0.009 0.001 TRP B 40 HIS 0.003 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00564 (11091) covalent geometry : angle 0.61789 (15073) hydrogen bonds : bond 0.05907 ( 639) hydrogen bonds : angle 4.99891 ( 1848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.430 Fit side-chains REVERT: A 409 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7972 (mm) REVERT: B 77 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7274 (tm) REVERT: B 569 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.7015 (mp) REVERT: C 161 LYS cc_start: 0.8003 (tttp) cc_final: 0.7473 (ttmt) REVERT: D 1 MET cc_start: 0.5015 (OUTLIER) cc_final: 0.4363 (mpt) outliers start: 43 outliers final: 16 residues processed: 142 average time/residue: 0.5287 time to fit residues: 81.8015 Evaluate side-chains 118 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 134 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 92 optimal weight: 30.0000 chunk 137 optimal weight: 0.4980 chunk 84 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.179952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104376 restraints weight = 12673.133| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.71 r_work: 0.3071 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11091 Z= 0.138 Angle : 0.529 7.307 15073 Z= 0.271 Chirality : 0.040 0.170 1807 Planarity : 0.003 0.047 1909 Dihedral : 8.083 77.604 1611 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.35 % Allowed : 19.47 % Favored : 77.18 % 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: 0.52 (0.22), residues: 1441 helix: 1.19 (0.18), residues: 852 sheet: -0.29 (0.54), residues: 109 loop : -0.96 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.025 0.001 TYR A 381 PHE 0.015 0.001 PHE A 392 TRP 0.008 0.001 TRP B 40 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00317 (11091) covalent geometry : angle 0.52856 (15073) hydrogen bonds : bond 0.04774 ( 639) hydrogen bonds : angle 4.56587 ( 1848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8880 (mmp) cc_final: 0.8456 (mmp) REVERT: B 77 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7313 (tm) REVERT: B 125 GLN cc_start: 0.5919 (OUTLIER) cc_final: 0.5510 (mp10) REVERT: B 383 MET cc_start: 0.3827 (tpt) cc_final: 0.0706 (mmt) REVERT: B 457 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6186 (m-80) REVERT: B 569 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6959 (mp) REVERT: C 161 LYS cc_start: 0.8065 (tttp) cc_final: 0.7535 (ttmt) REVERT: D 1 MET cc_start: 0.4989 (OUTLIER) cc_final: 0.4305 (mpt) outliers start: 38 outliers final: 14 residues processed: 136 average time/residue: 0.5446 time to fit residues: 80.6726 Evaluate side-chains 121 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 457 PHE Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 11 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 64 optimal weight: 30.0000 chunk 49 optimal weight: 0.0000 chunk 37 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 50.0000 chunk 131 optimal weight: 0.9980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.181859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106700 restraints weight = 12687.406| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.76 r_work: 0.3122 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11091 Z= 0.108 Angle : 0.501 8.954 15073 Z= 0.255 Chirality : 0.039 0.147 1807 Planarity : 0.003 0.046 1909 Dihedral : 7.878 74.401 1610 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.61 % Allowed : 18.68 % Favored : 77.71 % 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: 0.79 (0.23), residues: 1441 helix: 1.46 (0.18), residues: 854 sheet: -0.28 (0.55), residues: 109 loop : -0.95 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 402 TYR 0.023 0.001 TYR A 381 PHE 0.016 0.001 PHE A 392 TRP 0.008 0.001 TRP B 40 HIS 0.001 0.000 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00234 (11091) covalent geometry : angle 0.50086 (15073) hydrogen bonds : bond 0.04076 ( 639) hydrogen bonds : angle 4.31404 ( 1848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8898 (mmp) cc_final: 0.8581 (mmp) REVERT: A 513 GLN cc_start: 0.7806 (mt0) cc_final: 0.7549 (mt0) REVERT: B 207 VAL cc_start: 0.8411 (t) cc_final: 0.8210 (p) REVERT: B 383 MET cc_start: 0.3962 (tpt) cc_final: 0.1304 (mmt) REVERT: B 457 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.6217 (m-80) REVERT: B 470 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.6101 (mm) REVERT: C 31 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8611 (mm110) REVERT: C 161 LYS cc_start: 0.8129 (tttp) cc_final: 0.7609 (ttmp) REVERT: D 1 MET cc_start: 0.4715 (OUTLIER) cc_final: 0.4102 (mmp) outliers start: 41 outliers final: 13 residues processed: 142 average time/residue: 0.5235 time to fit residues: 81.3983 Evaluate side-chains 121 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 457 PHE Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 111 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 129 optimal weight: 0.4980 chunk 89 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.181218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107354 restraints weight = 12606.668| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.67 r_work: 0.3139 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11091 Z= 0.133 Angle : 0.520 9.959 15073 Z= 0.262 Chirality : 0.040 0.184 1807 Planarity : 0.003 0.049 1909 Dihedral : 7.865 76.946 1608 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.35 % Allowed : 19.12 % Favored : 77.53 % 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: 0.87 (0.23), residues: 1441 helix: 1.52 (0.18), residues: 856 sheet: -0.31 (0.55), residues: 109 loop : -0.92 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 382 TYR 0.024 0.001 TYR A 381 PHE 0.018 0.001 PHE A 392 TRP 0.007 0.001 TRP B 40 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00309 (11091) covalent geometry : angle 0.51955 (15073) hydrogen bonds : bond 0.04284 ( 639) hydrogen bonds : angle 4.25482 ( 1848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8860 (mmp) cc_final: 0.8475 (mmp) REVERT: B 77 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7432 (tm) REVERT: B 125 GLN cc_start: 0.5978 (OUTLIER) cc_final: 0.5551 (mp10) REVERT: B 207 VAL cc_start: 0.8455 (t) cc_final: 0.8243 (p) REVERT: B 383 MET cc_start: 0.3265 (tpt) cc_final: 0.0918 (mmt) REVERT: B 457 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.6161 (m-80) REVERT: C 31 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8626 (mm110) REVERT: C 161 LYS cc_start: 0.8145 (tttp) cc_final: 0.7634 (ttmp) REVERT: D 1 MET cc_start: 0.4823 (OUTLIER) cc_final: 0.4208 (mmp) outliers start: 38 outliers final: 14 residues processed: 139 average time/residue: 0.5772 time to fit residues: 87.3513 Evaluate side-chains 120 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 457 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.0060 chunk 128 optimal weight: 0.0370 chunk 20 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.182942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109333 restraints weight = 12715.466| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.71 r_work: 0.3172 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11091 Z= 0.106 Angle : 0.501 10.334 15073 Z= 0.252 Chirality : 0.039 0.167 1807 Planarity : 0.003 0.047 1909 Dihedral : 7.705 74.066 1608 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.78 % Favored : 97.15 % Rotamer: Outliers : 2.91 % Allowed : 19.74 % Favored : 77.36 % 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: 1.02 (0.23), residues: 1441 helix: 1.69 (0.18), residues: 857 sheet: -0.50 (0.54), residues: 111 loop : -0.89 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.023 0.001 TYR A 381 PHE 0.019 0.001 PHE A 392 TRP 0.007 0.001 TRP B 40 HIS 0.001 0.000 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00231 (11091) covalent geometry : angle 0.50062 (15073) hydrogen bonds : bond 0.03795 ( 639) hydrogen bonds : angle 4.09968 ( 1848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8910 (mmp) cc_final: 0.8615 (mmp) REVERT: B 383 MET cc_start: 0.3683 (tpt) cc_final: 0.1529 (mmt) REVERT: B 457 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6209 (m-80) REVERT: C 31 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8648 (mm110) REVERT: C 75 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7753 (pmm) REVERT: C 161 LYS cc_start: 0.8169 (tttp) cc_final: 0.7651 (ttmt) REVERT: D 1 MET cc_start: 0.4678 (OUTLIER) cc_final: 0.4088 (mmp) outliers start: 33 outliers final: 18 residues processed: 136 average time/residue: 0.5728 time to fit residues: 84.8945 Evaluate side-chains 124 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 457 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 123 optimal weight: 0.2980 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.181755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107944 restraints weight = 12719.423| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.69 r_work: 0.3151 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11091 Z= 0.129 Angle : 0.524 11.137 15073 Z= 0.263 Chirality : 0.040 0.150 1807 Planarity : 0.003 0.049 1909 Dihedral : 7.787 76.307 1608 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.08 % Allowed : 19.82 % Favored : 77.09 % 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: 0.97 (0.23), residues: 1441 helix: 1.66 (0.18), residues: 857 sheet: -0.54 (0.54), residues: 111 loop : -0.93 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 202 TYR 0.024 0.001 TYR A 381 PHE 0.019 0.001 PHE A 392 TRP 0.006 0.001 TRP B 40 HIS 0.001 0.000 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00300 (11091) covalent geometry : angle 0.52428 (15073) hydrogen bonds : bond 0.04085 ( 639) hydrogen bonds : angle 4.14503 ( 1848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: B 140 ILE cc_start: 0.2363 (OUTLIER) cc_final: 0.1965 (mp) REVERT: B 383 MET cc_start: 0.4029 (tpt) cc_final: 0.1867 (mmt) REVERT: B 457 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: C 31 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8642 (mm110) REVERT: C 75 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7738 (pmm) REVERT: C 161 LYS cc_start: 0.8181 (tttp) cc_final: 0.7661 (ttmt) REVERT: D 1 MET cc_start: 0.4693 (OUTLIER) cc_final: 0.4111 (mmp) outliers start: 35 outliers final: 18 residues processed: 134 average time/residue: 0.5651 time to fit residues: 82.3303 Evaluate side-chains 120 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 457 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.181632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107815 restraints weight = 12652.504| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.70 r_work: 0.3152 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11091 Z= 0.127 Angle : 0.525 8.757 15073 Z= 0.264 Chirality : 0.040 0.150 1807 Planarity : 0.003 0.049 1909 Dihedral : 7.847 78.467 1608 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 3.00 % Allowed : 19.74 % Favored : 77.27 % 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: 0.97 (0.23), residues: 1441 helix: 1.67 (0.18), residues: 857 sheet: -0.58 (0.53), residues: 111 loop : -0.94 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 202 TYR 0.024 0.001 TYR A 381 PHE 0.020 0.001 PHE A 392 TRP 0.007 0.001 TRP B 40 HIS 0.001 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00295 (11091) covalent geometry : angle 0.52510 (15073) hydrogen bonds : bond 0.04069 ( 639) hydrogen bonds : angle 4.10889 ( 1848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7388 (tm) REVERT: B 140 ILE cc_start: 0.2489 (OUTLIER) cc_final: 0.2108 (mp) REVERT: B 383 MET cc_start: 0.4075 (tpt) cc_final: 0.1924 (mmt) REVERT: B 457 PHE cc_start: 0.6825 (OUTLIER) cc_final: 0.6269 (m-80) REVERT: C 31 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8636 (mm110) REVERT: C 75 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7760 (pmm) REVERT: C 161 LYS cc_start: 0.8174 (tttp) cc_final: 0.7654 (ttmt) REVERT: D 1 MET cc_start: 0.4782 (OUTLIER) cc_final: 0.4206 (mmp) outliers start: 34 outliers final: 18 residues processed: 131 average time/residue: 0.5763 time to fit residues: 82.1258 Evaluate side-chains 123 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 457 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 108 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.0020 chunk 127 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.182302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108792 restraints weight = 12666.364| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.70 r_work: 0.3164 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11091 Z= 0.118 Angle : 0.523 12.450 15073 Z= 0.262 Chirality : 0.039 0.150 1807 Planarity : 0.003 0.049 1909 Dihedral : 7.855 88.059 1608 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 2.64 % Allowed : 20.00 % Favored : 77.36 % 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: 1.03 (0.23), residues: 1441 helix: 1.73 (0.18), residues: 858 sheet: -0.63 (0.52), residues: 111 loop : -0.91 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 202 TYR 0.023 0.001 TYR A 381 PHE 0.020 0.001 PHE A 392 TRP 0.007 0.001 TRP B 40 HIS 0.002 0.000 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00269 (11091) covalent geometry : angle 0.52259 (15073) hydrogen bonds : bond 0.03892 ( 639) hydrogen bonds : angle 4.05334 ( 1848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.418 Fit side-chains REVERT: A 501 MET cc_start: 0.8887 (mmp) cc_final: 0.8589 (mmp) REVERT: B 140 ILE cc_start: 0.2302 (OUTLIER) cc_final: 0.1905 (mp) REVERT: B 383 MET cc_start: 0.3903 (tpt) cc_final: 0.1791 (mmt) REVERT: B 457 PHE cc_start: 0.6801 (OUTLIER) cc_final: 0.6244 (m-80) REVERT: C 31 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8644 (mm110) REVERT: C 75 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7711 (pmm) REVERT: C 161 LYS cc_start: 0.8182 (tttp) cc_final: 0.7653 (ttmt) outliers start: 30 outliers final: 18 residues processed: 126 average time/residue: 0.5269 time to fit residues: 72.5974 Evaluate side-chains 120 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 457 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain D residue 6 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 102 optimal weight: 0.0170 chunk 134 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 69 optimal weight: 40.0000 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.182271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108836 restraints weight = 12670.282| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.66 r_work: 0.3164 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11091 Z= 0.120 Angle : 0.525 11.892 15073 Z= 0.263 Chirality : 0.039 0.147 1807 Planarity : 0.003 0.049 1909 Dihedral : 7.822 80.655 1608 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 2.64 % Allowed : 20.35 % Favored : 77.00 % 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: 1.04 (0.23), residues: 1441 helix: 1.73 (0.18), residues: 857 sheet: -0.55 (0.53), residues: 111 loop : -0.92 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 394 TYR 0.024 0.001 TYR A 381 PHE 0.017 0.001 PHE A 392 TRP 0.007 0.001 TRP B 40 HIS 0.002 0.000 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00275 (11091) covalent geometry : angle 0.52482 (15073) hydrogen bonds : bond 0.03936 ( 639) hydrogen bonds : angle 4.05594 ( 1848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.417 Fit side-chains REVERT: B 77 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7414 (tm) REVERT: B 140 ILE cc_start: 0.2454 (OUTLIER) cc_final: 0.2023 (mp) REVERT: B 383 MET cc_start: 0.3771 (tpt) cc_final: 0.1659 (mmt) REVERT: B 457 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.6184 (m-80) REVERT: C 31 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8641 (mm110) REVERT: C 75 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7760 (pmm) REVERT: C 161 LYS cc_start: 0.8205 (tttp) cc_final: 0.7681 (ttmt) outliers start: 30 outliers final: 19 residues processed: 129 average time/residue: 0.5198 time to fit residues: 73.3226 Evaluate side-chains 123 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 457 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain D residue 6 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 94 optimal weight: 0.0970 chunk 139 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.181671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108123 restraints weight = 12688.335| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.68 r_work: 0.3155 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11091 Z= 0.130 Angle : 0.532 9.382 15073 Z= 0.268 Chirality : 0.040 0.149 1807 Planarity : 0.003 0.049 1909 Dihedral : 7.829 77.399 1608 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 2.38 % Allowed : 20.44 % Favored : 77.18 % 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: 1.01 (0.23), residues: 1441 helix: 1.69 (0.18), residues: 858 sheet: -0.51 (0.53), residues: 111 loop : -0.91 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 394 TYR 0.024 0.001 TYR A 381 PHE 0.012 0.001 PHE A 373 TRP 0.006 0.001 TRP B 40 HIS 0.002 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00303 (11091) covalent geometry : angle 0.53175 (15073) hydrogen bonds : bond 0.04066 ( 639) hydrogen bonds : angle 4.07846 ( 1848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5513.99 seconds wall clock time: 94 minutes 16.44 seconds (5656.44 seconds total)