Starting phenix.real_space_refine on Sun Aug 24 09:42:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yn1_39411/08_2025/8yn1_39411.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yn1_39411/08_2025/8yn1_39411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yn1_39411/08_2025/8yn1_39411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yn1_39411/08_2025/8yn1_39411.map" model { file = "/net/cci-nas-00/data/ceres_data/8yn1_39411/08_2025/8yn1_39411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yn1_39411/08_2025/8yn1_39411.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8627 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 62 5.16 5 C 7762 2.51 5 N 2047 2.21 5 O 2310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12186 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4720 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 21, 'TRANS': 558} Chain breaks: 1 Chain: "B" Number of atoms: 4149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4149 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 16, 'TRANS': 492} Chain breaks: 2 Chain: "C" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3251 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 391} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'APR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.42, per 1000 atoms: 0.20 Number of scatterers: 12186 At special positions: 0 Unit cell: (121.55, 110.5, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 5 15.00 O 2310 8.00 N 2047 7.00 C 7762 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 590.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 9 sheets defined 56.0% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 10 through 24 Processing helix chain 'A' and resid 87 through 98 removed outlier: 3.600A pdb=" N ASP A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 103 through 113 removed outlier: 3.592A pdb=" N SER A 113 " --> pdb=" O MET A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 140 removed outlier: 3.599A pdb=" N LEU A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 163 through 173 removed outlier: 3.536A pdb=" N SER A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 removed outlier: 5.640A pdb=" N MET A 193 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 194 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.739A pdb=" N VAL A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.827A pdb=" N VAL A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 246 Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.267A pdb=" N LEU A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 297 removed outlier: 3.926A pdb=" N PHE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.581A pdb=" N SER A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.946A pdb=" N ILE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 326 removed outlier: 3.614A pdb=" N LEU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 removed outlier: 4.031A pdb=" N THR A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 381 removed outlier: 3.638A pdb=" N GLN A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.892A pdb=" N LEU A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 415 through 441 Processing helix chain 'A' and resid 447 through 450 Processing helix chain 'A' and resid 451 through 476 Proline residue: A 467 - end of helix removed outlier: 3.683A pdb=" N HIS A 476 " --> pdb=" O ASN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.659A pdb=" N ARG A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 507 removed outlier: 3.744A pdb=" N ILE A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 removed outlier: 3.706A pdb=" N GLU A 551 " --> pdb=" O CYS A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 581 removed outlier: 3.724A pdb=" N VAL A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ARG A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'B' and resid 4 through 20 removed outlier: 3.637A pdb=" N GLY B 20 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 removed outlier: 4.222A pdb=" N SER B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 136 removed outlier: 5.119A pdb=" N THR B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.531A pdb=" N SER B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'B' and resid 192 through 196 Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.742A pdb=" N VAL B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 317 removed outlier: 3.874A pdb=" N MET B 293 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASN B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 334 through 360 removed outlier: 3.773A pdb=" N ILE B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER B 346 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 396 Proline residue: B 387 - end of helix Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.629A pdb=" N VAL B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 420 " --> pdb=" O TRP B 416 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 461 Processing helix chain 'B' and resid 466 through 489 removed outlier: 3.712A pdb=" N LYS B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 498 removed outlier: 3.588A pdb=" N LEU B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 515 removed outlier: 3.652A pdb=" N LYS B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 527 Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.680A pdb=" N TYR B 533 " --> pdb=" O TYR B 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 418 removed outlier: 3.686A pdb=" N GLU C 414 " --> pdb=" O PRO C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 422 Processing helix chain 'C' and resid 430 through 442 Processing helix chain 'C' and resid 444 through 458 Processing helix chain 'C' and resid 484 through 494 removed outlier: 3.515A pdb=" N ARG C 488 " --> pdb=" O HIS C 484 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 494 " --> pdb=" O LEU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 563 through 569 removed outlier: 3.623A pdb=" N ILE C 566 " --> pdb=" O PRO C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 596 Processing helix chain 'C' and resid 612 through 617 removed outlier: 4.252A pdb=" N GLN C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 648 Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.503A pdb=" N SER C 670 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 672 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 696 Processing helix chain 'C' and resid 714 through 720 Processing helix chain 'C' and resid 740 through 744 removed outlier: 3.595A pdb=" N LEU C 744 " --> pdb=" O ILE C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 767 removed outlier: 3.501A pdb=" N VAL C 764 " --> pdb=" O PRO C 761 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 767 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 784 removed outlier: 4.559A pdb=" N LEU C 781 " --> pdb=" O GLU C 777 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG C 784 " --> pdb=" O LEU C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 789 Processing helix chain 'C' and resid 803 through 808 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 35 removed outlier: 3.830A pdb=" N GLY A 121 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 179 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL A 274 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN A 181 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER A 276 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL A 183 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 61 removed outlier: 3.519A pdb=" N GLY B 144 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 218 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 87 removed outlier: 3.548A pdb=" N PHE B 106 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 182 removed outlier: 4.415A pdb=" N GLY B 181 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 428 through 429 Processing sheet with id=AA7, first strand: chain 'C' and resid 505 through 509 removed outlier: 6.815A pdb=" N LEU C 528 " --> pdb=" O VAL C 552 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ASN C 554 " --> pdb=" O LEU C 528 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE C 530 " --> pdb=" O ASN C 554 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU C 551 " --> pdb=" O THR C 576 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR C 578 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C 553 " --> pdb=" O THR C 578 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 575 " --> pdb=" O ARG C 603 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLU C 605 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 577 " --> pdb=" O GLU C 605 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 559 through 561 removed outlier: 6.395A pdb=" N ALA C 585 " --> pdb=" O SER C 608 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 749 through 751 removed outlier: 6.470A pdb=" N ILE C 750 " --> pdb=" O LYS C 773 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS C 774 " --> pdb=" O GLN C 795 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1629 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3758 1.34 - 1.45: 1949 1.45 - 1.57: 6633 1.57 - 1.69: 8 1.69 - 1.81: 94 Bond restraints: 12442 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.448 -0.060 1.00e-02 1.00e+04 3.64e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.332 0.055 1.00e-02 1.00e+04 3.07e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.463 -0.054 1.00e-02 1.00e+04 2.87e+01 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.55e+01 bond pdb=" O3A APR A 701 " pdb=" PA APR A 701 " ideal model delta sigma weight residual 1.648 1.573 0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 12437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 16573 3.01 - 6.01: 199 6.01 - 9.02: 23 9.02 - 12.02: 2 12.02 - 15.03: 2 Bond angle restraints: 16799 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 124.84 15.03 1.00e+00 1.00e+00 2.26e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 123.12 13.71 1.00e+00 1.00e+00 1.88e+02 angle pdb=" C5 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 126.80 119.28 7.52 1.00e+00 1.00e+00 5.66e+01 angle pdb=" N3 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 127.04 134.78 -7.74 1.15e+00 7.59e-01 4.54e+01 angle pdb=" N1 ATP B 601 " pdb=" C2 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 128.69 122.80 5.89 1.00e+00 1.00e+00 3.47e+01 ... (remaining 16794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6771 17.91 - 35.82: 663 35.82 - 53.73: 128 53.73 - 71.63: 17 71.63 - 89.54: 19 Dihedral angle restraints: 7598 sinusoidal: 3204 harmonic: 4394 Sorted by residual: dihedral pdb=" CA HIS A 122 " pdb=" C HIS A 122 " pdb=" N SER A 123 " pdb=" CA SER A 123 " ideal model delta harmonic sigma weight residual -180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ALA B 145 " pdb=" C ALA B 145 " pdb=" N ALA B 146 " pdb=" CA ALA B 146 " ideal model delta harmonic sigma weight residual -180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ILE B 163 " pdb=" C ILE B 163 " pdb=" N GLU B 164 " pdb=" CA GLU B 164 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 7595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1243 0.049 - 0.097: 497 0.097 - 0.146: 108 0.146 - 0.195: 7 0.195 - 0.243: 1 Chirality restraints: 1856 Sorted by residual: chirality pdb=" CB VAL B 317 " pdb=" CA VAL B 317 " pdb=" CG1 VAL B 317 " pdb=" CG2 VAL B 317 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR B 162 " pdb=" CA THR B 162 " pdb=" OG1 THR B 162 " pdb=" CG2 THR B 162 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.52 -0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 1853 not shown) Planarity restraints: 2127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 406 " -0.025 2.00e-02 2.50e+03 3.18e-02 2.03e+01 pdb=" CG TYR A 406 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR A 406 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR A 406 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 406 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 406 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 406 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 406 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 321 " -0.011 2.00e-02 2.50e+03 1.97e-02 7.74e+00 pdb=" CG TYR B 321 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 321 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 321 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 321 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 321 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 321 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 321 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 560 " 0.013 2.00e-02 2.50e+03 1.69e-02 5.70e+00 pdb=" CG TYR A 560 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 560 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 560 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 560 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 560 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 560 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 560 " -0.004 2.00e-02 2.50e+03 ... (remaining 2124 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 313 2.70 - 3.25: 11846 3.25 - 3.80: 18253 3.80 - 4.35: 24679 4.35 - 4.90: 41059 Nonbonded interactions: 96150 Sorted by model distance: nonbonded pdb=" O LEU B 189 " pdb=" ND2 ASN B 195 " model vdw 2.145 3.120 nonbonded pdb=" O GLU A 322 " pdb=" OG SER A 326 " model vdw 2.175 3.040 nonbonded pdb=" O LEU B 160 " pdb=" NH1 ARG B 194 " model vdw 2.180 3.120 nonbonded pdb=" O LEU C 511 " pdb=" OG1 THR C 514 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP A 187 " pdb=" OH TYR A 320 " model vdw 2.216 3.040 ... (remaining 96145 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.110 Find NCS groups from input model: 0.070 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.008 0.075 12443 Z= 0.369 Angle : 0.911 15.030 16799 Z= 0.527 Chirality : 0.051 0.243 1856 Planarity : 0.006 0.053 2127 Dihedral : 15.153 89.542 4742 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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 aren not related in a simple way. whole: -1.49 (0.20), residues: 1483 helix: -0.50 (0.19), residues: 719 sheet: -0.11 (0.40), residues: 175 loop : -1.79 (0.23), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 784 TYR 0.074 0.004 TYR A 406 PHE 0.022 0.003 PHE A 548 TRP 0.012 0.002 TRP B 352 HIS 0.008 0.002 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00831 (12442) covalent geometry : angle 0.91134 (16799) hydrogen bonds : bond 0.19472 ( 588) hydrogen bonds : angle 6.58428 ( 1629) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.315 Fit side-chains REVERT: A 144 ASN cc_start: 0.7886 (p0) cc_final: 0.7625 (p0) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1255 time to fit residues: 28.4546 Evaluate side-chains 145 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN B 33 HIS B 457 GLN C 483 GLN C 795 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.165831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.138199 restraints weight = 15148.934| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.06 r_work: 0.3166 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12443 Z= 0.167 Angle : 0.608 6.493 16799 Z= 0.327 Chirality : 0.043 0.143 1856 Planarity : 0.005 0.042 2127 Dihedral : 7.455 75.554 1699 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.88 % Allowed : 5.66 % Favored : 93.46 % 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 aren not related in a simple way. whole: -0.72 (0.21), residues: 1483 helix: 0.26 (0.19), residues: 716 sheet: 0.31 (0.40), residues: 175 loop : -1.60 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 784 TYR 0.035 0.002 TYR A 406 PHE 0.015 0.002 PHE A 548 TRP 0.013 0.001 TRP B 352 HIS 0.006 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00376 (12442) covalent geometry : angle 0.60793 (16799) hydrogen bonds : bond 0.06894 ( 588) hydrogen bonds : angle 4.98013 ( 1629) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.498 Fit side-chains REVERT: A 427 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7907 (mt-10) REVERT: B 362 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7623 (ttt180) REVERT: C 616 GLN cc_start: 0.6236 (mm-40) cc_final: 0.5076 (pt0) REVERT: C 739 GLN cc_start: 0.7357 (mp10) cc_final: 0.7135 (mm-40) outliers start: 12 outliers final: 6 residues processed: 166 average time/residue: 0.1245 time to fit residues: 28.4773 Evaluate side-chains 152 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 478 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 0.0370 chunk 98 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 333 ASN B 33 HIS B 195 ASN B 457 GLN C 795 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.171191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143270 restraints weight = 15333.020| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.97 r_work: 0.3284 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12443 Z= 0.106 Angle : 0.488 6.993 16799 Z= 0.264 Chirality : 0.040 0.129 1856 Planarity : 0.004 0.046 2127 Dihedral : 6.294 83.172 1699 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.96 % Allowed : 8.01 % Favored : 91.04 % 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 aren not related in a simple way. whole: -0.17 (0.21), residues: 1483 helix: 0.77 (0.20), residues: 718 sheet: 0.60 (0.39), residues: 178 loop : -1.44 (0.22), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 784 TYR 0.016 0.001 TYR A 406 PHE 0.017 0.001 PHE B 290 TRP 0.013 0.001 TRP B 352 HIS 0.006 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00205 (12442) covalent geometry : angle 0.48833 (16799) hydrogen bonds : bond 0.04667 ( 588) hydrogen bonds : angle 4.46217 ( 1629) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 HIS cc_start: 0.7521 (t-90) cc_final: 0.6973 (t70) REVERT: A 246 GLU cc_start: 0.6486 (pt0) cc_final: 0.6258 (pt0) outliers start: 13 outliers final: 6 residues processed: 164 average time/residue: 0.1101 time to fit residues: 25.0264 Evaluate side-chains 138 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 780 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 476 HIS B 33 HIS C 795 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.168769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140917 restraints weight = 15134.288| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.06 r_work: 0.3209 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12443 Z= 0.125 Angle : 0.516 6.419 16799 Z= 0.275 Chirality : 0.041 0.144 1856 Planarity : 0.004 0.046 2127 Dihedral : 6.491 83.610 1699 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.03 % Allowed : 9.85 % Favored : 89.13 % 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 aren not related in a simple way. whole: 0.05 (0.21), residues: 1483 helix: 0.92 (0.20), residues: 718 sheet: 0.77 (0.39), residues: 188 loop : -1.34 (0.23), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 100 TYR 0.024 0.001 TYR A 406 PHE 0.012 0.001 PHE A 548 TRP 0.009 0.001 TRP B 352 HIS 0.006 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00270 (12442) covalent geometry : angle 0.51616 (16799) hydrogen bonds : bond 0.05385 ( 588) hydrogen bonds : angle 4.41673 ( 1629) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 HIS cc_start: 0.7543 (t-90) cc_final: 0.6975 (t70) REVERT: A 246 GLU cc_start: 0.6696 (pt0) cc_final: 0.6364 (pt0) REVERT: C 671 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: C 748 LYS cc_start: 0.6915 (mmtt) cc_final: 0.6529 (mmmt) REVERT: C 798 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6858 (pt0) outliers start: 14 outliers final: 10 residues processed: 159 average time/residue: 0.1279 time to fit residues: 28.0757 Evaluate side-chains 148 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 780 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 37 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 333 ASN B 33 HIS B 457 GLN C 795 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.168322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141686 restraints weight = 15233.756| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.13 r_work: 0.3207 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12443 Z= 0.123 Angle : 0.507 6.344 16799 Z= 0.271 Chirality : 0.040 0.132 1856 Planarity : 0.004 0.046 2127 Dihedral : 6.471 84.420 1699 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.62 % Allowed : 10.43 % Favored : 87.95 % 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 aren not related in a simple way. whole: 0.15 (0.22), residues: 1483 helix: 0.98 (0.20), residues: 721 sheet: 0.84 (0.39), residues: 188 loop : -1.27 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 100 TYR 0.021 0.001 TYR A 406 PHE 0.019 0.001 PHE B 290 TRP 0.010 0.001 TRP B 352 HIS 0.005 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00266 (12442) covalent geometry : angle 0.50748 (16799) hydrogen bonds : bond 0.05315 ( 588) hydrogen bonds : angle 4.38775 ( 1629) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 206 HIS cc_start: 0.7596 (t-90) cc_final: 0.7064 (t70) REVERT: A 246 GLU cc_start: 0.6705 (pt0) cc_final: 0.6411 (pt0) REVERT: B 457 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: C 489 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6857 (tm-30) REVERT: C 671 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: C 748 LYS cc_start: 0.6939 (mmtt) cc_final: 0.6555 (mmmt) REVERT: C 798 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6897 (pt0) outliers start: 22 outliers final: 14 residues processed: 163 average time/residue: 0.1355 time to fit residues: 30.3382 Evaluate side-chains 158 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 780 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 45 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 121 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 333 ASN B 33 HIS B 457 GLN C 471 HIS C 795 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.168743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.141872 restraints weight = 15179.183| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.10 r_work: 0.3207 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12443 Z= 0.120 Angle : 0.504 6.403 16799 Z= 0.268 Chirality : 0.040 0.134 1856 Planarity : 0.004 0.047 2127 Dihedral : 6.439 84.638 1699 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.84 % Allowed : 11.02 % Favored : 87.14 % 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 aren not related in a simple way. whole: 0.23 (0.22), residues: 1483 helix: 1.02 (0.20), residues: 721 sheet: 0.91 (0.39), residues: 188 loop : -1.21 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 100 TYR 0.020 0.001 TYR A 406 PHE 0.012 0.001 PHE A 548 TRP 0.011 0.001 TRP B 352 HIS 0.005 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00258 (12442) covalent geometry : angle 0.50383 (16799) hydrogen bonds : bond 0.05242 ( 588) hydrogen bonds : angle 4.36525 ( 1629) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 206 HIS cc_start: 0.7600 (t-90) cc_final: 0.7057 (t70) REVERT: A 246 GLU cc_start: 0.6734 (pt0) cc_final: 0.6429 (pt0) REVERT: A 312 ARG cc_start: 0.7982 (ttt-90) cc_final: 0.7769 (ttt-90) REVERT: C 489 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6879 (tm-30) REVERT: C 671 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: C 748 LYS cc_start: 0.6924 (mmtt) cc_final: 0.6539 (mmmt) REVERT: C 798 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6895 (pt0) outliers start: 25 outliers final: 20 residues processed: 162 average time/residue: 0.1400 time to fit residues: 31.2620 Evaluate side-chains 161 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 780 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 67 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 333 ASN B 33 HIS B 457 GLN C 795 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.170040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143989 restraints weight = 15143.543| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.95 r_work: 0.3263 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12443 Z= 0.107 Angle : 0.486 6.437 16799 Z= 0.259 Chirality : 0.039 0.131 1856 Planarity : 0.004 0.047 2127 Dihedral : 6.277 84.535 1699 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.69 % Allowed : 11.39 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.22), residues: 1483 helix: 1.14 (0.20), residues: 720 sheet: 0.89 (0.39), residues: 190 loop : -1.14 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 100 TYR 0.016 0.001 TYR A 406 PHE 0.021 0.001 PHE B 290 TRP 0.012 0.001 TRP B 352 HIS 0.004 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00218 (12442) covalent geometry : angle 0.48617 (16799) hydrogen bonds : bond 0.04807 ( 588) hydrogen bonds : angle 4.29800 ( 1629) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 206 HIS cc_start: 0.7588 (t-90) cc_final: 0.7099 (t70) REVERT: A 246 GLU cc_start: 0.6496 (pt0) cc_final: 0.6219 (pt0) REVERT: A 327 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7853 (ttt) REVERT: C 489 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6854 (tm-30) REVERT: C 671 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.6458 (mp0) REVERT: C 748 LYS cc_start: 0.6839 (mmtt) cc_final: 0.6468 (mmmt) REVERT: C 798 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6946 (pt0) outliers start: 23 outliers final: 18 residues processed: 160 average time/residue: 0.1255 time to fit residues: 27.4644 Evaluate side-chains 157 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 780 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 127 optimal weight: 0.0870 chunk 134 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 285 ASN A 333 ASN B 33 HIS C 795 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.170334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.143381 restraints weight = 15206.104| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.98 r_work: 0.3258 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12443 Z= 0.105 Angle : 0.481 6.587 16799 Z= 0.256 Chirality : 0.039 0.131 1856 Planarity : 0.004 0.047 2127 Dihedral : 6.191 84.313 1699 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.62 % Allowed : 11.39 % Favored : 86.99 % 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 aren not related in a simple way. whole: 0.47 (0.22), residues: 1483 helix: 1.20 (0.20), residues: 720 sheet: 1.03 (0.39), residues: 190 loop : -1.07 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 100 TYR 0.015 0.001 TYR A 406 PHE 0.011 0.001 PHE A 548 TRP 0.012 0.001 TRP B 352 HIS 0.004 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00212 (12442) covalent geometry : angle 0.48083 (16799) hydrogen bonds : bond 0.04654 ( 588) hydrogen bonds : angle 4.26275 ( 1629) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 206 HIS cc_start: 0.7613 (t-90) cc_final: 0.7081 (t70) REVERT: A 246 GLU cc_start: 0.6451 (pt0) cc_final: 0.6208 (pt0) REVERT: A 327 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7867 (ttt) REVERT: C 489 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6891 (tm-30) REVERT: C 671 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: C 748 LYS cc_start: 0.6808 (mmtt) cc_final: 0.6438 (mmmt) REVERT: C 798 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6980 (pt0) outliers start: 22 outliers final: 17 residues processed: 155 average time/residue: 0.1131 time to fit residues: 24.3880 Evaluate side-chains 155 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 780 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 285 ASN A 333 ASN C 795 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.166437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.139502 restraints weight = 15075.220| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.10 r_work: 0.3180 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12443 Z= 0.174 Angle : 0.578 6.939 16799 Z= 0.305 Chirality : 0.043 0.155 1856 Planarity : 0.004 0.043 2127 Dihedral : 6.836 84.462 1699 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.69 % Allowed : 11.39 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.22), residues: 1483 helix: 0.97 (0.20), residues: 721 sheet: 1.05 (0.39), residues: 188 loop : -1.14 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 100 TYR 0.026 0.002 TYR A 406 PHE 0.022 0.002 PHE B 290 TRP 0.009 0.001 TRP B 158 HIS 0.008 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00407 (12442) covalent geometry : angle 0.57850 (16799) hydrogen bonds : bond 0.06373 ( 588) hydrogen bonds : angle 4.50910 ( 1629) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 206 HIS cc_start: 0.7637 (t-90) cc_final: 0.7100 (t70) REVERT: A 246 GLU cc_start: 0.6862 (pt0) cc_final: 0.6525 (pt0) REVERT: A 327 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7926 (ttt) REVERT: C 489 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6895 (tm-30) REVERT: C 671 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: C 748 LYS cc_start: 0.6923 (mmtt) cc_final: 0.6504 (mmmt) REVERT: C 798 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6933 (pt0) outliers start: 23 outliers final: 16 residues processed: 161 average time/residue: 0.1191 time to fit residues: 26.7251 Evaluate side-chains 159 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 780 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 129 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 chunk 46 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 285 ASN A 333 ASN B 33 HIS B 457 GLN C 795 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.169456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143083 restraints weight = 15160.025| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.94 r_work: 0.3292 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12443 Z= 0.110 Angle : 0.496 6.354 16799 Z= 0.264 Chirality : 0.040 0.131 1856 Planarity : 0.004 0.051 2127 Dihedral : 6.336 85.105 1699 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.54 % Allowed : 11.68 % Favored : 86.77 % 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 aren not related in a simple way. whole: 0.47 (0.22), residues: 1483 helix: 1.17 (0.20), residues: 720 sheet: 1.05 (0.39), residues: 190 loop : -1.04 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 100 TYR 0.015 0.001 TYR A 406 PHE 0.010 0.001 PHE A 548 TRP 0.013 0.001 TRP B 352 HIS 0.005 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00228 (12442) covalent geometry : angle 0.49584 (16799) hydrogen bonds : bond 0.04896 ( 588) hydrogen bonds : angle 4.32251 ( 1629) Misc. bond : bond 0.00010 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.448 Fit side-chains REVERT: A 206 HIS cc_start: 0.7787 (t-90) cc_final: 0.7344 (t70) REVERT: A 246 GLU cc_start: 0.6811 (pt0) cc_final: 0.6586 (pt0) REVERT: A 320 TYR cc_start: 0.8228 (m-80) cc_final: 0.7725 (m-80) REVERT: A 327 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7836 (ttt) REVERT: C 671 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: C 748 LYS cc_start: 0.6951 (mmtt) cc_final: 0.6650 (mmmt) REVERT: C 798 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7101 (pt0) outliers start: 21 outliers final: 16 residues processed: 150 average time/residue: 0.1181 time to fit residues: 24.5891 Evaluate side-chains 150 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 543 MET Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 671 GLU Chi-restraints excluded: chain C residue 780 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 285 ASN A 333 ASN B 457 GLN C 795 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.167632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.140949 restraints weight = 15098.156| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.93 r_work: 0.3281 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12443 Z= 0.146 Angle : 0.543 6.416 16799 Z= 0.287 Chirality : 0.041 0.161 1856 Planarity : 0.004 0.044 2127 Dihedral : 6.557 85.068 1699 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.47 % Allowed : 11.76 % Favored : 86.77 % 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 aren not related in a simple way. whole: 0.40 (0.22), residues: 1483 helix: 1.08 (0.20), residues: 720 sheet: 1.08 (0.39), residues: 188 loop : -1.06 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 100 TYR 0.022 0.002 TYR A 406 PHE 0.023 0.002 PHE B 290 TRP 0.009 0.001 TRP B 352 HIS 0.007 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00333 (12442) covalent geometry : angle 0.54337 (16799) hydrogen bonds : bond 0.05691 ( 588) hydrogen bonds : angle 4.40179 ( 1629) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2487.87 seconds wall clock time: 43 minutes 23.49 seconds (2603.49 seconds total)