Starting phenix.real_space_refine on Thu Jul 2 21:11:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kck_22811/07_2026/7kck_22811.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kck_22811/07_2026/7kck_22811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kck_22811/07_2026/7kck_22811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kck_22811/07_2026/7kck_22811.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kck_22811/07_2026/7kck_22811.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kck_22811/07_2026/7kck_22811.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kck_22811/07_2026/7kck_22811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kck_22811/07_2026/7kck_22811.map" } resolution = 3.26 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= 0.003 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 425 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 6 5.49 5 Mg 2 5.21 5 S 43 5.16 5 C 6203 2.51 5 N 1710 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 9825 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4856 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 588} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4903 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 594} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.15, per 1000 atoms: 0.22 Number of scatterers: 9825 At special positions: 0 Unit cell: (94.424, 86.284, 131.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 43 16.00 P 6 15.00 Mg 2 11.99 O 1859 8.00 N 1710 7.00 C 6203 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: 0.99 Conformation dependent library (CDL) restraints added in 343.5 milliseconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 46.9% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.606A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.307A pdb=" N ARG A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 178 through 186 removed outlier: 3.663A pdb=" N ALA A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 removed outlier: 3.788A pdb=" N MET A 210 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 265 removed outlier: 4.004A pdb=" N LYS A 262 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLU A 263 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.670A pdb=" N HIS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 313 " --> pdb=" O TRP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 410 through 433 removed outlier: 3.927A pdb=" N LEU A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 455 removed outlier: 3.911A pdb=" N GLU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 443 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.636A pdb=" N ASP A 463 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.588A pdb=" N ARG A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 511 through 517 removed outlier: 3.587A pdb=" N GLU A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET A 517 " --> pdb=" O TYR A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 540 removed outlier: 3.846A pdb=" N LEU A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 removed outlier: 3.820A pdb=" N ILE A 554 " --> pdb=" O VAL A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 550 through 554' Processing helix chain 'A' and resid 575 through 590 removed outlier: 3.713A pdb=" N GLU A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 removed outlier: 4.090A pdb=" N HIS A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 removed outlier: 3.988A pdb=" N ALA A 635 " --> pdb=" O GLN A 631 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLN A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 removed outlier: 3.976A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 removed outlier: 3.859A pdb=" N ASP A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 699 removed outlier: 3.843A pdb=" N VAL A 690 " --> pdb=" O PRO A 686 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 691 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 698 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 110 through 134 removed outlier: 4.265A pdb=" N ARG B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 178 through 186 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.626A pdb=" N PHE B 264 " --> pdb=" O CYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.559A pdb=" N TYR B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 357 removed outlier: 3.591A pdb=" N SER B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 408 through 433 Processing helix chain 'B' and resid 433 through 455 removed outlier: 6.326A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.885A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 462 " --> pdb=" O GLN B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 489 removed outlier: 3.666A pdb=" N ARG B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 511 through 517 Processing helix chain 'B' and resid 518 through 520 No H-bonds generated for 'chain 'B' and resid 518 through 520' Processing helix chain 'B' and resid 531 through 540 Processing helix chain 'B' and resid 550 through 557 removed outlier: 3.812A pdb=" N VAL B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 590 removed outlier: 3.755A pdb=" N GLU B 580 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 624 removed outlier: 3.868A pdb=" N MET B 624 " --> pdb=" O HIS B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 639 removed outlier: 3.913A pdb=" N LEU B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 660 removed outlier: 3.885A pdb=" N ASN B 655 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 681 removed outlier: 3.538A pdb=" N GLN B 666 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 701 removed outlier: 3.561A pdb=" N VAL B 690 " --> pdb=" O PRO B 686 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY B 691 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 3.899A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 7.184A pdb=" N GLN A 91 " --> pdb=" O ILE B 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.997A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.997A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS B 88 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 331 removed outlier: 3.998A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU A 365 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 481 through 482 removed outlier: 3.550A pdb=" N GLU A 471 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR A 498 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N CYS A 527 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 500 " --> pdb=" O CYS A 527 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 597 through 599 removed outlier: 6.163A pdb=" N LYS A 598 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 333 removed outlier: 3.555A pdb=" N TYR B 327 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA B 364 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N SER B 393 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR B 366 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 481 through 482 removed outlier: 4.086A pdb=" N GLU B 471 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N LEU B 525 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR B 498 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N CYS B 527 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 500 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 499 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 597 through 599 removed outlier: 6.573A pdb=" N LYS B 598 " --> pdb=" O ILE B 644 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1290 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: 1.85 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: 1.23 - 1.34: 3248 1.34 - 1.46: 2033 1.46 - 1.58: 4626 1.58 - 1.69: 10 1.69 - 1.81: 78 Bond restraints: 9995 Sorted by residual: bond pdb=" O3A ANP A 803 " pdb=" PB ANP A 803 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" O3A ANP B 803 " pdb=" PB ANP B 803 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" N3B ANP B 803 " pdb=" PG ANP B 803 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" N3B ANP A 803 " pdb=" PG ANP A 803 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" O5' ANP A 803 " pdb=" PA ANP A 803 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 9990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 13395 3.27 - 6.54: 83 6.54 - 9.80: 6 9.80 - 13.07: 2 13.07 - 16.34: 2 Bond angle restraints: 13488 Sorted by residual: angle pdb=" PB ANP A 803 " pdb=" N3B ANP A 803 " pdb=" PG ANP A 803 " ideal model delta sigma weight residual 126.95 110.61 16.34 3.00e+00 1.11e-01 2.97e+01 angle pdb=" PB ANP B 803 " pdb=" N3B ANP B 803 " pdb=" PG ANP B 803 " ideal model delta sigma weight residual 126.95 110.67 16.28 3.00e+00 1.11e-01 2.94e+01 angle pdb=" O1B ANP A 803 " pdb=" PB ANP A 803 " pdb=" O2B ANP A 803 " ideal model delta sigma weight residual 120.08 109.00 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N SER A 401 " pdb=" CA SER A 401 " pdb=" C SER A 401 " ideal model delta sigma weight residual 112.97 109.09 3.88 1.06e+00 8.90e-01 1.34e+01 angle pdb=" O1B ANP B 803 " pdb=" PB ANP B 803 " pdb=" O2B ANP B 803 " ideal model delta sigma weight residual 120.08 109.12 10.96 3.00e+00 1.11e-01 1.33e+01 ... (remaining 13483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5412 17.95 - 35.89: 558 35.89 - 53.84: 101 53.84 - 71.79: 22 71.79 - 89.74: 12 Dihedral angle restraints: 6105 sinusoidal: 2522 harmonic: 3583 Sorted by residual: dihedral pdb=" CA ALA A 608 " pdb=" C ALA A 608 " pdb=" N MET A 609 " pdb=" CA MET A 609 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LEU A 613 " pdb=" C LEU A 613 " pdb=" N GLU A 614 " pdb=" CA GLU A 614 " ideal model delta harmonic sigma weight residual -180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TYR B 277 " pdb=" C TYR B 277 " pdb=" N SER B 278 " pdb=" CA SER B 278 " ideal model delta harmonic sigma weight residual 180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 6102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1305 0.056 - 0.111: 192 0.111 - 0.167: 20 0.167 - 0.223: 0 0.223 - 0.279: 2 Chirality restraints: 1519 Sorted by residual: chirality pdb=" C3' ANP B 803 " pdb=" C2' ANP B 803 " pdb=" C4' ANP B 803 " pdb=" O3' ANP B 803 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' ANP A 803 " pdb=" C2' ANP A 803 " pdb=" C4' ANP A 803 " pdb=" O3' ANP A 803 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ASP B 378 " pdb=" N ASP B 378 " pdb=" C ASP B 378 " pdb=" CB ASP B 378 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 1516 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 511 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO A 512 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 685 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO B 686 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 686 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 686 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 475 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 476 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 476 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 476 " -0.020 5.00e-02 4.00e+02 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.63: 136 2.63 - 3.26: 10282 3.26 - 3.89: 19847 3.89 - 4.51: 27225 4.51 - 5.14: 41830 Nonbonded interactions: 99320 Sorted by model distance: nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 801 " model vdw 2.008 2.170 nonbonded pdb="MG MG A 801 " pdb=" O3G ANP A 803 " model vdw 2.009 2.170 nonbonded pdb="MG MG B 801 " pdb=" O3G ANP B 803 " model vdw 2.013 2.170 nonbonded pdb=" OD1 ASN A 119 " pdb="MG MG A 801 " model vdw 2.038 2.170 nonbonded pdb=" O1B ANP A 803 " pdb=" O2A ANP A 803 " model vdw 2.161 3.040 ... (remaining 99315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 70 through 554 or resid 573 through 626 or resid 631 throu \ gh 803)) selection = (chain 'B' and (resid 70 through 351 or resid 363 through 554 or resid 573 throu \ gh 803)) } 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.310 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.004 0.144 9995 Z= 0.205 Angle : 0.657 16.340 13488 Z= 0.326 Chirality : 0.041 0.279 1519 Planarity : 0.004 0.071 1714 Dihedral : 15.175 89.736 3777 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.09 % Allowed : 0.56 % Favored : 99.34 % 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 (0.25), residues: 1206 helix: 0.40 (0.24), residues: 495 sheet: 0.30 (0.41), residues: 182 loop : -0.90 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 412 TYR 0.009 0.001 TYR B 218 PHE 0.016 0.001 PHE B 531 TRP 0.008 0.001 TRP A 299 HIS 0.002 0.000 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 ( 9995) covalent geometry : angle 0.65679 / 0.33 (13488) hydrogen bonds : bond 0.24540 / 16.82 ( 440) hydrogen bonds : angle 8.41919 / 6.00 ( 1290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.388 Fit side-chains REVERT: A 699 LYS cc_start: 0.7914 (ptpt) cc_final: 0.7120 (tptt) REVERT: B 290 ARG cc_start: 0.7154 (mmp-170) cc_final: 0.6926 (mmp-170) REVERT: B 348 MET cc_start: 0.7744 (ppp) cc_final: 0.7443 (ppp) REVERT: B 537 LEU cc_start: 0.8798 (mt) cc_final: 0.8537 (mt) REVERT: B 677 MET cc_start: 0.8486 (mmt) cc_final: 0.8084 (mmt) outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.0992 time to fit residues: 18.9005 Evaluate side-chains 106 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.131532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102738 restraints weight = 15843.597| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.52 r_work: 0.3176 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9995 Z= 0.208 Angle : 0.633 9.298 13488 Z= 0.322 Chirality : 0.045 0.171 1519 Planarity : 0.004 0.053 1714 Dihedral : 5.448 58.237 1343 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.94 % Allowed : 10.83 % Favored : 88.23 % 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: -0.16 (0.24), residues: 1206 helix: 0.59 (0.24), residues: 504 sheet: 0.16 (0.40), residues: 177 loop : -0.81 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 593 TYR 0.018 0.002 TYR A 218 PHE 0.017 0.002 PHE A 441 TRP 0.009 0.002 TRP A 585 HIS 0.006 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 ( 9995) covalent geometry : angle 0.63269 / 0.32 (13488) hydrogen bonds : bond 0.03991 / 2.71 ( 440) hydrogen bonds : angle 5.45387 / 3.77 ( 1290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.363 Fit side-chains REVERT: A 349 LYS cc_start: 0.7599 (pttt) cc_final: 0.7117 (ptpp) REVERT: A 699 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7582 (tptt) REVERT: B 290 ARG cc_start: 0.7960 (mmp-170) cc_final: 0.7610 (mmp-170) REVERT: B 348 MET cc_start: 0.8346 (ppp) cc_final: 0.8111 (ppp) REVERT: B 352 MET cc_start: 0.7743 (tpp) cc_final: 0.7218 (mpp) REVERT: B 537 LEU cc_start: 0.8984 (mt) cc_final: 0.8635 (mt) REVERT: B 677 MET cc_start: 0.9023 (mmt) cc_final: 0.8445 (mpp) outliers start: 10 outliers final: 6 residues processed: 126 average time/residue: 0.0971 time to fit residues: 17.6128 Evaluate side-chains 104 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 36 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 530 GLN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 256 HIS ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.131151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.102819 restraints weight = 15736.815| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.53 r_work: 0.3186 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9995 Z= 0.159 Angle : 0.570 9.311 13488 Z= 0.291 Chirality : 0.043 0.187 1519 Planarity : 0.004 0.043 1714 Dihedral : 5.223 59.966 1342 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.51 % Allowed : 14.41 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1206 helix: 0.74 (0.24), residues: 506 sheet: 0.17 (0.40), residues: 168 loop : -0.83 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 634 TYR 0.012 0.001 TYR A 286 PHE 0.014 0.001 PHE A 441 TRP 0.011 0.001 TRP A 231 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 9995) covalent geometry : angle 0.57024 / 0.29 (13488) hydrogen bonds : bond 0.03602 / 2.44 ( 440) hydrogen bonds : angle 5.14518 / 3.53 ( 1290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.376 Fit side-chains REVERT: A 349 LYS cc_start: 0.7600 (pttt) cc_final: 0.7121 (ptpp) REVERT: A 583 MET cc_start: 0.6426 (tpp) cc_final: 0.5970 (tpp) REVERT: A 597 VAL cc_start: 0.9039 (t) cc_final: 0.8693 (t) REVERT: A 699 LYS cc_start: 0.8187 (ptpt) cc_final: 0.7548 (tptt) REVERT: B 290 ARG cc_start: 0.7893 (mmp-170) cc_final: 0.7688 (mmp-170) REVERT: B 352 MET cc_start: 0.7855 (tpp) cc_final: 0.7407 (mpp) REVERT: B 537 LEU cc_start: 0.9006 (mt) cc_final: 0.8650 (mt) REVERT: B 598 LYS cc_start: 0.7775 (pptt) cc_final: 0.6939 (ptpp) REVERT: B 677 MET cc_start: 0.9028 (mmt) cc_final: 0.8533 (mpp) outliers start: 16 outliers final: 9 residues processed: 131 average time/residue: 0.0861 time to fit residues: 16.1289 Evaluate side-chains 113 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 613 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 14 optimal weight: 0.3980 chunk 93 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 39 optimal weight: 0.0270 chunk 8 optimal weight: 4.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 675 ASN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 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 = 0.3764 r_free = 0.3764 target = 0.134051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106013 restraints weight = 16019.472| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.54 r_work: 0.3223 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9995 Z= 0.107 Angle : 0.536 10.154 13488 Z= 0.270 Chirality : 0.041 0.181 1519 Planarity : 0.003 0.036 1714 Dihedral : 4.842 53.174 1342 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.22 % Allowed : 17.33 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.25), residues: 1206 helix: 1.06 (0.24), residues: 494 sheet: 0.27 (0.40), residues: 167 loop : -0.70 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 491 TYR 0.011 0.001 TYR B 344 PHE 0.014 0.001 PHE A 441 TRP 0.014 0.001 TRP A 231 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9995) covalent geometry : angle 0.53574 / 0.27 (13488) hydrogen bonds : bond 0.03058 / 2.07 ( 440) hydrogen bonds : angle 4.79757 / 3.30 ( 1290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.403 Fit side-chains REVERT: A 349 LYS cc_start: 0.7510 (pttt) cc_final: 0.7094 (ptpp) REVERT: A 597 VAL cc_start: 0.8978 (t) cc_final: 0.8739 (t) REVERT: A 699 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7585 (tptt) REVERT: B 290 ARG cc_start: 0.7825 (mmp-170) cc_final: 0.7392 (mmp-170) REVERT: B 340 ARG cc_start: 0.8295 (mmt-90) cc_final: 0.8081 (mmt180) REVERT: B 352 MET cc_start: 0.7933 (tpp) cc_final: 0.7417 (mpp) REVERT: B 537 LEU cc_start: 0.9003 (mt) cc_final: 0.8620 (mt) REVERT: B 598 LYS cc_start: 0.7697 (pptt) cc_final: 0.6944 (ptpt) REVERT: B 677 MET cc_start: 0.9006 (mmt) cc_final: 0.8523 (mpp) outliers start: 13 outliers final: 8 residues processed: 136 average time/residue: 0.0851 time to fit residues: 16.1150 Evaluate side-chains 121 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 114 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.099131 restraints weight = 15988.809| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.40 r_work: 0.3121 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9995 Z= 0.265 Angle : 0.647 9.430 13488 Z= 0.326 Chirality : 0.045 0.182 1519 Planarity : 0.004 0.035 1714 Dihedral : 5.446 57.207 1342 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.17 % Allowed : 18.64 % Favored : 79.19 % 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: -0.29 (0.24), residues: 1206 helix: 0.58 (0.23), residues: 528 sheet: -0.33 (0.38), residues: 171 loop : -0.87 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 593 TYR 0.014 0.002 TYR B 286 PHE 0.014 0.002 PHE A 239 TRP 0.011 0.002 TRP A 231 HIS 0.007 0.001 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.26 ( 9995) covalent geometry : angle 0.64734 / 0.33 (13488) hydrogen bonds : bond 0.03524 / 2.35 ( 440) hydrogen bonds : angle 5.14758 / 3.54 ( 1290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.365 Fit side-chains REVERT: A 313 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: A 349 LYS cc_start: 0.7739 (pttt) cc_final: 0.7266 (ptpp) REVERT: A 699 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7695 (tptt) REVERT: B 312 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7924 (mm-30) REVERT: B 537 LEU cc_start: 0.9009 (mt) cc_final: 0.8635 (mt) REVERT: B 598 LYS cc_start: 0.8072 (pptt) cc_final: 0.7210 (ptpt) REVERT: B 677 MET cc_start: 0.9038 (mmt) cc_final: 0.8503 (tpp) outliers start: 23 outliers final: 18 residues processed: 129 average time/residue: 0.0815 time to fit residues: 15.3247 Evaluate side-chains 123 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 683 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 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 = 0.3727 r_free = 0.3727 target = 0.131347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103202 restraints weight = 16014.132| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.46 r_work: 0.3190 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9995 Z= 0.119 Angle : 0.552 10.606 13488 Z= 0.279 Chirality : 0.042 0.189 1519 Planarity : 0.003 0.035 1714 Dihedral : 5.011 56.627 1342 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.07 % Allowed : 19.02 % Favored : 78.91 % 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: 0.02 (0.25), residues: 1206 helix: 0.88 (0.24), residues: 514 sheet: -0.13 (0.39), residues: 168 loop : -0.74 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 623 TYR 0.012 0.001 TYR B 206 PHE 0.011 0.001 PHE B 112 TRP 0.015 0.001 TRP A 231 HIS 0.003 0.001 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9995) covalent geometry : angle 0.55212 / 0.28 (13488) hydrogen bonds : bond 0.03000 / 2.02 ( 440) hydrogen bonds : angle 4.82287 / 3.32 ( 1290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.333 Fit side-chains REVERT: A 349 LYS cc_start: 0.7561 (pttt) cc_final: 0.7147 (ptpp) REVERT: A 699 LYS cc_start: 0.8223 (ptpt) cc_final: 0.7682 (tptt) REVERT: B 98 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9075 (mm) REVERT: B 312 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7888 (mm-30) REVERT: B 340 ARG cc_start: 0.8294 (mmt-90) cc_final: 0.8039 (mmt180) REVERT: B 352 MET cc_start: 0.7971 (tpp) cc_final: 0.7429 (mpp) REVERT: B 537 LEU cc_start: 0.9007 (mt) cc_final: 0.8629 (mt) REVERT: B 598 LYS cc_start: 0.7863 (pptt) cc_final: 0.7064 (ptpt) REVERT: B 677 MET cc_start: 0.9014 (mmt) cc_final: 0.8519 (mpp) REVERT: B 695 GLU cc_start: 0.7961 (pp20) cc_final: 0.7582 (pp20) outliers start: 22 outliers final: 13 residues processed: 133 average time/residue: 0.0872 time to fit residues: 16.7649 Evaluate side-chains 126 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 683 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 78 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 675 ASN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 GLN ** 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 = 0.3726 r_free = 0.3726 target = 0.131420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103599 restraints weight = 15921.067| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.51 r_work: 0.3183 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9995 Z= 0.125 Angle : 0.555 10.401 13488 Z= 0.281 Chirality : 0.042 0.186 1519 Planarity : 0.003 0.033 1714 Dihedral : 4.924 53.664 1342 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.26 % Allowed : 19.77 % Favored : 77.97 % 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: 0.06 (0.25), residues: 1206 helix: 0.94 (0.24), residues: 514 sheet: -0.15 (0.39), residues: 171 loop : -0.74 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 491 TYR 0.011 0.001 TYR B 206 PHE 0.022 0.001 PHE B 531 TRP 0.013 0.001 TRP A 231 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9995) covalent geometry : angle 0.55514 / 0.28 (13488) hydrogen bonds : bond 0.03017 / 2.04 ( 440) hydrogen bonds : angle 4.73990 / 3.26 ( 1290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.428 Fit side-chains REVERT: A 110 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: A 349 LYS cc_start: 0.7533 (pttt) cc_final: 0.7143 (ptpp) REVERT: A 583 MET cc_start: 0.5870 (mmt) cc_final: 0.5574 (tpp) REVERT: A 699 LYS cc_start: 0.8216 (ptpt) cc_final: 0.7703 (tptt) REVERT: B 98 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9070 (mm) REVERT: B 163 MET cc_start: 0.8883 (mtm) cc_final: 0.8561 (mtm) REVERT: B 352 MET cc_start: 0.8013 (tpp) cc_final: 0.7474 (mpp) REVERT: B 537 LEU cc_start: 0.9004 (mt) cc_final: 0.8624 (mt) REVERT: B 580 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7483 (mt-10) REVERT: B 598 LYS cc_start: 0.7916 (pptt) cc_final: 0.7104 (ptpt) REVERT: B 677 MET cc_start: 0.9020 (mmt) cc_final: 0.8561 (tpp) REVERT: B 695 GLU cc_start: 0.7918 (pp20) cc_final: 0.7538 (pp20) outliers start: 24 outliers final: 17 residues processed: 135 average time/residue: 0.1019 time to fit residues: 20.0085 Evaluate side-chains 126 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 683 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 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 = 0.3702 r_free = 0.3702 target = 0.129532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101456 restraints weight = 15930.311| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.43 r_work: 0.3159 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9995 Z= 0.140 Angle : 0.575 12.140 13488 Z= 0.288 Chirality : 0.042 0.190 1519 Planarity : 0.003 0.032 1714 Dihedral : 4.951 53.535 1342 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.17 % Allowed : 20.15 % Favored : 77.68 % 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: 0.05 (0.25), residues: 1206 helix: 0.92 (0.24), residues: 514 sheet: -0.06 (0.39), residues: 168 loop : -0.75 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 491 TYR 0.011 0.001 TYR B 206 PHE 0.018 0.001 PHE B 531 TRP 0.012 0.001 TRP A 231 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9995) covalent geometry : angle 0.57501 / 0.29 (13488) hydrogen bonds : bond 0.03034 / 2.05 ( 440) hydrogen bonds : angle 4.74585 / 3.27 ( 1290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: A 583 MET cc_start: 0.5948 (mmt) cc_final: 0.5681 (tpp) REVERT: A 699 LYS cc_start: 0.8201 (ptpt) cc_final: 0.7700 (tptt) REVERT: B 352 MET cc_start: 0.8029 (tpp) cc_final: 0.7494 (mpp) REVERT: B 537 LEU cc_start: 0.8965 (mt) cc_final: 0.8603 (mt) REVERT: B 580 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7426 (mt-10) REVERT: B 598 LYS cc_start: 0.7898 (pptt) cc_final: 0.7085 (ptpt) REVERT: B 677 MET cc_start: 0.9011 (mmt) cc_final: 0.8607 (tpp) REVERT: B 695 GLU cc_start: 0.7973 (pp20) cc_final: 0.7599 (pp20) outliers start: 23 outliers final: 19 residues processed: 130 average time/residue: 0.1022 time to fit residues: 19.0973 Evaluate side-chains 130 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 683 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 116 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 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 = 0.3707 r_free = 0.3707 target = 0.129904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102332 restraints weight = 15787.216| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.44 r_work: 0.3182 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9995 Z= 0.155 Angle : 0.584 10.375 13488 Z= 0.293 Chirality : 0.043 0.187 1519 Planarity : 0.003 0.031 1714 Dihedral : 4.997 53.020 1342 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.07 % Allowed : 20.43 % Favored : 77.50 % 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: -0.12 (0.25), residues: 1206 helix: 0.78 (0.24), residues: 525 sheet: -0.22 (0.39), residues: 171 loop : -0.86 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 491 TYR 0.010 0.001 TYR B 206 PHE 0.011 0.001 PHE B 112 TRP 0.012 0.001 TRP A 231 HIS 0.002 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 9995) covalent geometry : angle 0.58359 / 0.29 (13488) hydrogen bonds : bond 0.03074 / 2.08 ( 440) hydrogen bonds : angle 4.79877 / 3.31 ( 1290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8350 (pt0) REVERT: A 583 MET cc_start: 0.5985 (mmt) cc_final: 0.5643 (tpp) REVERT: A 699 LYS cc_start: 0.8221 (ptpt) cc_final: 0.7712 (tptt) REVERT: B 352 MET cc_start: 0.8022 (tpp) cc_final: 0.7451 (mpp) REVERT: B 537 LEU cc_start: 0.9007 (mt) cc_final: 0.8641 (mt) REVERT: B 580 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7447 (mt-10) REVERT: B 598 LYS cc_start: 0.7975 (pptt) cc_final: 0.7152 (ptpt) REVERT: B 677 MET cc_start: 0.8998 (mmt) cc_final: 0.8560 (tpp) REVERT: B 695 GLU cc_start: 0.7933 (pp20) cc_final: 0.7566 (pp20) outliers start: 22 outliers final: 18 residues processed: 128 average time/residue: 0.1067 time to fit residues: 19.4789 Evaluate side-chains 128 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 683 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 116 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 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 = 0.3741 r_free = 0.3741 target = 0.132617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.104683 restraints weight = 15721.682| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.42 r_work: 0.3213 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9995 Z= 0.114 Angle : 0.560 10.925 13488 Z= 0.280 Chirality : 0.042 0.191 1519 Planarity : 0.003 0.030 1714 Dihedral : 4.727 47.456 1342 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.51 % Allowed : 20.90 % Favored : 77.59 % 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: 0.08 (0.25), residues: 1206 helix: 0.97 (0.24), residues: 511 sheet: 0.01 (0.39), residues: 169 loop : -0.80 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 634 TYR 0.012 0.001 TYR A 218 PHE 0.012 0.001 PHE B 112 TRP 0.015 0.001 TRP A 231 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 9995) covalent geometry : angle 0.55958 / 0.28 (13488) hydrogen bonds : bond 0.02902 / 1.98 ( 440) hydrogen bonds : angle 4.64813 / 3.21 ( 1290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7386 (pttt) cc_final: 0.7037 (ptpp) REVERT: A 583 MET cc_start: 0.5909 (mmt) cc_final: 0.5546 (tpp) REVERT: A 623 ARG cc_start: 0.6863 (mtm110) cc_final: 0.6356 (ttp-110) REVERT: A 699 LYS cc_start: 0.8211 (ptpt) cc_final: 0.7878 (tptt) REVERT: B 352 MET cc_start: 0.8141 (tpp) cc_final: 0.7607 (mpp) REVERT: B 517 MET cc_start: 0.8571 (mmm) cc_final: 0.8088 (tpp) REVERT: B 537 LEU cc_start: 0.8971 (mt) cc_final: 0.8608 (mt) REVERT: B 580 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7466 (mt-10) REVERT: B 598 LYS cc_start: 0.7917 (pptt) cc_final: 0.6949 (ptpp) REVERT: B 677 MET cc_start: 0.9030 (mmt) cc_final: 0.8575 (tpp) outliers start: 16 outliers final: 15 residues processed: 131 average time/residue: 0.1070 time to fit residues: 19.8284 Evaluate side-chains 130 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 683 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 53 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 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 = 0.3722 r_free = 0.3722 target = 0.131067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103297 restraints weight = 15920.704| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.43 r_work: 0.3186 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9995 Z= 0.119 Angle : 0.568 10.775 13488 Z= 0.284 Chirality : 0.042 0.182 1519 Planarity : 0.003 0.030 1714 Dihedral : 4.682 45.587 1342 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.41 % Allowed : 20.90 % Favored : 77.68 % 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: 0.14 (0.25), residues: 1206 helix: 1.02 (0.24), residues: 510 sheet: -0.09 (0.39), residues: 178 loop : -0.71 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 623 TYR 0.014 0.001 TYR A 218 PHE 0.012 0.001 PHE B 112 TRP 0.013 0.001 TRP A 231 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9995) covalent geometry : angle 0.56838 / 0.28 (13488) hydrogen bonds : bond 0.02903 / 1.97 ( 440) hydrogen bonds : angle 4.60130 / 3.18 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2096.05 seconds wall clock time: 36 minutes 57.83 seconds (2217.83 seconds total)