Starting phenix.real_space_refine on Fri Jul 3 01:08:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zwo_74914/07_2026/9zwo_74914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zwo_74914/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9zwo_74914/07_2026/9zwo_74914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zwo_74914/07_2026/9zwo_74914.map" model { file = "/net/cci-nas-00/data/ceres_data/9zwo_74914/07_2026/9zwo_74914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zwo_74914/07_2026/9zwo_74914.cif" } 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 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: 2.18, per 1000 atoms: 0.20 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: 0.79 Conformation dependent library (CDL) restraints added in 403.6 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: 0.31 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: 1.35 Time building geometry restraints manager: 1.07 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: 3.330 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.600 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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/Z covalent geometry : bond 0.00234 / 0.10 (11091) covalent geometry : angle 0.46599 / 0.24 (15073) hydrogen bonds : bond 0.25120 / 17.08 ( 639) hydrogen bonds : angle 7.76527 / 5.72 ( 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 : 0.406 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: 0.4893 time to fit residues: 58.0029 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 : 0.288 ------------------------------------------------------------------------------- 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... B 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.177784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101490 restraints weight = 12545.958| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.75 r_work: 0.3034 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 11091 Z= 0.235 Angle : 0.612 6.593 15073 Z= 0.318 Chirality : 0.044 0.174 1807 Planarity : 0.004 0.045 1909 Dihedral : 8.385 82.058 1618 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.61 % Allowed : 18.24 % Favored : 78.15 % 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: 0.31 (0.22), residues: 1441 helix: 0.97 (0.18), residues: 840 sheet: -0.16 (0.53), residues: 107 loop : -0.95 (0.28), residues: 494 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 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (11091) covalent geometry : angle 0.61169 / 0.32 (15073) hydrogen bonds : bond 0.06275 / 4.31 ( 639) hydrogen bonds : angle 5.06214 / 3.71 ( 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 147 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.316 Fit side-chains REVERT: B 77 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7331 (tm) REVERT: C 161 LYS cc_start: 0.8050 (tttp) cc_final: 0.7547 (ttmt) REVERT: D 1 MET cc_start: 0.5045 (OUTLIER) cc_final: 0.4419 (mpt) outliers start: 41 outliers final: 16 residues processed: 138 average time/residue: 0.4308 time to fit residues: 65.0221 Evaluate side-chains 115 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 5 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 92 optimal weight: 40.0000 chunk 137 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.0030 chunk 56 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.180295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105809 restraints weight = 12707.582| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.72 r_work: 0.3114 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11091 Z= 0.120 Angle : 0.515 7.383 15073 Z= 0.264 Chirality : 0.039 0.167 1807 Planarity : 0.003 0.045 1909 Dihedral : 7.957 75.867 1611 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.08 % Allowed : 19.38 % 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: 0.60 (0.22), residues: 1441 helix: 1.27 (0.18), residues: 852 sheet: -0.28 (0.54), residues: 109 loop : -0.97 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 402 TYR 0.024 0.001 TYR A 381 PHE 0.014 0.001 PHE A 392 TRP 0.008 0.001 TRP B 40 HIS 0.002 0.000 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (11091) covalent geometry : angle 0.51485 / 0.26 (15073) hydrogen bonds : bond 0.04527 / 3.12 ( 639) hydrogen bonds : angle 4.53617 / 3.30 ( 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: 35 poor density : 107 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8890 (mmp) cc_final: 0.8411 (mmp) REVERT: B 77 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7290 (tm) REVERT: B 383 MET cc_start: 0.3565 (tpt) cc_final: 0.0478 (mmt) REVERT: C 31 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8665 (mm110) REVERT: C 161 LYS cc_start: 0.8040 (tttp) cc_final: 0.7512 (ttmt) REVERT: D 1 MET cc_start: 0.5014 (OUTLIER) cc_final: 0.4233 (mpt) outliers start: 35 outliers final: 14 residues processed: 137 average time/residue: 0.4219 time to fit residues: 63.3285 Evaluate side-chains 118 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLN 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 77 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 434 VAL 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 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: 0.9980 chunk 101 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 49 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 69 optimal weight: 50.0000 chunk 131 optimal weight: 0.2980 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.179426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103680 restraints weight = 12701.298| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.73 r_work: 0.3066 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11091 Z= 0.159 Angle : 0.540 8.637 15073 Z= 0.275 Chirality : 0.041 0.153 1807 Planarity : 0.003 0.050 1909 Dihedral : 8.093 78.851 1611 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.61 % Allowed : 19.12 % 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: 0.64 (0.22), residues: 1441 helix: 1.33 (0.18), residues: 851 sheet: -0.30 (0.55), residues: 109 loop : -0.99 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 326 TYR 0.025 0.001 TYR A 381 PHE 0.016 0.001 PHE A 392 TRP 0.008 0.001 TRP B 40 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (11091) covalent geometry : angle 0.54031 / 0.27 (15073) hydrogen bonds : bond 0.04696 / 3.24 ( 639) hydrogen bonds : angle 4.46390 / 3.26 ( 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 : 0.248 Fit side-chains revert: symmetry clash REVERT: A 501 MET cc_start: 0.8861 (mmp) cc_final: 0.8456 (mmp) REVERT: B 77 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7336 (tm) REVERT: B 125 GLN cc_start: 0.5892 (OUTLIER) cc_final: 0.5502 (mp10) REVERT: B 383 MET cc_start: 0.4057 (tpt) cc_final: 0.1376 (mmt) REVERT: B 457 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.6237 (m-80) REVERT: C 31 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8661 (mm110) REVERT: C 161 LYS cc_start: 0.8090 (tttp) cc_final: 0.7577 (ttmp) REVERT: D 1 MET cc_start: 0.5046 (OUTLIER) cc_final: 0.4364 (mpt) outliers start: 41 outliers final: 15 residues processed: 143 average time/residue: 0.4451 time to fit residues: 69.6567 Evaluate side-chains 119 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 125 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 457 PHE Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 590 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 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: 4.9990 chunk 118 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 chunk 89 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4091 r_free = 0.4091 target = 0.179094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104629 restraints weight = 12599.014| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.71 r_work: 0.3080 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11091 Z= 0.146 Angle : 0.535 10.831 15073 Z= 0.270 Chirality : 0.040 0.185 1807 Planarity : 0.003 0.050 1909 Dihedral : 8.140 78.574 1610 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.70 % Allowed : 18.94 % 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: 0.75 (0.22), residues: 1441 helix: 1.41 (0.18), residues: 854 sheet: -0.32 (0.55), residues: 109 loop : -0.93 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 326 TYR 0.025 0.001 TYR A 381 PHE 0.019 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/Z covalent geometry : bond 0.00343 / 0.15 (11091) covalent geometry : angle 0.53511 / 0.27 (15073) hydrogen bonds : bond 0.04439 / 3.07 ( 639) hydrogen bonds : angle 4.33788 / 3.16 ( 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 145 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 501 MET cc_start: 0.8850 (mmp) cc_final: 0.8458 (mmp) REVERT: B 383 MET cc_start: 0.3321 (tpt) cc_final: 0.0983 (mmt) REVERT: B 457 PHE cc_start: 0.6692 (OUTLIER) cc_final: 0.6197 (m-80) REVERT: C 31 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8649 (mm110) REVERT: C 161 LYS cc_start: 0.8079 (tttp) cc_final: 0.7560 (ttmp) REVERT: D 1 MET cc_start: 0.4710 (OUTLIER) cc_final: 0.4011 (mpt) outliers start: 42 outliers final: 16 residues processed: 137 average time/residue: 0.4621 time to fit residues: 69.1024 Evaluate side-chains 117 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 134 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 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 645 THR Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 72 THR 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: 0.8980 chunk 23 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 27 optimal weight: 0.0570 chunk 128 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN ** A 114 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 = 0.4115 r_free = 0.4115 target = 0.181191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105985 restraints weight = 12674.339| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.76 r_work: 0.3106 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1868 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= 0.114 Angle : 0.511 10.310 15073 Z= 0.258 Chirality : 0.039 0.165 1807 Planarity : 0.003 0.048 1909 Dihedral : 7.861 75.428 1608 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 2.91 % Allowed : 19.21 % Favored : 77.89 % 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: 1.65 (0.18), residues: 851 sheet: -0.47 (0.55), residues: 111 loop : -0.89 (0.28), residues: 479 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 0.008 0.001 TRP B 40 HIS 0.001 0.000 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (11091) covalent geometry : angle 0.51139 / 0.26 (15073) hydrogen bonds : bond 0.03957 / 2.73 ( 639) hydrogen bonds : angle 4.18101 / 3.04 ( 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 : 0.349 Fit side-chains revert: symmetry clash REVERT: A 501 MET cc_start: 0.8856 (mmp) cc_final: 0.8470 (mmp) REVERT: B 77 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7319 (tm) REVERT: B 383 MET cc_start: 0.3848 (tpt) cc_final: 0.1714 (mmt) REVERT: B 457 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6234 (m-80) REVERT: C 31 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8583 (mm110) REVERT: C 161 LYS cc_start: 0.8162 (tttp) cc_final: 0.7618 (ttmt) REVERT: D 1 MET cc_start: 0.4690 (OUTLIER) cc_final: 0.4085 (mmp) outliers start: 33 outliers final: 14 residues processed: 136 average time/residue: 0.4281 time to fit residues: 63.8383 Evaluate side-chains 119 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 193 VAL Chi-restraints excluded: chain B residue 215 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 15 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 121 VAL 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: 0.8980 chunk 4 optimal weight: 0.7980 chunk 123 optimal weight: 0.0970 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 30.0000 chunk 9 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 136 optimal weight: 0.3980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.180929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106154 restraints weight = 12677.446| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.74 r_work: 0.3103 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1919 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= 0.119 Angle : 0.515 6.754 15073 Z= 0.261 Chirality : 0.039 0.147 1807 Planarity : 0.003 0.049 1909 Dihedral : 7.866 80.936 1608 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.91 % Allowed : 19.47 % Favored : 77.62 % 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: 0.98 (0.23), residues: 1441 helix: 1.68 (0.18), residues: 853 sheet: -0.52 (0.54), residues: 111 loop : -0.93 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 89 TYR 0.024 0.001 TYR A 381 PHE 0.019 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/Z covalent geometry : bond 0.00271 / 0.12 (11091) covalent geometry : angle 0.51502 / 0.26 (15073) hydrogen bonds : bond 0.03988 / 2.75 ( 639) hydrogen bonds : angle 4.15526 / 3.03 ( 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 135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: B 77 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7297 (tm) REVERT: B 140 ILE cc_start: 0.2445 (OUTLIER) cc_final: 0.2008 (mp) REVERT: B 383 MET cc_start: 0.3810 (tpt) cc_final: 0.1616 (mmt) REVERT: B 457 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.6196 (m-80) REVERT: C 31 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8580 (mm110) REVERT: C 161 LYS cc_start: 0.8138 (tttp) cc_final: 0.7593 (ttmt) REVERT: D 1 MET cc_start: 0.4713 (OUTLIER) cc_final: 0.4100 (mmp) outliers start: 33 outliers final: 20 residues processed: 132 average time/residue: 0.4420 time to fit residues: 63.7595 Evaluate side-chains 123 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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 434 VAL Chi-restraints excluded: chain B residue 457 PHE Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 607 ILE 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 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: 0.7980 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 131 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 9 optimal weight: 0.0270 chunk 21 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN ** A 114 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 = 0.4124 r_free = 0.4124 target = 0.181827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108117 restraints weight = 12621.501| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.71 r_work: 0.3155 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11091 Z= 0.122 Angle : 0.525 11.977 15073 Z= 0.263 Chirality : 0.039 0.150 1807 Planarity : 0.003 0.049 1909 Dihedral : 7.927 89.237 1608 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 3.00 % Allowed : 19.21 % Favored : 77.80 % 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: 1.70 (0.18), residues: 852 sheet: -0.58 (0.53), residues: 111 loop : -0.96 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 89 TYR 0.024 0.001 TYR A 381 PHE 0.019 0.001 PHE A 392 TRP 0.007 0.001 TRP B 40 HIS 0.001 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (11091) covalent geometry : angle 0.52490 / 0.26 (15073) hydrogen bonds : bond 0.03990 / 2.76 ( 639) hydrogen bonds : angle 4.12403 / 3.01 ( 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 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 77 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7388 (tm) REVERT: B 125 GLN cc_start: 0.5495 (OUTLIER) cc_final: 0.5263 (mp10) REVERT: B 140 ILE cc_start: 0.2504 (OUTLIER) cc_final: 0.2117 (mp) REVERT: B 383 MET cc_start: 0.3984 (tpt) cc_final: 0.1916 (mmt) REVERT: B 457 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: C 31 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8639 (mm110) REVERT: C 75 MET cc_start: 0.8089 (pmt) cc_final: 0.7798 (pmm) REVERT: C 161 LYS cc_start: 0.8199 (tttp) cc_final: 0.7667 (ttmt) REVERT: D 1 MET cc_start: 0.4452 (OUTLIER) cc_final: 0.3847 (mmp) outliers start: 34 outliers final: 20 residues processed: 130 average time/residue: 0.4283 time to fit residues: 60.7412 Evaluate side-chains 122 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 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 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 434 VAL Chi-restraints excluded: chain B residue 457 PHE Chi-restraints excluded: chain B residue 607 ILE 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 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: 1.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 127 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.180552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104295 restraints weight = 12686.593| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.73 r_work: 0.3123 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11091 Z= 0.153 Angle : 0.546 8.002 15073 Z= 0.276 Chirality : 0.040 0.154 1807 Planarity : 0.003 0.051 1909 Dihedral : 8.026 79.906 1608 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 2.82 % Allowed : 19.56 % Favored : 77.62 % 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 (0.22), residues: 1441 helix: 1.59 (0.18), residues: 853 sheet: -0.53 (0.53), residues: 109 loop : -0.97 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.025 0.001 TYR A 381 PHE 0.021 0.001 PHE A 392 TRP 0.007 0.001 TRP C 32 HIS 0.002 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (11091) covalent geometry : angle 0.54555 / 0.28 (15073) hydrogen bonds : bond 0.04426 / 3.06 ( 639) hydrogen bonds : angle 4.19694 / 3.06 ( 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 132 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 501 MET cc_start: 0.8850 (mmp) cc_final: 0.8430 (mmp) REVERT: B 77 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7354 (tm) REVERT: B 140 ILE cc_start: 0.2611 (OUTLIER) cc_final: 0.2227 (mp) REVERT: B 383 MET cc_start: 0.4010 (tpt) cc_final: 0.1993 (mmt) REVERT: B 457 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: B 535 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6852 (mmt) REVERT: C 31 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8590 (mm110) REVERT: C 161 LYS cc_start: 0.8200 (tttp) cc_final: 0.7683 (ttmp) outliers start: 32 outliers final: 16 residues processed: 129 average time/residue: 0.4393 time to fit residues: 61.9383 Evaluate side-chains 117 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 313 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 457 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 607 ILE 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 113 SER 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: 1.9990 chunk 134 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN ** A 114 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 = 0.4102 r_free = 0.4102 target = 0.179477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.102917 restraints weight = 12781.423| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.77 r_work: 0.3067 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11091 Z= 0.171 Angle : 0.579 13.738 15073 Z= 0.290 Chirality : 0.041 0.177 1807 Planarity : 0.004 0.052 1909 Dihedral : 8.126 79.698 1608 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 2.29 % Allowed : 20.35 % 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: 0.79 (0.22), residues: 1441 helix: 1.50 (0.18), residues: 849 sheet: -0.48 (0.53), residues: 109 loop : -0.97 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 394 TYR 0.026 0.001 TYR A 381 PHE 0.020 0.001 PHE A 392 TRP 0.006 0.001 TRP B 40 HIS 0.002 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (11091) covalent geometry : angle 0.57948 / 0.29 (15073) hydrogen bonds : bond 0.04576 / 3.16 ( 639) hydrogen bonds : angle 4.24790 / 3.10 ( 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 124 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 501 MET cc_start: 0.8868 (mmp) cc_final: 0.8438 (mmp) REVERT: B 77 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7359 (tm) REVERT: B 383 MET cc_start: 0.3765 (tpt) cc_final: 0.1720 (mmt) REVERT: B 535 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6974 (mmt) REVERT: C 31 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8554 (mm110) REVERT: C 161 LYS cc_start: 0.8134 (tttp) cc_final: 0.7618 (ttmp) outliers start: 26 outliers final: 19 residues processed: 123 average time/residue: 0.4267 time to fit residues: 57.2516 Evaluate side-chains 119 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 506 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 193 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 607 ILE 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 113 SER 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: 0.7980 chunk 121 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 139 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.178884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105851 restraints weight = 12765.712| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.69 r_work: 0.3108 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2088 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= 0.141 Angle : 0.546 8.189 15073 Z= 0.275 Chirality : 0.040 0.153 1807 Planarity : 0.003 0.050 1909 Dihedral : 8.020 78.236 1608 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 2.11 % Allowed : 20.53 % 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: 0.87 (0.22), residues: 1441 helix: 1.58 (0.18), residues: 850 sheet: -0.49 (0.53), residues: 109 loop : -0.95 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 394 TYR 0.024 0.001 TYR A 381 PHE 0.016 0.001 PHE A 392 TRP 0.007 0.001 TRP B 40 HIS 0.002 0.001 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (11091) covalent geometry : angle 0.54570 / 0.28 (15073) hydrogen bonds : bond 0.04247 / 2.93 ( 639) hydrogen bonds : angle 4.17153 / 3.05 ( 1848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4132.06 seconds wall clock time: 70 minutes 49.15 seconds (4249.15 seconds total)