Starting phenix.real_space_refine on Wed Mar 4 02:56:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kck_22811/03_2026/7kck_22811.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kck_22811/03_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_22811/03_2026/7kck_22811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kck_22811/03_2026/7kck_22811.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kck_22811/03_2026/7kck_22811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kck_22811/03_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-5986/lib/python3.9/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: 2.31, per 1000 atoms: 0.24 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: 0.74 Conformation dependent library (CDL) restraints added in 396.9 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: 0.44 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: 1.51 Time building geometry restraints manager: 1.02 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: 5462 17.95 - 35.89: 558 35.89 - 53.84: 106 53.84 - 71.79: 23 71.79 - 89.74: 12 Dihedral angle restraints: 6161 sinusoidal: 2578 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 6158 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.010 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 15.215 89.736 3833 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 covalent geometry : bond 0.00410 ( 9995) covalent geometry : angle 0.65679 (13488) hydrogen bonds : bond 0.24540 ( 440) hydrogen bonds : angle 8.41919 ( 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 : 0.415 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: 0.0943 time to fit residues: 17.8234 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 : 0.393 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3729 r_free = 0.3729 target = 0.131193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102702 restraints weight = 15778.713| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.49 r_work: 0.3170 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9995 Z= 0.208 Angle : 0.636 9.469 13488 Z= 0.324 Chirality : 0.045 0.172 1519 Planarity : 0.004 0.052 1714 Dihedral : 6.071 59.372 1399 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 10.00 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: -0.17 (0.24), residues: 1206 helix: 0.58 (0.24), residues: 504 sheet: 0.15 (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 A 634 TYR 0.018 0.002 TYR A 218 PHE 0.017 0.002 PHE A 441 TRP 0.009 0.002 TRP A 299 HIS 0.006 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 9995) covalent geometry : angle 0.63606 (13488) hydrogen bonds : bond 0.03871 ( 440) hydrogen bonds : angle 5.41553 ( 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 133 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7617 (pttt) cc_final: 0.7128 (ptpp) REVERT: A 699 LYS cc_start: 0.8181 (ptpt) cc_final: 0.7593 (tptt) REVERT: B 290 ARG cc_start: 0.7968 (mmp-170) cc_final: 0.7618 (mmp-170) REVERT: B 352 MET cc_start: 0.7784 (tpp) cc_final: 0.7274 (mpp) REVERT: B 531 PHE cc_start: 0.8471 (m-10) cc_final: 0.8111 (m-10) REVERT: B 537 LEU cc_start: 0.8978 (mt) cc_final: 0.8622 (mt) REVERT: B 554 ILE cc_start: 0.8569 (mm) cc_final: 0.8321 (mm) REVERT: B 598 LYS cc_start: 0.7801 (pptt) cc_final: 0.6918 (ptpp) REVERT: B 677 MET cc_start: 0.9017 (mmt) cc_final: 0.8410 (mpp) outliers start: 10 outliers final: 6 residues processed: 128 average time/residue: 0.1008 time to fit residues: 18.5160 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 : 0.389 ------------------------------------------------------------------------------- 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: 6.9990 chunk 32 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3744 r_free = 0.3744 target = 0.132490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104338 restraints weight = 15832.316| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.39 r_work: 0.3204 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2010 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= 0.137 Angle : 0.555 9.420 13488 Z= 0.283 Chirality : 0.042 0.185 1519 Planarity : 0.004 0.042 1714 Dihedral : 5.680 53.268 1398 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.32 % Allowed : 13.84 % Favored : 84.84 % 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: -0.03 (0.24), residues: 1206 helix: 0.76 (0.24), residues: 506 sheet: 0.26 (0.40), residues: 167 loop : -0.81 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 634 TYR 0.011 0.001 TYR B 206 PHE 0.013 0.001 PHE A 441 TRP 0.012 0.001 TRP A 231 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9995) covalent geometry : angle 0.55538 (13488) hydrogen bonds : bond 0.03529 ( 440) hydrogen bonds : angle 5.07159 ( 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: 14 poor density : 121 time to evaluate : 0.422 Fit side-chains REVERT: A 349 LYS cc_start: 0.7563 (pttt) cc_final: 0.7094 (ptpp) REVERT: A 583 MET cc_start: 0.6382 (tpp) cc_final: 0.5944 (tpp) REVERT: A 597 VAL cc_start: 0.9032 (t) cc_final: 0.8685 (t) REVERT: A 699 LYS cc_start: 0.8184 (ptpt) cc_final: 0.7407 (tptt) REVERT: B 290 ARG cc_start: 0.7878 (mmp-170) cc_final: 0.7526 (mmp-170) REVERT: B 352 MET cc_start: 0.7831 (tpp) cc_final: 0.7372 (mpp) REVERT: B 537 LEU cc_start: 0.9011 (mt) cc_final: 0.8651 (mt) REVERT: B 598 LYS cc_start: 0.7734 (pptt) cc_final: 0.6890 (ptpp) REVERT: B 677 MET cc_start: 0.9028 (mmt) cc_final: 0.8574 (mpp) outliers start: 14 outliers final: 8 residues processed: 132 average time/residue: 0.1049 time to fit residues: 19.8083 Evaluate side-chains 113 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 14 optimal weight: 0.0000 chunk 93 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 39 optimal weight: 0.0770 chunk 8 optimal weight: 4.9990 overall best weight: 0.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3760 r_free = 0.3760 target = 0.133804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105531 restraints weight = 16019.580| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.49 r_work: 0.3221 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2164 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= 0.111 Angle : 0.539 9.746 13488 Z= 0.272 Chirality : 0.041 0.180 1519 Planarity : 0.003 0.037 1714 Dihedral : 5.405 47.353 1398 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.32 % Allowed : 16.38 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1206 helix: 1.07 (0.24), residues: 494 sheet: 0.32 (0.41), residues: 167 loop : -0.69 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 491 TYR 0.012 0.001 TYR B 344 PHE 0.011 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 covalent geometry : bond 0.00256 ( 9995) covalent geometry : angle 0.53935 (13488) hydrogen bonds : bond 0.03068 ( 440) hydrogen bonds : angle 4.79212 ( 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 137 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7492 (pttt) cc_final: 0.7081 (ptpp) REVERT: A 597 VAL cc_start: 0.8997 (t) cc_final: 0.8760 (t) REVERT: A 699 LYS cc_start: 0.8179 (ptpt) cc_final: 0.7582 (tptt) REVERT: B 290 ARG cc_start: 0.7852 (mmp-170) cc_final: 0.7421 (mmp-170) REVERT: B 352 MET cc_start: 0.7895 (tpp) cc_final: 0.7366 (mpp) REVERT: B 537 LEU cc_start: 0.9002 (mt) cc_final: 0.8623 (mt) REVERT: B 598 LYS cc_start: 0.7696 (pptt) cc_final: 0.6876 (ptpp) REVERT: B 677 MET cc_start: 0.9012 (mmt) cc_final: 0.8538 (mpp) outliers start: 14 outliers final: 9 residues processed: 134 average time/residue: 0.1003 time to fit residues: 19.0937 Evaluate side-chains 123 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 273 VAL 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: 4.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3670 r_free = 0.3670 target = 0.126932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.098496 restraints weight = 16036.476| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.47 r_work: 0.3119 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 9995 Z= 0.276 Angle : 0.657 9.076 13488 Z= 0.331 Chirality : 0.046 0.184 1519 Planarity : 0.004 0.035 1714 Dihedral : 6.114 56.608 1398 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.17 % Allowed : 18.55 % Favored : 79.28 % 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: -0.27 (0.24), residues: 1206 helix: 0.59 (0.23), residues: 528 sheet: -0.30 (0.39), residues: 171 loop : -0.88 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 491 TYR 0.015 0.002 TYR B 286 PHE 0.015 0.002 PHE B 531 TRP 0.012 0.002 TRP A 299 HIS 0.005 0.001 HIS B 538 Details of bonding type rmsd covalent geometry : bond 0.00651 ( 9995) covalent geometry : angle 0.65651 (13488) hydrogen bonds : bond 0.03561 ( 440) hydrogen bonds : angle 5.13992 ( 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 133 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.391 Fit side-chains REVERT: A 286 TYR cc_start: 0.8364 (m-80) cc_final: 0.8159 (m-80) REVERT: A 349 LYS cc_start: 0.7711 (pttt) cc_final: 0.7235 (ptpp) REVERT: A 699 LYS cc_start: 0.8203 (ptpt) cc_final: 0.7698 (tptt) REVERT: B 312 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7986 (mm-30) REVERT: B 537 LEU cc_start: 0.9006 (mt) cc_final: 0.8641 (mt) REVERT: B 598 LYS cc_start: 0.8079 (pptt) cc_final: 0.7216 (ptpt) REVERT: B 677 MET cc_start: 0.9043 (mmt) cc_final: 0.8517 (tpp) outliers start: 23 outliers final: 17 residues processed: 126 average time/residue: 0.1000 time to fit residues: 18.1954 Evaluate side-chains 120 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3725 r_free = 0.3725 target = 0.131306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.103503 restraints weight = 15947.430| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.46 r_work: 0.3191 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9995 Z= 0.117 Angle : 0.553 10.502 13488 Z= 0.279 Chirality : 0.042 0.184 1519 Planarity : 0.003 0.035 1714 Dihedral : 5.524 47.806 1398 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.07 % Allowed : 18.83 % Favored : 79.10 % 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: 0.03 (0.25), residues: 1206 helix: 0.86 (0.24), residues: 517 sheet: -0.06 (0.40), residues: 167 loop : -0.73 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 623 TYR 0.012 0.001 TYR B 206 PHE 0.011 0.001 PHE B 112 TRP 0.014 0.001 TRP A 231 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9995) covalent geometry : angle 0.55337 (13488) hydrogen bonds : bond 0.03012 ( 440) hydrogen bonds : angle 4.82226 ( 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 136 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.404 Fit side-chains REVERT: A 349 LYS cc_start: 0.7560 (pttt) cc_final: 0.7173 (ptpp) REVERT: A 699 LYS cc_start: 0.8222 (ptpt) cc_final: 0.7681 (tptt) REVERT: B 352 MET cc_start: 0.7978 (tpp) cc_final: 0.7414 (mpp) REVERT: B 537 LEU cc_start: 0.8999 (mt) cc_final: 0.8616 (mt) REVERT: B 598 LYS cc_start: 0.7855 (pptt) cc_final: 0.7050 (ptpt) REVERT: B 677 MET cc_start: 0.9026 (mmt) cc_final: 0.8542 (mpp) REVERT: B 695 GLU cc_start: 0.7965 (pp20) cc_final: 0.7586 (pp20) outliers start: 22 outliers final: 15 residues processed: 130 average time/residue: 0.0961 time to fit residues: 17.9760 Evaluate side-chains 122 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 28 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 0.0050 chunk 59 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3732 r_free = 0.3732 target = 0.131929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104004 restraints weight = 15950.832| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.52 r_work: 0.3194 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9995 Z= 0.119 Angle : 0.546 10.363 13488 Z= 0.276 Chirality : 0.042 0.184 1519 Planarity : 0.003 0.033 1714 Dihedral : 5.406 44.396 1398 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.88 % Allowed : 19.49 % Favored : 78.63 % 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: 0.93 (0.24), residues: 517 sheet: -0.15 (0.39), residues: 171 loop : -0.74 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 623 TYR 0.011 0.001 TYR B 206 PHE 0.018 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 covalent geometry : bond 0.00278 ( 9995) covalent geometry : angle 0.54596 (13488) hydrogen bonds : bond 0.02976 ( 440) hydrogen bonds : angle 4.72696 ( 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 137 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7519 (pttt) cc_final: 0.7126 (ptpp) REVERT: A 583 MET cc_start: 0.5929 (mmt) cc_final: 0.5630 (tpp) REVERT: A 699 LYS cc_start: 0.8218 (ptpt) cc_final: 0.7663 (tptt) REVERT: B 98 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9077 (mm) REVERT: B 163 MET cc_start: 0.8875 (mtm) cc_final: 0.8560 (mtm) REVERT: B 348 MET cc_start: 0.8290 (ppp) cc_final: 0.8008 (ppp) REVERT: B 352 MET cc_start: 0.8089 (tpp) cc_final: 0.7514 (mpp) REVERT: B 537 LEU cc_start: 0.8997 (mt) cc_final: 0.8617 (mt) REVERT: B 598 LYS cc_start: 0.7891 (pptt) cc_final: 0.7083 (ptpt) REVERT: B 677 MET cc_start: 0.9019 (mmt) cc_final: 0.8588 (tpp) REVERT: B 695 GLU cc_start: 0.7928 (pp20) cc_final: 0.7558 (pp20) outliers start: 20 outliers final: 16 residues processed: 133 average time/residue: 0.0874 time to fit residues: 16.6009 Evaluate side-chains 129 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 657 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 98 LEU 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 379 ILE Chi-restraints excluded: chain B residue 610 VAL 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: 6.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 75 optimal weight: 0.0770 chunk 92 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 GLN ** 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 = 0.3684 r_free = 0.3684 target = 0.128084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.099639 restraints weight = 16008.943| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.47 r_work: 0.3136 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9995 Z= 0.204 Angle : 0.601 10.026 13488 Z= 0.305 Chirality : 0.044 0.179 1519 Planarity : 0.004 0.033 1714 Dihedral : 5.812 51.131 1398 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.07 % Allowed : 19.40 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1206 helix: 0.71 (0.24), residues: 527 sheet: -0.36 (0.39), residues: 171 loop : -0.85 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 491 TYR 0.012 0.002 TYR A 218 PHE 0.012 0.002 PHE B 239 TRP 0.013 0.002 TRP A 299 HIS 0.003 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 9995) covalent geometry : angle 0.60102 (13488) hydrogen bonds : bond 0.03294 ( 440) hydrogen bonds : angle 4.96135 ( 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 131 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8390 (pt0) REVERT: A 583 MET cc_start: 0.6182 (mmt) cc_final: 0.5902 (tpp) REVERT: A 699 LYS cc_start: 0.8230 (ptpt) cc_final: 0.7746 (tptt) REVERT: B 98 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9098 (mm) REVERT: B 537 LEU cc_start: 0.8995 (mt) cc_final: 0.8627 (mt) REVERT: B 580 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7481 (mt-10) REVERT: B 598 LYS cc_start: 0.8024 (pptt) cc_final: 0.7188 (ptpt) REVERT: B 677 MET cc_start: 0.9052 (mmt) cc_final: 0.8529 (tpp) REVERT: B 695 GLU cc_start: 0.7936 (pp20) cc_final: 0.7548 (pp20) outliers start: 22 outliers final: 18 residues processed: 125 average time/residue: 0.0905 time to fit residues: 16.2644 Evaluate side-chains 124 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 501 CYS 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: 1.9990 chunk 105 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3718 r_free = 0.3718 target = 0.130775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102704 restraints weight = 15838.189| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.46 r_work: 0.3181 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9995 Z= 0.122 Angle : 0.562 12.379 13488 Z= 0.284 Chirality : 0.042 0.189 1519 Planarity : 0.003 0.031 1714 Dihedral : 5.478 45.255 1398 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.17 % Allowed : 19.02 % Favored : 78.81 % 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: 0.04 (0.25), residues: 1206 helix: 0.93 (0.24), residues: 514 sheet: -0.12 (0.40), residues: 168 loop : -0.77 (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 0.022 0.001 PHE B 531 TRP 0.013 0.002 TRP A 231 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9995) covalent geometry : angle 0.56221 (13488) hydrogen bonds : bond 0.03033 ( 440) hydrogen bonds : angle 4.79844 ( 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 136 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8337 (pt0) REVERT: A 583 MET cc_start: 0.6125 (mmt) cc_final: 0.5705 (tpp) REVERT: A 623 ARG cc_start: 0.6941 (mtm110) cc_final: 0.6468 (ttp-110) REVERT: A 699 LYS cc_start: 0.8224 (ptpt) cc_final: 0.7701 (tptt) REVERT: B 98 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9072 (mm) REVERT: B 352 MET cc_start: 0.8090 (tpp) cc_final: 0.7481 (mpp) REVERT: B 537 LEU cc_start: 0.8970 (mt) cc_final: 0.8604 (mt) REVERT: B 580 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7476 (mt-10) REVERT: B 598 LYS cc_start: 0.7973 (pptt) cc_final: 0.7137 (ptpt) REVERT: B 677 MET cc_start: 0.9026 (mmt) cc_final: 0.8625 (tpp) REVERT: B 695 GLU cc_start: 0.7937 (pp20) cc_final: 0.7594 (pp20) outliers start: 23 outliers final: 20 residues processed: 129 average time/residue: 0.0925 time to fit residues: 16.8981 Evaluate side-chains 130 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 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 365 LEU Chi-restraints excluded: chain B residue 379 ILE 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: 0.5980 chunk 92 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 14 optimal weight: 0.1980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3730 r_free = 0.3730 target = 0.131748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104322 restraints weight = 15714.618| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.43 r_work: 0.3200 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9995 Z= 0.116 Angle : 0.548 8.200 13488 Z= 0.278 Chirality : 0.042 0.187 1519 Planarity : 0.003 0.031 1714 Dihedral : 5.328 44.808 1398 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.88 % Allowed : 19.68 % Favored : 78.44 % 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: 0.10 (0.25), residues: 1206 helix: 1.01 (0.24), residues: 511 sheet: -0.10 (0.39), residues: 175 loop : -0.77 (0.28), residues: 520 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 0.012 0.001 PHE B 112 TRP 0.015 0.002 TRP A 231 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9995) covalent geometry : angle 0.54838 (13488) hydrogen bonds : bond 0.02946 ( 440) hydrogen bonds : angle 4.67351 ( 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 132 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8324 (pt0) REVERT: A 583 MET cc_start: 0.5923 (mmt) cc_final: 0.5662 (tpp) REVERT: A 623 ARG cc_start: 0.6824 (mtm110) cc_final: 0.6467 (ttp-110) REVERT: A 699 LYS cc_start: 0.8210 (ptpt) cc_final: 0.7856 (tptt) REVERT: B 352 MET cc_start: 0.8149 (tpp) cc_final: 0.7576 (mpp) REVERT: B 517 MET cc_start: 0.8589 (mmm) cc_final: 0.8126 (tpp) REVERT: B 537 LEU cc_start: 0.8966 (mt) cc_final: 0.8606 (mt) REVERT: B 580 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7577 (mt-10) REVERT: B 598 LYS cc_start: 0.7878 (pptt) cc_final: 0.6931 (ptpp) REVERT: B 677 MET cc_start: 0.9004 (mmt) cc_final: 0.8552 (mpp) outliers start: 20 outliers final: 18 residues processed: 126 average time/residue: 0.1063 time to fit residues: 19.0587 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 : 0.395 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 53 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3712 r_free = 0.3712 target = 0.130209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102404 restraints weight = 15961.421| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.49 r_work: 0.3170 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9995 Z= 0.149 Angle : 0.576 8.516 13488 Z= 0.290 Chirality : 0.043 0.180 1519 Planarity : 0.003 0.047 1714 Dihedral : 5.484 45.923 1398 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.07 % Allowed : 19.77 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1206 helix: 0.94 (0.24), residues: 513 sheet: -0.27 (0.39), residues: 177 loop : -0.70 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 593 TYR 0.010 0.001 TYR B 327 PHE 0.042 0.002 PHE B 531 TRP 0.016 0.002 TRP B 585 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9995) covalent geometry : angle 0.57570 (13488) hydrogen bonds : bond 0.03055 ( 440) hydrogen bonds : angle 4.75849 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2089.03 seconds wall clock time: 36 minutes 40.09 seconds (2200.09 seconds total)