Starting phenix.real_space_refine on Fri Jun 13 08:30:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8olx_16964/06_2025/8olx_16964.cif Found real_map, /net/cci-nas-00/data/ceres_data/8olx_16964/06_2025/8olx_16964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8olx_16964/06_2025/8olx_16964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8olx_16964/06_2025/8olx_16964.map" model { file = "/net/cci-nas-00/data/ceres_data/8olx_16964/06_2025/8olx_16964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8olx_16964/06_2025/8olx_16964.cif" } resolution = 3.1 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 1 5.21 5 S 65 5.16 5 C 9068 2.51 5 N 2488 2.21 5 O 2823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14492 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 863, 6832 Classifications: {'peptide': 863} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 836} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 6709 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 836, 6706 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 25, 'TRANS': 810} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 836, 6706 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 25, 'TRANS': 810} Chain breaks: 5 bond proxies already assigned to first conformer: 6825 Chain: "C" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 515 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.83, per 1000 atoms: 0.95 Number of scatterers: 14492 At special positions: 0 Unit cell: (93.2484, 118.846, 169.127, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 65 16.00 P 47 15.00 Mg 1 11.99 O 2823 8.00 N 2488 7.00 C 9068 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: 4.08 Conformation dependent library (CDL) restraints added in 2.6 seconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3230 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 10 sheets defined 54.6% alpha, 12.3% beta 18 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 6.19 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.741A pdb=" N VAL A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.998A pdb=" N VAL A 63 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.511A pdb=" N GLU A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 219 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.761A pdb=" N LEU A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.584A pdb=" N PHE A 286 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.775A pdb=" N TYR A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.623A pdb=" N ILE A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.929A pdb=" N ARG A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 400 through 422 Proline residue: A 415 - end of helix removed outlier: 3.542A pdb=" N GLU A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 445 removed outlier: 3.601A pdb=" N VAL A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 475 through 504 Processing helix chain 'A' and resid 529 through 534 removed outlier: 4.558A pdb=" N ARG A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 587 removed outlier: 3.651A pdb=" N THR A 568 " --> pdb=" O THR A 564 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 614 Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.516A pdb=" N VAL A 644 " --> pdb=" O CYS A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 692 Processing helix chain 'A' and resid 724 through 739 Processing helix chain 'A' and resid 755 through 773 Processing helix chain 'A' and resid 784 through 793 removed outlier: 3.954A pdb=" N ALA A 789 " --> pdb=" O GLU A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 834 removed outlier: 3.606A pdb=" N ALA A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 852 Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 900 through 919 removed outlier: 4.110A pdb=" N GLU A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 922 No H-bonds generated for 'chain 'A' and resid 920 through 922' Processing helix chain 'B' and resid 230 through 243 removed outlier: 3.922A pdb=" N GLN B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.958A pdb=" N GLU B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 removed outlier: 3.544A pdb=" N HIS B 293 " --> pdb=" O ARG B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.620A pdb=" N LYS B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 459 through 463 Processing helix chain 'B' and resid 464 through 476 Processing helix chain 'B' and resid 490 through 495 Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.510A pdb=" N GLU B 512 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 removed outlier: 3.621A pdb=" N MET B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 570 through 582 Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 606 through 615 Processing helix chain 'B' and resid 620 through 630 Processing helix chain 'B' and resid 634 through 655 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 673 Processing helix chain 'B' and resid 674 through 679 Processing helix chain 'B' and resid 680 through 686 Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 709 through 738 removed outlier: 4.412A pdb=" N LYS B 713 " --> pdb=" O PHE B 709 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 714 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 730 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 815 Processing helix chain 'B' and resid 817 through 841 Processing helix chain 'B' and resid 864 through 871 removed outlier: 3.517A pdb=" N VAL B 869 " --> pdb=" O PRO B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 919 removed outlier: 4.302A pdb=" N SER B 903 " --> pdb=" O MET B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 966 removed outlier: 3.756A pdb=" N GLU B 955 " --> pdb=" O THR B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1000 Processing helix chain 'B' and resid 1011 through 1016 removed outlier: 4.073A pdb=" N CYS B1015 " --> pdb=" O TYR B1011 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1011 through 1016' Processing helix chain 'B' and resid 1017 through 1020 Processing helix chain 'B' and resid 1068 through 1076 Processing helix chain 'B' and resid 1079 through 1113 removed outlier: 3.511A pdb=" N LEU B1083 " --> pdb=" O PRO B1079 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.335A pdb=" N HIS A 46 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG A 35 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A 34 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TYR A 103 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU A 36 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ASN A 105 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASP A 38 " --> pdb=" O ASN A 105 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS A 104 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU A 119 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 5.746A pdb=" N VAL A 147 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG A 159 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 302 removed outlier: 6.898A pdb=" N LYS A 301 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA A 710 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS A 707 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 746 " --> pdb=" O CYS A 707 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 709 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ASP A 748 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG A 711 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 745 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA A 781 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 747 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N HIS A 665 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N PHE A 664 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 800 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE A 666 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 802 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR A 668 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ALA A 804 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLN A 816 " --> pdb=" O THR A 803 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LEU A 805 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU A 814 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 511 through 514 removed outlier: 6.645A pdb=" N LYS A 550 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 653 through 655 removed outlier: 5.565A pdb=" N ASN A 653 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA A 636 " --> pdb=" O ASN A 653 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER A 637 " --> pdb=" O CYS A 697 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS A 697 " --> pdb=" O SER A 637 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 283 through 286 removed outlier: 6.184A pdb=" N VAL B 247 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 307 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N CYS B 249 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLN B 309 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLU B 251 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 332 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS B 308 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU B 330 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 454 through 458 removed outlier: 6.786A pdb=" N TYR B 367 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU B 426 " --> pdb=" O TYR B 367 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU B 369 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU B 428 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE B 371 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 400 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 536 through 537 removed outlier: 3.624A pdb=" N ILE B 935 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLY B 934 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE B 973 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG B 938 " --> pdb=" O ASP B 975 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET B1030 " --> pdb=" O THR B 895 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 745 through 747 removed outlier: 7.765A pdb=" N VAL B 747 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU B 751 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 754 " --> pdb=" O PHE B 780 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 880 through 885 removed outlier: 6.996A pdb=" N THR B 882 " --> pdb=" O LYS B 860 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS B 860 " --> pdb=" O THR B 882 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU B 884 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 858 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) 705 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 7.41 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3881 1.34 - 1.46: 4136 1.46 - 1.58: 6621 1.58 - 1.70: 87 1.70 - 1.82: 105 Bond restraints: 14830 Sorted by residual: bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.390 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C1' DG D 42 " pdb=" N9 DG D 42 " ideal model delta sigma weight residual 1.460 1.376 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C1' G C 26 " pdb=" N9 G C 26 " ideal model delta sigma weight residual 1.460 1.376 0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C1' G C 21 " pdb=" N9 G C 21 " ideal model delta sigma weight residual 1.460 1.377 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C1' DG D 38 " pdb=" N9 DG D 38 " ideal model delta sigma weight residual 1.460 1.379 0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 14825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 20089 3.77 - 7.53: 98 7.53 - 11.30: 3 11.30 - 15.07: 0 15.07 - 18.83: 1 Bond angle restraints: 20191 Sorted by residual: angle pdb=" N PRO A 415 " pdb=" CD PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 103.20 84.37 18.83 1.50e+00 4.44e-01 1.58e+02 angle pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 112.00 105.06 6.94 1.40e+00 5.10e-01 2.46e+01 angle pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 103.25 98.17 5.08 1.05e+00 9.07e-01 2.34e+01 angle pdb=" CA ASP B 320 " pdb=" CB ASP B 320 " pdb=" CG ASP B 320 " ideal model delta sigma weight residual 112.60 116.86 -4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" CA ASP B 705 " pdb=" CB ASP B 705 " pdb=" CG ASP B 705 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 ... (remaining 20186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.41: 8159 29.41 - 58.81: 699 58.81 - 88.22: 54 88.22 - 117.62: 4 117.62 - 147.03: 1 Dihedral angle restraints: 8917 sinusoidal: 3947 harmonic: 4970 Sorted by residual: dihedral pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " pdb=" O2A ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 87.03 -147.03 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" CD ARG B 979 " pdb=" NE ARG B 979 " pdb=" CZ ARG B 979 " pdb=" NH1 ARG B 979 " ideal model delta sinusoidal sigma weight residual 0.00 -50.78 50.78 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 57.59 -117.59 1 2.00e+01 2.50e-03 3.51e+01 ... (remaining 8914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1555 0.075 - 0.150: 677 0.150 - 0.226: 72 0.226 - 0.301: 4 0.301 - 0.376: 2 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CB PRO A 415 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA MET A 492 " pdb=" N MET A 492 " pdb=" C MET A 492 " pdb=" CB MET A 492 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA PRO A 591 " pdb=" N PRO A 591 " pdb=" C PRO A 591 " pdb=" CB PRO A 591 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 2307 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 979 " 0.827 9.50e-02 1.11e+02 3.71e-01 8.36e+01 pdb=" NE ARG B 979 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG B 979 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 979 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 979 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 414 " 0.018 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU A 414 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU A 414 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO A 415 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 414 " 0.055 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO A 415 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " 0.043 5.00e-02 4.00e+02 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 135 2.57 - 3.16: 11879 3.16 - 3.74: 24133 3.74 - 4.32: 32496 4.32 - 4.90: 52517 Nonbonded interactions: 121160 Sorted by model distance: nonbonded pdb=" NZ LYS B 757 " pdb=" C7 DT C 20 " model vdw 1.992 3.540 nonbonded pdb=" OG SER A 676 " pdb="MG MG A1000 " model vdw 2.063 2.170 nonbonded pdb="MG MG A1000 " pdb=" O1B ADP A1001 " model vdw 2.088 2.170 nonbonded pdb=" NH2 ARG B 574 " pdb=" OE1 GLU B 622 " model vdw 2.125 3.120 nonbonded pdb=" OG1 THR B 230 " pdb=" OE1 GLU B 233 " model vdw 2.174 3.040 ... (remaining 121155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.39 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: 141.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 50.090 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.007 0.100 14830 Z= 0.426 Angle : 0.966 18.833 20191 Z= 0.616 Chirality : 0.074 0.376 2310 Planarity : 0.009 0.371 2416 Dihedral : 19.708 147.026 5687 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.00 % Allowed : 25.90 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.21), residues: 1674 helix: 0.88 (0.18), residues: 795 sheet: -0.83 (0.36), residues: 211 loop : -1.30 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 807 HIS 0.007 0.002 HIS B 614 PHE 0.025 0.003 PHE B 752 TYR 0.017 0.004 TYR B 236 ARG 0.012 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.15866 ( 751) hydrogen bonds : angle 6.10087 ( 2087) covalent geometry : bond 0.00685 (14830) covalent geometry : angle 0.96569 (20191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 394 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7482 (p) REVERT: A 67 MET cc_start: 0.7949 (ttt) cc_final: 0.7643 (ttt) REVERT: A 159 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6926 (mtm-85) REVERT: A 254 ASN cc_start: 0.6863 (t0) cc_final: 0.6582 (t0) REVERT: A 313 PHE cc_start: 0.7516 (m-10) cc_final: 0.7283 (m-10) REVERT: A 471 LYS cc_start: 0.8322 (ptpt) cc_final: 0.8097 (ttmt) REVERT: A 574 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: A 658 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7398 (mt-10) REVERT: B 320 ASP cc_start: 0.8545 (p0) cc_final: 0.8283 (p0) REVERT: B 445 SER cc_start: 0.7952 (t) cc_final: 0.7324 (m) REVERT: B 452 ARG cc_start: 0.8177 (ttt-90) cc_final: 0.7821 (ttt-90) REVERT: B 812 GLU cc_start: 0.8022 (tp30) cc_final: 0.7653 (tp30) REVERT: B 985 ASP cc_start: 0.8280 (m-30) cc_final: 0.7925 (t0) outliers start: 30 outliers final: 16 residues processed: 411 average time/residue: 0.2990 time to fit residues: 172.5251 Evaluate side-chains 403 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 384 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.8980 chunk 131 optimal weight: 0.0040 chunk 72 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 135 optimal weight: 0.0570 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 overall best weight: 0.4710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 242 ASN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN A 377 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN A 799 ASN A 824 GLN B 243 HIS B 309 GLN B 538 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 GLN B 826 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 HIS B1027 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.163888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133111 restraints weight = 28962.458| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.87 r_work: 0.3516 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14830 Z= 0.151 Angle : 0.605 7.611 20191 Z= 0.322 Chirality : 0.042 0.153 2310 Planarity : 0.004 0.047 2416 Dihedral : 17.429 127.720 2344 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.66 % Allowed : 25.30 % Favored : 72.04 % 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: -0.06 (0.21), residues: 1674 helix: 1.03 (0.18), residues: 812 sheet: -0.75 (0.37), residues: 202 loop : -1.10 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 562 HIS 0.005 0.001 HIS B 984 PHE 0.022 0.002 PHE B 752 TYR 0.016 0.001 TYR A 678 ARG 0.005 0.001 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 751) hydrogen bonds : angle 4.58029 ( 2087) covalent geometry : bond 0.00331 (14830) covalent geometry : angle 0.60492 (20191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 395 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7611 (ttt) cc_final: 0.7383 (ttt) REVERT: A 97 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7593 (mm-40) REVERT: A 215 GLN cc_start: 0.7497 (tm-30) cc_final: 0.7098 (tm-30) REVERT: A 246 LYS cc_start: 0.8079 (tppt) cc_final: 0.7866 (tppt) REVERT: A 313 PHE cc_start: 0.7546 (m-10) cc_final: 0.7203 (m-10) REVERT: A 334 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7433 (mtpp) REVERT: A 351 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7195 (mpp) REVERT: A 430 LYS cc_start: 0.5861 (mmmt) cc_final: 0.5406 (mmmt) REVERT: A 471 LYS cc_start: 0.7941 (ptpt) cc_final: 0.7703 (ttmt) REVERT: A 481 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7969 (mp) REVERT: A 514 ASP cc_start: 0.7763 (t0) cc_final: 0.7498 (t0) REVERT: A 530 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5577 (mp0) REVERT: A 562 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7146 (mm-30) REVERT: A 567 LYS cc_start: 0.8207 (tppp) cc_final: 0.7981 (tppp) REVERT: A 569 GLU cc_start: 0.7583 (tp30) cc_final: 0.7239 (tp30) REVERT: A 658 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7443 (mt-10) REVERT: A 691 ILE cc_start: 0.8409 (tt) cc_final: 0.7900 (pt) REVERT: A 799 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8551 (p0) REVERT: B 264 GLU cc_start: 0.7245 (mp0) cc_final: 0.6922 (mp0) REVERT: B 445 SER cc_start: 0.7931 (t) cc_final: 0.7622 (m) REVERT: B 508 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7895 (ttmm) REVERT: B 550 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7812 (p0) REVERT: B 606 SER cc_start: 0.7807 (m) cc_final: 0.7296 (p) REVERT: B 709 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: B 860 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7951 (ttpt) REVERT: B 899 MET cc_start: 0.6121 (ppp) cc_final: 0.5652 (ppp) REVERT: B 961 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7037 (mm-30) REVERT: B 969 GLN cc_start: 0.8277 (mp10) cc_final: 0.8058 (mp10) REVERT: B 1063 ILE cc_start: 0.7682 (mm) cc_final: 0.7431 (mm) outliers start: 40 outliers final: 17 residues processed: 412 average time/residue: 0.3846 time to fit residues: 223.2611 Evaluate side-chains 398 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 373 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 908 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 4 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 86 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 147 optimal weight: 0.0020 chunk 14 optimal weight: 0.7980 chunk 167 optimal weight: 10.0000 overall best weight: 0.5706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 288 GLN A 395 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135130 restraints weight = 20392.548| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.28 r_work: 0.3561 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14830 Z= 0.152 Angle : 0.576 6.825 20191 Z= 0.306 Chirality : 0.041 0.165 2310 Planarity : 0.004 0.052 2416 Dihedral : 17.183 121.047 2309 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.73 % Allowed : 26.03 % Favored : 71.24 % 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: 0.06 (0.21), residues: 1674 helix: 1.13 (0.18), residues: 813 sheet: -0.72 (0.36), residues: 208 loop : -1.04 (0.26), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 807 HIS 0.005 0.001 HIS B 781 PHE 0.020 0.002 PHE A 760 TYR 0.013 0.001 TYR B 236 ARG 0.007 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 751) hydrogen bonds : angle 4.41189 ( 2087) covalent geometry : bond 0.00338 (14830) covalent geometry : angle 0.57592 (20191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 388 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7514 (ttt) cc_final: 0.7276 (ttt) REVERT: A 97 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7496 (mm-40) REVERT: A 119 LEU cc_start: 0.8284 (tp) cc_final: 0.7987 (tp) REVERT: A 160 GLN cc_start: 0.7534 (tt0) cc_final: 0.7153 (tt0) REVERT: A 215 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7028 (tm-30) REVERT: A 246 LYS cc_start: 0.8008 (tppt) cc_final: 0.7766 (tppt) REVERT: A 261 MET cc_start: 0.7944 (tmm) cc_final: 0.7677 (tmm) REVERT: A 298 GLN cc_start: 0.8048 (mt0) cc_final: 0.7743 (mt0) REVERT: A 313 PHE cc_start: 0.7526 (m-10) cc_final: 0.7138 (m-10) REVERT: A 351 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7053 (mpp) REVERT: A 371 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7791 (mm-30) REVERT: A 402 GLN cc_start: 0.7040 (tt0) cc_final: 0.6579 (tp40) REVERT: A 430 LYS cc_start: 0.5791 (mmmt) cc_final: 0.5039 (mmmt) REVERT: A 471 LYS cc_start: 0.7904 (ptpt) cc_final: 0.7697 (ttmt) REVERT: A 481 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7992 (mp) REVERT: A 530 GLU cc_start: 0.5870 (OUTLIER) cc_final: 0.5542 (mp0) REVERT: A 562 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7094 (mm-30) REVERT: A 567 LYS cc_start: 0.8186 (tppp) cc_final: 0.7951 (tppp) REVERT: A 569 GLU cc_start: 0.7496 (tp30) cc_final: 0.7024 (tp30) REVERT: A 658 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7350 (mt-10) REVERT: A 691 ILE cc_start: 0.8372 (tt) cc_final: 0.7876 (pt) REVERT: A 728 GLU cc_start: 0.6697 (tm-30) cc_final: 0.6474 (tm-30) REVERT: A 824 GLN cc_start: 0.7796 (pm20) cc_final: 0.7417 (pm20) REVERT: A 850 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7496 (tm-30) REVERT: B 417 ARG cc_start: 0.7711 (mpt180) cc_final: 0.7425 (mmt180) REVERT: B 445 SER cc_start: 0.7966 (t) cc_final: 0.7285 (m) REVERT: B 452 ARG cc_start: 0.7279 (ttt-90) cc_final: 0.7071 (ttt-90) REVERT: B 508 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7784 (ttmm) REVERT: B 550 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7883 (p0) REVERT: B 606 SER cc_start: 0.7816 (m) cc_final: 0.7453 (p) REVERT: B 860 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7949 (ptpt) REVERT: B 899 MET cc_start: 0.6114 (ppp) cc_final: 0.5732 (ppp) REVERT: B 961 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6916 (mm-30) REVERT: B 1063 ILE cc_start: 0.7664 (mm) cc_final: 0.7418 (mm) outliers start: 41 outliers final: 21 residues processed: 410 average time/residue: 0.4265 time to fit residues: 247.5515 Evaluate side-chains 403 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 377 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 1057 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 166 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 85 optimal weight: 40.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN B 271 ASN B 613 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.161980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132724 restraints weight = 22983.907| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.48 r_work: 0.3528 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14830 Z= 0.219 Angle : 0.611 9.975 20191 Z= 0.322 Chirality : 0.043 0.176 2310 Planarity : 0.004 0.059 2416 Dihedral : 17.192 125.635 2309 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.79 % Allowed : 25.83 % Favored : 70.37 % 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: -0.04 (0.21), residues: 1674 helix: 1.02 (0.18), residues: 814 sheet: -0.79 (0.35), residues: 216 loop : -1.04 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 807 HIS 0.004 0.001 HIS B 781 PHE 0.033 0.002 PHE A 232 TYR 0.046 0.002 TYR B 334 ARG 0.006 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 751) hydrogen bonds : angle 4.41248 ( 2087) covalent geometry : bond 0.00493 (14830) covalent geometry : angle 0.61140 (20191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 389 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7576 (ttt) cc_final: 0.7337 (ttt) REVERT: A 97 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7503 (mm-40) REVERT: A 119 LEU cc_start: 0.8315 (tp) cc_final: 0.8010 (tp) REVERT: A 160 GLN cc_start: 0.7541 (tt0) cc_final: 0.7168 (tt0) REVERT: A 261 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7236 (tmm) REVERT: A 298 GLN cc_start: 0.8120 (mt0) cc_final: 0.7794 (mt0) REVERT: A 334 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7486 (mtpp) REVERT: A 371 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7832 (mm-30) REVERT: A 402 GLN cc_start: 0.7108 (tt0) cc_final: 0.6694 (tp40) REVERT: A 430 LYS cc_start: 0.6012 (mmmt) cc_final: 0.5239 (mmmt) REVERT: A 471 LYS cc_start: 0.7977 (ptpt) cc_final: 0.7769 (ttmt) REVERT: A 514 ASP cc_start: 0.7615 (t0) cc_final: 0.7413 (t0) REVERT: A 530 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.5475 (mp0) REVERT: A 562 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7133 (mm-30) REVERT: A 567 LYS cc_start: 0.8227 (tppp) cc_final: 0.7977 (tppp) REVERT: A 569 GLU cc_start: 0.7527 (tp30) cc_final: 0.7005 (tp30) REVERT: A 658 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7490 (mt-10) REVERT: A 691 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7926 (pt) REVERT: A 726 MET cc_start: 0.7975 (tpt) cc_final: 0.7688 (tpp) REVERT: A 728 GLU cc_start: 0.6743 (tm-30) cc_final: 0.6516 (tm-30) REVERT: A 799 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8455 (p0) REVERT: B 264 GLU cc_start: 0.7237 (mp0) cc_final: 0.6949 (mp0) REVERT: B 407 ASP cc_start: 0.6793 (t0) cc_final: 0.6418 (t70) REVERT: B 445 SER cc_start: 0.8008 (t) cc_final: 0.7305 (m) REVERT: B 508 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7810 (ttmm) REVERT: B 550 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7813 (p0) REVERT: B 606 SER cc_start: 0.7883 (m) cc_final: 0.7326 (p) REVERT: B 753 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.6068 (ptp) REVERT: B 856 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8210 (ttmm) REVERT: B 899 MET cc_start: 0.6198 (ppp) cc_final: 0.5882 (ppp) REVERT: B 961 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6997 (mm-30) REVERT: B 1063 ILE cc_start: 0.7823 (mm) cc_final: 0.7585 (mm) outliers start: 57 outliers final: 30 residues processed: 416 average time/residue: 0.2959 time to fit residues: 174.8322 Evaluate side-chains 412 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 375 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 653 ASN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 1057 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 138 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 161 optimal weight: 0.0030 chunk 31 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 582 GLN B 613 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS B 729 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.164522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134692 restraints weight = 25120.401| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.65 r_work: 0.3542 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14830 Z= 0.138 Angle : 0.573 9.827 20191 Z= 0.302 Chirality : 0.041 0.163 2310 Planarity : 0.004 0.057 2416 Dihedral : 17.046 125.165 2309 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.60 % Allowed : 27.03 % Favored : 69.37 % 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: 0.10 (0.21), residues: 1674 helix: 1.20 (0.18), residues: 813 sheet: -0.74 (0.36), residues: 207 loop : -1.06 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1111 HIS 0.006 0.001 HIS B 984 PHE 0.020 0.001 PHE A 760 TYR 0.038 0.002 TYR B 334 ARG 0.009 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 751) hydrogen bonds : angle 4.28864 ( 2087) covalent geometry : bond 0.00311 (14830) covalent geometry : angle 0.57289 (20191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 383 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.7363 (m-80) cc_final: 0.6985 (m-80) REVERT: A 67 MET cc_start: 0.7532 (ttt) cc_final: 0.7271 (ttt) REVERT: A 97 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7473 (mm-40) REVERT: A 119 LEU cc_start: 0.8295 (tp) cc_final: 0.7995 (tp) REVERT: A 160 GLN cc_start: 0.7507 (tt0) cc_final: 0.7130 (tt0) REVERT: A 261 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7740 (tmm) REVERT: A 298 GLN cc_start: 0.8040 (mt0) cc_final: 0.7731 (mt0) REVERT: A 371 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7806 (mm-30) REVERT: A 402 GLN cc_start: 0.6958 (tt0) cc_final: 0.6628 (tp40) REVERT: A 430 LYS cc_start: 0.5960 (mmmt) cc_final: 0.4967 (mmmt) REVERT: A 471 LYS cc_start: 0.7944 (ptpt) cc_final: 0.7732 (ttmt) REVERT: A 514 ASP cc_start: 0.7716 (t0) cc_final: 0.7443 (t0) REVERT: A 515 SER cc_start: 0.8295 (m) cc_final: 0.7872 (t) REVERT: A 530 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.5485 (mp0) REVERT: A 555 LYS cc_start: 0.8983 (tmmt) cc_final: 0.8774 (tmmt) REVERT: A 562 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7161 (mm-30) REVERT: A 567 LYS cc_start: 0.8196 (tppp) cc_final: 0.7954 (tppp) REVERT: A 569 GLU cc_start: 0.7562 (tp30) cc_final: 0.7053 (tp30) REVERT: A 658 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7461 (mt-10) REVERT: A 659 LYS cc_start: 0.8317 (ttmt) cc_final: 0.8086 (ttmt) REVERT: A 691 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7843 (pt) REVERT: A 726 MET cc_start: 0.7926 (tpt) cc_final: 0.7622 (tpp) REVERT: B 264 GLU cc_start: 0.7214 (mp0) cc_final: 0.6939 (mp0) REVERT: B 417 ARG cc_start: 0.7682 (mpt180) cc_final: 0.7336 (mmt180) REVERT: B 445 SER cc_start: 0.7890 (t) cc_final: 0.7258 (m) REVERT: B 453 ILE cc_start: 0.8585 (tt) cc_final: 0.8319 (pt) REVERT: B 508 LYS cc_start: 0.8051 (ttmm) cc_final: 0.7789 (ttmm) REVERT: B 550 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7933 (p0) REVERT: B 709 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: B 812 GLU cc_start: 0.7701 (tp30) cc_final: 0.7395 (tp30) REVERT: B 856 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8179 (ttmm) REVERT: B 899 MET cc_start: 0.6105 (ppp) cc_final: 0.5796 (ppp) REVERT: B 1063 ILE cc_start: 0.7716 (mm) cc_final: 0.7477 (mm) outliers start: 54 outliers final: 26 residues processed: 414 average time/residue: 0.3609 time to fit residues: 213.1867 Evaluate side-chains 407 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 376 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 129 optimal weight: 0.0060 chunk 94 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN A 395 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 690 GLN B 582 GLN B 613 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.164041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.133584 restraints weight = 29053.889| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.89 r_work: 0.3515 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14830 Z= 0.153 Angle : 0.584 9.071 20191 Z= 0.306 Chirality : 0.041 0.166 2310 Planarity : 0.004 0.056 2416 Dihedral : 16.935 131.361 2309 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.46 % Allowed : 26.70 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.12 (0.21), residues: 1674 helix: 1.21 (0.18), residues: 814 sheet: -0.76 (0.36), residues: 210 loop : -1.04 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1111 HIS 0.010 0.001 HIS B 647 PHE 0.022 0.002 PHE A 760 TYR 0.039 0.002 TYR B 334 ARG 0.009 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 751) hydrogen bonds : angle 4.25830 ( 2087) covalent geometry : bond 0.00345 (14830) covalent geometry : angle 0.58384 (20191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 380 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.7500 (m-80) cc_final: 0.7077 (m-80) REVERT: A 67 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7348 (ttt) REVERT: A 97 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7526 (mm-40) REVERT: A 119 LEU cc_start: 0.8317 (tp) cc_final: 0.8024 (tp) REVERT: A 160 GLN cc_start: 0.7509 (tt0) cc_final: 0.7139 (tt0) REVERT: A 215 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7103 (tm-30) REVERT: A 216 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8335 (tp) REVERT: A 261 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7741 (tmm) REVERT: A 298 GLN cc_start: 0.8098 (mt0) cc_final: 0.7750 (mt0) REVERT: A 371 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 402 GLN cc_start: 0.7125 (tt0) cc_final: 0.6784 (tp40) REVERT: A 430 LYS cc_start: 0.6059 (mmmt) cc_final: 0.5211 (mmmt) REVERT: A 482 ARG cc_start: 0.8074 (tpp80) cc_final: 0.7555 (tpp80) REVERT: A 514 ASP cc_start: 0.7784 (t0) cc_final: 0.7501 (t0) REVERT: A 515 SER cc_start: 0.8440 (m) cc_final: 0.7926 (t) REVERT: A 530 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.5460 (mp0) REVERT: A 555 LYS cc_start: 0.8983 (tmmt) cc_final: 0.8756 (tmmt) REVERT: A 562 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7165 (mm-30) REVERT: A 567 LYS cc_start: 0.8208 (tppp) cc_final: 0.7971 (tppp) REVERT: A 569 GLU cc_start: 0.7616 (tp30) cc_final: 0.7115 (tp30) REVERT: A 658 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7548 (mt-10) REVERT: A 659 LYS cc_start: 0.8352 (ttmt) cc_final: 0.8070 (ttmt) REVERT: A 691 ILE cc_start: 0.8387 (tt) cc_final: 0.7865 (pt) REVERT: A 726 MET cc_start: 0.7957 (tpt) cc_final: 0.7667 (tpp) REVERT: A 728 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6495 (tm-30) REVERT: A 729 MET cc_start: 0.7879 (mmm) cc_final: 0.7414 (mmm) REVERT: B 264 GLU cc_start: 0.7252 (mp0) cc_final: 0.6825 (mp0) REVERT: B 417 ARG cc_start: 0.7747 (mpt180) cc_final: 0.7483 (mmt180) REVERT: B 445 SER cc_start: 0.7884 (t) cc_final: 0.7248 (m) REVERT: B 550 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7935 (p0) REVERT: B 606 SER cc_start: 0.7851 (m) cc_final: 0.7298 (p) REVERT: B 613 ASN cc_start: 0.7938 (m-40) cc_final: 0.7455 (m110) REVERT: B 709 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: B 856 LYS cc_start: 0.8478 (ttmt) cc_final: 0.8211 (ttmm) REVERT: B 860 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8036 (ptmm) REVERT: B 898 ASN cc_start: 0.7851 (t0) cc_final: 0.7388 (t0) REVERT: B 899 MET cc_start: 0.6166 (ppp) cc_final: 0.5862 (ppp) REVERT: B 1063 ILE cc_start: 0.7713 (mm) cc_final: 0.7486 (mm) REVERT: B 1092 GLU cc_start: 0.7632 (tp30) cc_final: 0.7089 (tp30) outliers start: 52 outliers final: 31 residues processed: 408 average time/residue: 0.4206 time to fit residues: 246.5602 Evaluate side-chains 410 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 372 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 171 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 119 optimal weight: 0.0980 chunk 65 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 0.0870 chunk 124 optimal weight: 0.7980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 582 GLN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 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 = 0.4112 r_free = 0.4112 target = 0.165084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.135821 restraints weight = 22689.770| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.48 r_work: 0.3566 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14830 Z= 0.135 Angle : 0.575 8.852 20191 Z= 0.302 Chirality : 0.041 0.163 2310 Planarity : 0.004 0.056 2416 Dihedral : 16.846 134.401 2309 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.46 % Allowed : 26.70 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.21), residues: 1674 helix: 1.30 (0.18), residues: 813 sheet: -0.83 (0.36), residues: 220 loop : -1.01 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1111 HIS 0.006 0.001 HIS B 647 PHE 0.027 0.001 PHE A 760 TYR 0.032 0.001 TYR B 334 ARG 0.009 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 751) hydrogen bonds : angle 4.22325 ( 2087) covalent geometry : bond 0.00305 (14830) covalent geometry : angle 0.57545 (20191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 388 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7601 (ttm110) cc_final: 0.7316 (ttm110) REVERT: A 43 TYR cc_start: 0.7477 (m-80) cc_final: 0.7005 (m-80) REVERT: A 67 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7319 (ttt) REVERT: A 97 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7453 (mt0) REVERT: A 119 LEU cc_start: 0.8283 (tp) cc_final: 0.7985 (tp) REVERT: A 160 GLN cc_start: 0.7479 (tt0) cc_final: 0.7094 (tt0) REVERT: A 215 GLN cc_start: 0.7520 (tm-30) cc_final: 0.6967 (tm-30) REVERT: A 216 ILE cc_start: 0.8508 (tp) cc_final: 0.8155 (tp) REVERT: A 246 LYS cc_start: 0.7983 (tppt) cc_final: 0.7681 (tppt) REVERT: A 261 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7768 (tmm) REVERT: A 298 GLN cc_start: 0.8075 (mt0) cc_final: 0.7708 (mt0) REVERT: A 371 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7809 (mm-30) REVERT: A 402 GLN cc_start: 0.7039 (tt0) cc_final: 0.6729 (tp40) REVERT: A 430 LYS cc_start: 0.6018 (mmmt) cc_final: 0.4880 (mmtt) REVERT: A 482 ARG cc_start: 0.8054 (tpp80) cc_final: 0.7528 (tpp80) REVERT: A 515 SER cc_start: 0.8532 (m) cc_final: 0.7979 (t) REVERT: A 530 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5432 (mp0) REVERT: A 555 LYS cc_start: 0.8960 (tmmt) cc_final: 0.8721 (tmmt) REVERT: A 562 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7168 (mm-30) REVERT: A 567 LYS cc_start: 0.8175 (tppp) cc_final: 0.7935 (tppp) REVERT: A 569 GLU cc_start: 0.7502 (tp30) cc_final: 0.6980 (tp30) REVERT: A 658 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7546 (mt-10) REVERT: A 726 MET cc_start: 0.7903 (tpt) cc_final: 0.7622 (tpp) REVERT: A 728 GLU cc_start: 0.6855 (tm-30) cc_final: 0.6567 (tm-30) REVERT: A 813 MET cc_start: 0.8293 (mmt) cc_final: 0.7931 (mmt) REVERT: B 417 ARG cc_start: 0.7698 (mpt180) cc_final: 0.7435 (mmt180) REVERT: B 445 SER cc_start: 0.7871 (t) cc_final: 0.7228 (m) REVERT: B 550 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.7989 (p0) REVERT: B 606 SER cc_start: 0.7797 (m) cc_final: 0.7244 (p) REVERT: B 709 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: B 856 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8167 (ttmm) REVERT: B 860 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7969 (ptmm) REVERT: B 898 ASN cc_start: 0.7805 (t0) cc_final: 0.7361 (t0) REVERT: B 899 MET cc_start: 0.6130 (ppp) cc_final: 0.5863 (ppp) REVERT: B 1063 ILE cc_start: 0.7676 (mm) cc_final: 0.7474 (mm) outliers start: 52 outliers final: 32 residues processed: 419 average time/residue: 0.3205 time to fit residues: 191.3694 Evaluate side-chains 412 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 374 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1096 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 156 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 164 optimal weight: 0.4980 chunk 74 optimal weight: 0.0060 chunk 7 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 147 optimal weight: 0.1980 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 582 GLN B 613 ASN B 630 HIS B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.166263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134691 restraints weight = 35458.940| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.28 r_work: 0.3521 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14830 Z= 0.121 Angle : 0.579 8.643 20191 Z= 0.303 Chirality : 0.040 0.160 2310 Planarity : 0.004 0.059 2416 Dihedral : 16.758 135.957 2309 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.93 % Allowed : 27.36 % Favored : 69.71 % 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: 0.34 (0.21), residues: 1674 helix: 1.42 (0.18), residues: 813 sheet: -0.81 (0.35), residues: 228 loop : -0.90 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1111 HIS 0.008 0.001 HIS B 647 PHE 0.042 0.001 PHE A 42 TYR 0.023 0.001 TYR B 334 ARG 0.009 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 751) hydrogen bonds : angle 4.15145 ( 2087) covalent geometry : bond 0.00271 (14830) covalent geometry : angle 0.57859 (20191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 381 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7643 (ttm110) cc_final: 0.7365 (ttm110) REVERT: A 43 TYR cc_start: 0.7469 (m-80) cc_final: 0.7072 (m-80) REVERT: A 67 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7407 (ttt) REVERT: A 97 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7566 (mt0) REVERT: A 106 ARG cc_start: 0.7551 (tpp-160) cc_final: 0.7344 (mmt90) REVERT: A 119 LEU cc_start: 0.8305 (tp) cc_final: 0.7999 (tp) REVERT: A 160 GLN cc_start: 0.7483 (tt0) cc_final: 0.7113 (tt0) REVERT: A 215 GLN cc_start: 0.7549 (tm-30) cc_final: 0.6975 (tm-30) REVERT: A 216 ILE cc_start: 0.8553 (tp) cc_final: 0.8158 (tp) REVERT: A 218 GLN cc_start: 0.7666 (mt0) cc_final: 0.7347 (mm-40) REVERT: A 261 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7869 (tmm) REVERT: A 298 GLN cc_start: 0.8046 (mt0) cc_final: 0.7722 (mt0) REVERT: A 299 TYR cc_start: 0.8567 (m-80) cc_final: 0.8287 (m-80) REVERT: A 351 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7139 (mpp) REVERT: A 371 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 402 GLN cc_start: 0.7135 (tt0) cc_final: 0.6841 (tp40) REVERT: A 430 LYS cc_start: 0.6052 (mmmt) cc_final: 0.5124 (mmmt) REVERT: A 515 SER cc_start: 0.8391 (m) cc_final: 0.8103 (t) REVERT: A 530 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5426 (mp0) REVERT: A 555 LYS cc_start: 0.8960 (tmmt) cc_final: 0.8716 (tmmt) REVERT: A 562 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7176 (mm-30) REVERT: A 567 LYS cc_start: 0.8211 (tppp) cc_final: 0.7997 (tppp) REVERT: A 569 GLU cc_start: 0.7586 (tp30) cc_final: 0.7110 (tp30) REVERT: A 658 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7492 (mt-10) REVERT: A 691 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7792 (pt) REVERT: A 728 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6697 (tm-30) REVERT: A 809 GLU cc_start: 0.7225 (tp30) cc_final: 0.6625 (tp30) REVERT: A 813 MET cc_start: 0.8339 (mmt) cc_final: 0.8035 (mmt) REVERT: A 899 MET cc_start: 0.1240 (tmt) cc_final: -0.1922 (ppp) REVERT: B 264 GLU cc_start: 0.7332 (mp0) cc_final: 0.6975 (mp0) REVERT: B 407 ASP cc_start: 0.6773 (t0) cc_final: 0.6388 (t70) REVERT: B 417 ARG cc_start: 0.7715 (mpt180) cc_final: 0.7391 (mmt180) REVERT: B 445 SER cc_start: 0.7810 (t) cc_final: 0.7213 (m) REVERT: B 550 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8048 (p0) REVERT: B 606 SER cc_start: 0.7818 (m) cc_final: 0.7264 (p) REVERT: B 683 GLU cc_start: 0.7493 (tp30) cc_final: 0.7285 (tp30) REVERT: B 856 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8199 (ttmm) REVERT: B 860 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7976 (ptmt) REVERT: B 863 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7894 (ptp90) REVERT: B 898 ASN cc_start: 0.7841 (t0) cc_final: 0.7412 (t0) REVERT: B 899 MET cc_start: 0.6138 (ppp) cc_final: 0.5861 (ppp) REVERT: B 964 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7860 (mtm110) REVERT: B 1077 ASP cc_start: 0.7684 (t0) cc_final: 0.7115 (t0) outliers start: 44 outliers final: 29 residues processed: 408 average time/residue: 0.2954 time to fit residues: 170.7021 Evaluate side-chains 410 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 374 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 169 optimal weight: 40.0000 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.162779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131854 restraints weight = 28927.697| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.89 r_work: 0.3500 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14830 Z= 0.217 Angle : 0.632 8.560 20191 Z= 0.329 Chirality : 0.043 0.173 2310 Planarity : 0.004 0.063 2416 Dihedral : 16.833 148.700 2307 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.80 % Allowed : 27.83 % Favored : 69.37 % 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: 0.16 (0.21), residues: 1674 helix: 1.21 (0.18), residues: 816 sheet: -0.84 (0.35), residues: 217 loop : -0.91 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 807 HIS 0.006 0.001 HIS B 647 PHE 0.041 0.002 PHE A 42 TYR 0.032 0.002 TYR B 334 ARG 0.009 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 751) hydrogen bonds : angle 4.29639 ( 2087) covalent geometry : bond 0.00490 (14830) covalent geometry : angle 0.63165 (20191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 376 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7588 (ttm110) cc_final: 0.7319 (ttm110) REVERT: A 38 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: A 67 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7381 (ttt) REVERT: A 97 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7560 (mt0) REVERT: A 106 ARG cc_start: 0.7561 (tpp-160) cc_final: 0.7325 (mmt90) REVERT: A 119 LEU cc_start: 0.8343 (tp) cc_final: 0.8033 (tp) REVERT: A 215 GLN cc_start: 0.7533 (tm-30) cc_final: 0.6948 (tm-30) REVERT: A 216 ILE cc_start: 0.8523 (tp) cc_final: 0.8124 (tp) REVERT: A 218 GLN cc_start: 0.7751 (mt0) cc_final: 0.7524 (mm-40) REVERT: A 246 LYS cc_start: 0.7974 (tppt) cc_final: 0.7672 (tppt) REVERT: A 261 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7815 (tmm) REVERT: A 298 GLN cc_start: 0.8137 (mt0) cc_final: 0.7821 (mt0) REVERT: A 371 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7864 (mm-30) REVERT: A 402 GLN cc_start: 0.7216 (tt0) cc_final: 0.6952 (tp40) REVERT: A 430 LYS cc_start: 0.6140 (mmmt) cc_final: 0.5186 (mmmt) REVERT: A 515 SER cc_start: 0.8405 (m) cc_final: 0.8162 (t) REVERT: A 530 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.5508 (mp0) REVERT: A 555 LYS cc_start: 0.8974 (tmmt) cc_final: 0.8732 (tmmt) REVERT: A 562 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7230 (mm-30) REVERT: A 567 LYS cc_start: 0.8189 (tppp) cc_final: 0.7959 (tppp) REVERT: A 569 GLU cc_start: 0.7559 (tp30) cc_final: 0.7047 (tp30) REVERT: A 658 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7600 (mt-10) REVERT: A 691 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7912 (pt) REVERT: A 779 MET cc_start: 0.7608 (mtp) cc_final: 0.7247 (mtp) REVERT: A 809 GLU cc_start: 0.7212 (tp30) cc_final: 0.6630 (tp30) REVERT: A 813 MET cc_start: 0.8401 (mmt) cc_final: 0.7988 (mmt) REVERT: A 899 MET cc_start: 0.1368 (tmt) cc_final: 0.1080 (tmt) REVERT: B 261 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7671 (mt-10) REVERT: B 264 GLU cc_start: 0.7288 (mp0) cc_final: 0.6944 (mp0) REVERT: B 445 SER cc_start: 0.7884 (t) cc_final: 0.7272 (m) REVERT: B 550 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7910 (p0) REVERT: B 606 SER cc_start: 0.7926 (m) cc_final: 0.7361 (p) REVERT: B 692 GLN cc_start: 0.7931 (tp40) cc_final: 0.7682 (tp40) REVERT: B 856 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8253 (ttmm) REVERT: B 860 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8147 (ptmt) REVERT: B 898 ASN cc_start: 0.7879 (t0) cc_final: 0.7443 (t0) REVERT: B 899 MET cc_start: 0.6188 (ppp) cc_final: 0.5924 (ppp) REVERT: B 1092 GLU cc_start: 0.7743 (tp30) cc_final: 0.7235 (tp30) outliers start: 42 outliers final: 27 residues processed: 401 average time/residue: 0.2965 time to fit residues: 168.4358 Evaluate side-chains 405 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 371 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 0.0970 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 112 optimal weight: 0.1980 chunk 67 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN B 582 GLN B 613 ASN B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 HIS B1027 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.164949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136222 restraints weight = 20329.574| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.30 r_work: 0.3580 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14830 Z= 0.147 Angle : 0.609 9.587 20191 Z= 0.317 Chirality : 0.041 0.178 2310 Planarity : 0.004 0.062 2416 Dihedral : 16.771 147.829 2307 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.60 % Allowed : 28.43 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.21), residues: 1674 helix: 1.29 (0.18), residues: 815 sheet: -0.89 (0.35), residues: 219 loop : -0.89 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1111 HIS 0.005 0.001 HIS B 647 PHE 0.035 0.002 PHE A 42 TYR 0.022 0.001 TYR B 334 ARG 0.010 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 751) hydrogen bonds : angle 4.25810 ( 2087) covalent geometry : bond 0.00334 (14830) covalent geometry : angle 0.60914 (20191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 376 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7549 (ttm110) cc_final: 0.7283 (ttm110) REVERT: A 43 TYR cc_start: 0.7512 (m-80) cc_final: 0.7090 (m-80) REVERT: A 97 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7474 (mt0) REVERT: A 106 ARG cc_start: 0.7534 (tpp-160) cc_final: 0.7107 (mmt90) REVERT: A 119 LEU cc_start: 0.8301 (tp) cc_final: 0.7992 (tp) REVERT: A 160 GLN cc_start: 0.7424 (tt0) cc_final: 0.7008 (tt0) REVERT: A 215 GLN cc_start: 0.7406 (tm-30) cc_final: 0.6792 (tm-30) REVERT: A 216 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8007 (tp) REVERT: A 218 GLN cc_start: 0.7636 (mt0) cc_final: 0.7387 (mm-40) REVERT: A 246 LYS cc_start: 0.7914 (tppt) cc_final: 0.7604 (tppt) REVERT: A 261 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7788 (tmm) REVERT: A 298 GLN cc_start: 0.8051 (mt0) cc_final: 0.7700 (mt0) REVERT: A 371 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 430 LYS cc_start: 0.6061 (mmmt) cc_final: 0.5252 (mmmt) REVERT: A 482 ARG cc_start: 0.8042 (tpp80) cc_final: 0.7789 (tpp80) REVERT: A 491 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7696 (mmmt) REVERT: A 515 SER cc_start: 0.8427 (m) cc_final: 0.8193 (t) REVERT: A 530 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5491 (mp0) REVERT: A 555 LYS cc_start: 0.8969 (tmmt) cc_final: 0.8720 (tmmt) REVERT: A 562 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7187 (mm-30) REVERT: A 567 LYS cc_start: 0.8139 (tppp) cc_final: 0.7918 (tppp) REVERT: A 569 GLU cc_start: 0.7451 (tp30) cc_final: 0.6942 (tp30) REVERT: A 658 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7476 (mt-10) REVERT: A 728 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6689 (tm-30) REVERT: A 729 MET cc_start: 0.7872 (mmm) cc_final: 0.7568 (mmm) REVERT: A 779 MET cc_start: 0.7473 (mtp) cc_final: 0.7117 (mtp) REVERT: A 809 GLU cc_start: 0.7129 (tp30) cc_final: 0.6560 (tp30) REVERT: A 813 MET cc_start: 0.8298 (mmt) cc_final: 0.7939 (mmt) REVERT: A 899 MET cc_start: 0.1241 (tmt) cc_final: 0.1027 (tmt) REVERT: B 261 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: B 264 GLU cc_start: 0.7213 (mp0) cc_final: 0.6863 (mp0) REVERT: B 445 SER cc_start: 0.7831 (t) cc_final: 0.7226 (m) REVERT: B 550 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.7948 (p0) REVERT: B 606 SER cc_start: 0.7799 (m) cc_final: 0.7250 (p) REVERT: B 613 ASN cc_start: 0.7901 (m-40) cc_final: 0.7457 (m110) REVERT: B 683 GLU cc_start: 0.7388 (tp30) cc_final: 0.7149 (tp30) REVERT: B 856 LYS cc_start: 0.8444 (ttmt) cc_final: 0.8180 (ttmm) REVERT: B 860 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8051 (ptmt) REVERT: B 863 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7724 (ptp90) REVERT: B 898 ASN cc_start: 0.7773 (t0) cc_final: 0.7352 (t0) REVERT: B 899 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.5842 (ppp) REVERT: B 1092 GLU cc_start: 0.7614 (tp30) cc_final: 0.7038 (tp30) outliers start: 39 outliers final: 27 residues processed: 398 average time/residue: 0.2987 time to fit residues: 168.2070 Evaluate side-chains 409 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 375 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1010 HIS Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 53 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 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 = 0.4105 r_free = 0.4105 target = 0.164502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133476 restraints weight = 30522.243| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.99 r_work: 0.3510 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14830 Z= 0.166 Angle : 0.634 12.102 20191 Z= 0.331 Chirality : 0.042 0.190 2310 Planarity : 0.004 0.066 2416 Dihedral : 16.782 151.053 2307 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.73 % Allowed : 28.70 % Favored : 68.58 % 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: 0.19 (0.21), residues: 1674 helix: 1.23 (0.18), residues: 816 sheet: -0.86 (0.35), residues: 225 loop : -0.88 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 807 HIS 0.007 0.001 HIS B1010 PHE 0.055 0.002 PHE B 752 TYR 0.039 0.002 TYR B1011 ARG 0.010 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 751) hydrogen bonds : angle 4.28284 ( 2087) covalent geometry : bond 0.00377 (14830) covalent geometry : angle 0.63423 (20191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10062.12 seconds wall clock time: 179 minutes 31.32 seconds (10771.32 seconds total)