Starting phenix.real_space_refine on Mon Jul 28 11:45:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kck_22811/07_2025/7kck_22811.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kck_22811/07_2025/7kck_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7kck_22811/07_2025/7kck_22811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kck_22811/07_2025/7kck_22811.map" model { file = "/net/cci-nas-00/data/ceres_data/7kck_22811/07_2025/7kck_22811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kck_22811/07_2025/7kck_22811.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.41, per 1000 atoms: 0.65 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: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.17 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: 3.61 Time building geometry restraints manager: 2.88 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 704 or resid 801 through 803)) selection = (chain 'B' and (resid 70 through 351 or resid 363 through 554 or resid 573 throu \ gh 704 or resid 801 through 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: 10.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.970 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 299 HIS 0.002 0.000 HIS A 506 PHE 0.016 0.001 PHE B 531 TYR 0.009 0.001 TYR B 218 ARG 0.006 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.24540 ( 440) hydrogen bonds : angle 8.41919 ( 1290) covalent geometry : bond 0.00410 ( 9995) covalent geometry : angle 0.65679 (13488) *********************** 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 : 1.166 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: 0.8083 (mmt) outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.2352 time to fit residues: 44.4290 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 : 1.068 ------------------------------------------------------------------------------- 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 102 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 256 HIS B 293 ASN B 420 GLN B 510 HIS B 538 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.128695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099876 restraints weight = 15846.041| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.49 r_work: 0.3138 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 9995 Z= 0.280 Angle : 0.683 9.368 13488 Z= 0.349 Chirality : 0.047 0.178 1519 Planarity : 0.005 0.055 1714 Dihedral : 6.353 58.548 1399 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.85 % Allowed : 11.30 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1206 helix: 0.49 (0.24), residues: 505 sheet: -0.00 (0.39), residues: 177 loop : -0.86 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 299 HIS 0.005 0.001 HIS B 506 PHE 0.017 0.002 PHE A 441 TYR 0.019 0.002 TYR A 218 ARG 0.006 0.001 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 440) hydrogen bonds : angle 5.64849 ( 1290) covalent geometry : bond 0.00655 ( 9995) covalent geometry : angle 0.68323 (13488) *********************** 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: 9 poor density : 124 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 348 MET cc_start: 0.7307 (tmm) cc_final: 0.7103 (tmm) REVERT: A 349 LYS cc_start: 0.7687 (pttt) cc_final: 0.7200 (ptpp) REVERT: A 699 LYS cc_start: 0.8227 (ptpt) cc_final: 0.7679 (tptt) REVERT: B 110 GLU cc_start: 0.8465 (pm20) cc_final: 0.8208 (pm20) REVERT: B 290 ARG cc_start: 0.7983 (mmp-170) cc_final: 0.7627 (mmp-170) REVERT: B 352 MET cc_start: 0.7753 (tpp) cc_final: 0.7240 (mpp) REVERT: B 531 PHE cc_start: 0.8464 (m-10) cc_final: 0.8138 (m-10) REVERT: B 537 LEU cc_start: 0.8980 (mt) cc_final: 0.8691 (mt) REVERT: B 554 ILE cc_start: 0.8575 (mm) cc_final: 0.8363 (mm) REVERT: B 598 LYS cc_start: 0.7980 (pptt) cc_final: 0.7678 (pptt) REVERT: B 677 MET cc_start: 0.8993 (mmt) cc_final: 0.8764 (tpp) outliers start: 9 outliers final: 7 residues processed: 128 average time/residue: 0.2688 time to fit residues: 49.3854 Evaluate side-chains 107 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 113 ILE 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 44 optimal weight: 5.9990 chunk 114 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104399 restraints weight = 16012.540| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.54 r_work: 0.3190 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2054 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= 0.120 Angle : 0.548 9.631 13488 Z= 0.281 Chirality : 0.042 0.177 1519 Planarity : 0.004 0.044 1714 Dihedral : 5.732 54.176 1398 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.04 % Allowed : 14.97 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1206 helix: 0.84 (0.24), residues: 495 sheet: 0.13 (0.39), residues: 173 loop : -0.74 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 231 HIS 0.004 0.001 HIS B 506 PHE 0.012 0.001 PHE A 441 TYR 0.015 0.001 TYR A 286 ARG 0.005 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 440) hydrogen bonds : angle 5.11487 ( 1290) covalent geometry : bond 0.00272 ( 9995) covalent geometry : angle 0.54843 (13488) *********************** 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 136 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 1.145 Fit side-chains REVERT: A 87 LYS cc_start: 0.8396 (tppt) cc_final: 0.8037 (mmtp) REVERT: A 348 MET cc_start: 0.7279 (tmm) cc_final: 0.6988 (tmm) REVERT: A 349 LYS cc_start: 0.7607 (pttt) cc_final: 0.7110 (ptpp) REVERT: A 583 MET cc_start: 0.6354 (tpp) cc_final: 0.6109 (tpp) REVERT: A 699 LYS cc_start: 0.8240 (ptpt) cc_final: 0.7434 (tptt) REVERT: B 290 ARG cc_start: 0.7921 (mmp-170) cc_final: 0.7559 (mmp-170) REVERT: B 352 MET cc_start: 0.7848 (tpp) cc_final: 0.7348 (mpp) REVERT: B 537 LEU cc_start: 0.9006 (mt) cc_final: 0.8647 (mt) REVERT: B 598 LYS cc_start: 0.7730 (pptt) cc_final: 0.6967 (ptpt) REVERT: B 677 MET cc_start: 0.9030 (mmt) cc_final: 0.8560 (mpp) outliers start: 11 outliers final: 5 residues processed: 133 average time/residue: 0.2141 time to fit residues: 40.7886 Evaluate side-chains 110 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 85 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 190 GLN B 373 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.124315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096397 restraints weight = 15997.124| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.45 r_work: 0.3080 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 9995 Z= 0.338 Angle : 0.717 8.710 13488 Z= 0.364 Chirality : 0.048 0.179 1519 Planarity : 0.005 0.041 1714 Dihedral : 6.588 56.100 1398 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.79 % Allowed : 18.17 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.24), residues: 1206 helix: 0.43 (0.23), residues: 517 sheet: -0.61 (0.38), residues: 178 loop : -0.97 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 231 HIS 0.005 0.001 HIS B 606 PHE 0.016 0.002 PHE A 239 TYR 0.019 0.002 TYR B 286 ARG 0.004 0.001 ARG B 593 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 440) hydrogen bonds : angle 5.46459 ( 1290) covalent geometry : bond 0.00799 ( 9995) covalent geometry : angle 0.71693 (13488) *********************** 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 127 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.092 Fit side-chains REVERT: A 348 MET cc_start: 0.7320 (tmm) cc_final: 0.6988 (tmm) REVERT: A 349 LYS cc_start: 0.7829 (pttt) cc_final: 0.7310 (ptpp) REVERT: A 699 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7667 (tptt) REVERT: B 163 MET cc_start: 0.9039 (mtm) cc_final: 0.8811 (mtp) REVERT: B 290 ARG cc_start: 0.8037 (mmp-170) cc_final: 0.7610 (mmp-170) REVERT: B 312 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7970 (mm-30) REVERT: B 537 LEU cc_start: 0.9017 (mt) cc_final: 0.8682 (mt) REVERT: B 598 LYS cc_start: 0.8163 (pptt) cc_final: 0.7250 (ptpt) outliers start: 19 outliers final: 13 residues processed: 121 average time/residue: 0.2195 time to fit residues: 37.7805 Evaluate side-chains 115 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 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 583 MET 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 601 LEU Chi-restraints excluded: chain B residue 613 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.128895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100660 restraints weight = 15807.287| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.39 r_work: 0.3157 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9995 Z= 0.121 Angle : 0.556 10.836 13488 Z= 0.282 Chirality : 0.042 0.178 1519 Planarity : 0.003 0.037 1714 Dihedral : 5.742 53.218 1398 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.79 % Allowed : 19.21 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1206 helix: 0.86 (0.24), residues: 509 sheet: -0.23 (0.40), residues: 167 loop : -0.82 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 231 HIS 0.004 0.001 HIS B 506 PHE 0.012 0.001 PHE B 531 TYR 0.013 0.001 TYR A 286 ARG 0.003 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 440) hydrogen bonds : angle 4.97895 ( 1290) covalent geometry : bond 0.00279 ( 9995) covalent geometry : angle 0.55566 (13488) *********************** 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 135 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.053 Fit side-chains REVERT: A 313 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: A 348 MET cc_start: 0.7375 (tmm) cc_final: 0.7028 (tmm) REVERT: A 349 LYS cc_start: 0.7677 (pttt) cc_final: 0.7122 (ptpp) REVERT: A 699 LYS cc_start: 0.8236 (ptpt) cc_final: 0.7620 (tptt) REVERT: B 163 MET cc_start: 0.8937 (mtm) cc_final: 0.8681 (mtp) REVERT: B 312 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7969 (mm-30) REVERT: B 537 LEU cc_start: 0.9011 (mt) cc_final: 0.8630 (mt) REVERT: B 580 GLU cc_start: 0.8621 (mm-30) cc_final: 0.7499 (mt-10) REVERT: B 598 LYS cc_start: 0.7878 (pptt) cc_final: 0.7072 (ptpt) outliers start: 19 outliers final: 11 residues processed: 131 average time/residue: 0.2259 time to fit residues: 42.3448 Evaluate side-chains 120 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 410 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 583 MET 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 683 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 115 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 85 optimal weight: 0.0040 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 HIS ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 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 = 0.3658 r_free = 0.3658 target = 0.126119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097585 restraints weight = 15893.728| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.47 r_work: 0.3101 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9995 Z= 0.205 Angle : 0.611 9.632 13488 Z= 0.308 Chirality : 0.044 0.184 1519 Planarity : 0.004 0.038 1714 Dihedral : 5.959 54.427 1398 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.64 % Allowed : 18.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1206 helix: 0.64 (0.24), residues: 529 sheet: -0.58 (0.38), residues: 177 loop : -0.92 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 231 HIS 0.003 0.001 HIS A 256 PHE 0.012 0.001 PHE A 441 TYR 0.012 0.002 TYR B 206 ARG 0.003 0.000 ARG B 593 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 440) hydrogen bonds : angle 5.06147 ( 1290) covalent geometry : bond 0.00485 ( 9995) covalent geometry : angle 0.61134 (13488) *********************** 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 138 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.698 Fit side-chains REVERT: A 348 MET cc_start: 0.7393 (tmm) cc_final: 0.7039 (tmm) REVERT: A 349 LYS cc_start: 0.7774 (pttt) cc_final: 0.7217 (ptpp) REVERT: A 699 LYS cc_start: 0.8225 (ptpt) cc_final: 0.7691 (tptt) REVERT: B 98 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9111 (mm) REVERT: B 163 MET cc_start: 0.8997 (mtm) cc_final: 0.8728 (mtp) REVERT: B 312 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7930 (mm-30) REVERT: B 379 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6683 (tt) REVERT: B 537 LEU cc_start: 0.9011 (mt) cc_final: 0.8637 (mt) REVERT: B 598 LYS cc_start: 0.7974 (pptt) cc_final: 0.7144 (ptpt) outliers start: 28 outliers final: 20 residues processed: 129 average time/residue: 0.2851 time to fit residues: 53.8096 Evaluate side-chains 129 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 272 ASP 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 491 ARG Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 583 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 36 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 68 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 60 optimal weight: 0.0470 chunk 87 optimal weight: 0.0030 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.4288 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.130285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102188 restraints weight = 16031.987| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.41 r_work: 0.3170 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9995 Z= 0.105 Angle : 0.551 10.673 13488 Z= 0.277 Chirality : 0.041 0.187 1519 Planarity : 0.003 0.035 1714 Dihedral : 5.435 44.679 1398 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.60 % Allowed : 20.06 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1206 helix: 0.92 (0.24), residues: 515 sheet: -0.16 (0.40), residues: 167 loop : -0.79 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 231 HIS 0.003 0.001 HIS B 506 PHE 0.013 0.001 PHE B 112 TYR 0.011 0.001 TYR B 206 ARG 0.004 0.000 ARG B 491 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 440) hydrogen bonds : angle 4.75286 ( 1290) covalent geometry : bond 0.00239 ( 9995) covalent geometry : angle 0.55079 (13488) *********************** 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 136 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.487 Fit side-chains REVERT: A 348 MET cc_start: 0.7395 (tmm) cc_final: 0.7043 (tmm) REVERT: A 349 LYS cc_start: 0.7639 (pttt) cc_final: 0.7079 (ptpp) REVERT: A 699 LYS cc_start: 0.8226 (ptpt) cc_final: 0.7682 (tptt) REVERT: B 98 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9089 (mm) REVERT: B 163 MET cc_start: 0.8934 (mtm) cc_final: 0.8657 (mtp) REVERT: B 352 MET cc_start: 0.8021 (tpp) cc_final: 0.7474 (mpp) REVERT: B 537 LEU cc_start: 0.8986 (mt) cc_final: 0.8609 (mt) REVERT: B 598 LYS cc_start: 0.7851 (pptt) cc_final: 0.7063 (ptpt) REVERT: B 677 MET cc_start: 0.9009 (mmt) cc_final: 0.8527 (tpp) outliers start: 17 outliers final: 13 residues processed: 133 average time/residue: 0.2564 time to fit residues: 48.6265 Evaluate side-chains 124 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 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 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 501 CYS Chi-restraints excluded: chain B residue 524 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 95 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097420 restraints weight = 16063.632| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.58 r_work: 0.3099 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9995 Z= 0.215 Angle : 0.614 9.994 13488 Z= 0.309 Chirality : 0.044 0.180 1519 Planarity : 0.004 0.037 1714 Dihedral : 5.838 50.944 1398 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.35 % Allowed : 20.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1206 helix: 0.68 (0.24), residues: 526 sheet: -0.53 (0.38), residues: 177 loop : -0.89 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 231 HIS 0.003 0.001 HIS A 506 PHE 0.034 0.002 PHE B 531 TYR 0.012 0.002 TYR B 206 ARG 0.004 0.000 ARG B 491 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 440) hydrogen bonds : angle 4.96110 ( 1290) covalent geometry : bond 0.00509 ( 9995) covalent geometry : angle 0.61386 (13488) *********************** 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 138 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: A 348 MET cc_start: 0.7363 (tmm) cc_final: 0.6976 (tmm) REVERT: A 349 LYS cc_start: 0.7756 (pttt) cc_final: 0.7166 (ptpp) REVERT: A 491 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6954 (tpt170) REVERT: A 699 LYS cc_start: 0.8241 (ptpt) cc_final: 0.7731 (tptt) REVERT: B 98 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9120 (mm) REVERT: B 379 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6683 (tt) REVERT: B 537 LEU cc_start: 0.9002 (mt) cc_final: 0.8624 (mt) REVERT: B 598 LYS cc_start: 0.8000 (pptt) cc_final: 0.7184 (ptpt) REVERT: B 695 GLU cc_start: 0.8008 (pp20) cc_final: 0.7626 (pp20) outliers start: 25 outliers final: 17 residues processed: 132 average time/residue: 0.2358 time to fit residues: 44.5078 Evaluate side-chains 127 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 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 491 ARG 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 501 CYS Chi-restraints excluded: chain B residue 524 VAL 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 57 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 0.0020 chunk 99 optimal weight: 3.9990 chunk 26 optimal weight: 0.0070 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0012 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.127969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099620 restraints weight = 16015.679| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.48 r_work: 0.3130 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2981 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= 0.140 Angle : 0.576 10.621 13488 Z= 0.289 Chirality : 0.042 0.189 1519 Planarity : 0.003 0.035 1714 Dihedral : 5.615 47.142 1398 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.07 % Allowed : 20.72 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1206 helix: 0.83 (0.24), residues: 515 sheet: -0.48 (0.39), residues: 177 loop : -0.82 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 231 HIS 0.003 0.001 HIS B 506 PHE 0.012 0.001 PHE B 112 TYR 0.011 0.001 TYR B 206 ARG 0.003 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 440) hydrogen bonds : angle 4.86189 ( 1290) covalent geometry : bond 0.00329 ( 9995) covalent geometry : angle 0.57608 (13488) *********************** 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 130 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.415 Fit side-chains REVERT: A 110 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8268 (pt0) REVERT: A 348 MET cc_start: 0.7366 (tmm) cc_final: 0.6968 (tmm) REVERT: A 349 LYS cc_start: 0.7722 (pttt) cc_final: 0.7136 (ptpp) REVERT: A 491 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.7076 (tpt170) REVERT: A 699 LYS cc_start: 0.8244 (ptpt) cc_final: 0.7713 (tptt) REVERT: B 98 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9107 (mm) REVERT: B 163 MET cc_start: 0.8992 (mtm) cc_final: 0.8730 (mtp) REVERT: B 537 LEU cc_start: 0.9006 (mt) cc_final: 0.8623 (mt) REVERT: B 598 LYS cc_start: 0.7940 (pptt) cc_final: 0.7160 (ptpt) REVERT: B 695 GLU cc_start: 0.7968 (pp20) cc_final: 0.7609 (pp20) outliers start: 22 outliers final: 16 residues processed: 125 average time/residue: 0.3259 time to fit residues: 61.2180 Evaluate side-chains 124 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 410 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 491 ARG 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 379 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 601 LEU 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 72 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.128974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.100925 restraints weight = 15962.119| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.46 r_work: 0.3155 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3020 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= 0.140 Angle : 0.582 10.673 13488 Z= 0.290 Chirality : 0.042 0.188 1519 Planarity : 0.003 0.035 1714 Dihedral : 5.564 46.871 1398 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.98 % Allowed : 20.81 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1206 helix: 0.85 (0.24), residues: 515 sheet: -0.45 (0.39), residues: 177 loop : -0.81 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 231 HIS 0.002 0.001 HIS B 506 PHE 0.024 0.001 PHE B 531 TYR 0.011 0.001 TYR B 206 ARG 0.003 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 440) hydrogen bonds : angle 4.79534 ( 1290) covalent geometry : bond 0.00332 ( 9995) covalent geometry : angle 0.58175 (13488) ********************** 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 129 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: A 348 MET cc_start: 0.7390 (tmm) cc_final: 0.7034 (tmm) REVERT: A 349 LYS cc_start: 0.7700 (pttt) cc_final: 0.7152 (ptpp) REVERT: A 491 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.7066 (tpt170) REVERT: A 583 MET cc_start: 0.6440 (tpp) cc_final: 0.6182 (tpp) REVERT: A 699 LYS cc_start: 0.8235 (ptpt) cc_final: 0.7722 (tptt) REVERT: B 98 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9102 (mm) REVERT: B 163 MET cc_start: 0.9024 (mtm) cc_final: 0.8762 (mtp) REVERT: B 537 LEU cc_start: 0.9002 (mt) cc_final: 0.8625 (mt) REVERT: B 598 LYS cc_start: 0.7991 (pptt) cc_final: 0.7187 (ptpt) REVERT: B 677 MET cc_start: 0.9032 (mmt) cc_final: 0.8648 (tpp) REVERT: B 695 GLU cc_start: 0.7949 (pp20) cc_final: 0.7593 (pp20) outliers start: 21 outliers final: 15 residues processed: 122 average time/residue: 0.2262 time to fit residues: 39.8337 Evaluate side-chains 124 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 410 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 491 ARG 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 379 ILE Chi-restraints excluded: chain B residue 524 VAL 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 92 optimal weight: 0.0050 chunk 43 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.130118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.102109 restraints weight = 16047.148| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.66 r_work: 0.3157 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3036 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= 0.111 Angle : 0.578 13.240 13488 Z= 0.282 Chirality : 0.042 0.190 1519 Planarity : 0.003 0.034 1714 Dihedral : 5.359 44.021 1398 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.69 % Allowed : 21.00 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1206 helix: 0.95 (0.24), residues: 515 sheet: -0.21 (0.39), residues: 174 loop : -0.78 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 585 HIS 0.003 0.001 HIS B 506 PHE 0.013 0.001 PHE B 112 TYR 0.010 0.001 TYR B 206 ARG 0.004 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.02912 ( 440) hydrogen bonds : angle 4.64423 ( 1290) covalent geometry : bond 0.00259 ( 9995) covalent geometry : angle 0.57752 (13488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4881.78 seconds wall clock time: 88 minutes 46.11 seconds (5326.11 seconds total)