Starting phenix.real_space_refine on Thu Jun 12 10:25:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ga5_51174/06_2025/9ga5_51174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ga5_51174/06_2025/9ga5_51174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ga5_51174/06_2025/9ga5_51174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ga5_51174/06_2025/9ga5_51174.map" model { file = "/net/cci-nas-00/data/ceres_data/9ga5_51174/06_2025/9ga5_51174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ga5_51174/06_2025/9ga5_51174_neut.cif" } resolution = 3.2 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= 0.002 sd= 0.028 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 Zn 4 6.06 5 P 75 5.49 5 S 40 5.16 5 C 8360 2.51 5 N 2446 2.21 5 O 2790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 13715 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6100 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 39, 'TRANS': 757} Chain breaks: 2 Chain: "B" Number of atoms: 6100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6100 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 39, 'TRANS': 757} Chain breaks: 2 Chain: "C" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 663 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "D" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 794 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4582 SG CYS A 753 61.595 30.456 100.785 1.00189.87 S ATOM 4602 SG CYS A 756 58.273 32.140 99.388 1.00184.26 S ATOM 4755 SG CYS A 776 59.276 28.844 98.064 1.00190.85 S ATOM 4777 SG CYS A 779 58.741 29.344 101.977 1.00188.07 S ATOM 1083 SG CYS A 282 52.868 84.607 83.473 1.00170.00 S ATOM 1105 SG CYS A 285 52.465 81.302 84.849 1.00165.89 S ATOM 2000 SG CYS A 412 55.014 83.727 86.606 1.00172.93 S ATOM 2020 SG CYS A 415 51.389 84.262 87.007 1.00167.05 S ATOM 10682 SG CYS B 753 58.932 80.626 58.715 1.00168.83 S ATOM 10702 SG CYS B 756 56.103 78.048 60.002 1.00167.21 S ATOM 10855 SG CYS B 776 56.096 81.265 61.270 1.00162.36 S ATOM 10877 SG CYS B 779 55.810 80.640 57.241 1.00161.65 S ATOM 7183 SG CYS B 282 54.601 26.603 76.638 1.00170.36 S ATOM 7205 SG CYS B 285 53.813 28.798 73.948 1.00174.96 S ATOM 8100 SG CYS B 412 55.774 25.605 72.945 1.00176.91 S ATOM 8120 SG CYS B 415 52.209 25.374 74.690 1.00165.13 S Time building chain proxies: 9.45, per 1000 atoms: 0.69 Number of scatterers: 13715 At special positions: 0 Unit cell: (99.12, 109.2, 149.52, 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) Zn 4 29.99 S 40 16.00 P 75 15.00 O 2790 8.00 N 2446 7.00 C 8360 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: 3.50 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 779 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 753 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 756 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 776 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 282 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 415 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 285 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 412 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 756 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 779 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 753 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 776 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 282 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 285 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 415 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 412 " Number of angles added : 24 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 13 sheets defined 47.1% alpha, 10.9% beta 27 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 4.92 Creating SS restraints... Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.772A pdb=" N TYR A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 58 No H-bonds generated for 'chain 'A' and resid 57 through 58' Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.634A pdb=" N ALA A 62 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A 63 " --> pdb=" O ALA A 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 59 through 63' Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.820A pdb=" N GLN A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.523A pdb=" N THR A 91 " --> pdb=" O GLN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 104 through 117 removed outlier: 3.545A pdb=" N TYR A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.565A pdb=" N VAL A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 312 through 317 removed outlier: 4.248A pdb=" N ASN A 317 " --> pdb=" O PRO A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 336 removed outlier: 4.191A pdb=" N TYR A 323 " --> pdb=" O HIS A 319 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 382 through 392 Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 421 through 424 Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 449 through 460 Processing helix chain 'A' and resid 463 through 488 removed outlier: 3.723A pdb=" N ILE A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLN A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 removed outlier: 3.556A pdb=" N LEU A 501 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 518 removed outlier: 3.750A pdb=" N GLY A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 550 removed outlier: 4.259A pdb=" N ARG A 539 " --> pdb=" O GLN A 535 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ARG A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 607 Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 691 through 695 Processing helix chain 'A' and resid 713 through 718 Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 785 through 790 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 816 through 830 removed outlier: 3.711A pdb=" N TYR A 822 " --> pdb=" O GLY A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 843 Processing helix chain 'A' and resid 844 through 859 removed outlier: 3.975A pdb=" N GLN A 858 " --> pdb=" O ALA A 854 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 859 " --> pdb=" O SER A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 893 Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 921 through 925 removed outlier: 3.628A pdb=" N GLY A 924 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 943 through 951 removed outlier: 4.189A pdb=" N GLU A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 43 Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.919A pdb=" N SER B 57 " --> pdb=" O ARG B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 318 through 319 No H-bonds generated for 'chain 'B' and resid 318 through 319' Processing helix chain 'B' and resid 320 through 336 removed outlier: 3.572A pdb=" N ALA B 334 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 removed outlier: 3.512A pdb=" N LEU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 396 through 405 removed outlier: 4.928A pdb=" N ARG B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR B 403 " --> pdb=" O MET B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 426 removed outlier: 3.655A pdb=" N ALA B 426 " --> pdb=" O PRO B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 463 through 488 removed outlier: 3.618A pdb=" N ILE B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 518 removed outlier: 3.682A pdb=" N GLY B 518 " --> pdb=" O GLN B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 550 removed outlier: 4.136A pdb=" N ARG B 539 " --> pdb=" O GLN B 535 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 596 removed outlier: 3.702A pdb=" N LEU B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 607 Processing helix chain 'B' and resid 659 through 665 Processing helix chain 'B' and resid 666 through 677 removed outlier: 3.755A pdb=" N ALA B 670 " --> pdb=" O ASP B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 695 removed outlier: 3.743A pdb=" N TYR B 694 " --> pdb=" O GLY B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 719 Processing helix chain 'B' and resid 719 through 730 removed outlier: 3.987A pdb=" N LYS B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 737 Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 785 through 790 Processing helix chain 'B' and resid 791 through 796 removed outlier: 7.227A pdb=" N LYS B 794 " --> pdb=" O VAL B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 804 Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 816 through 830 removed outlier: 4.434A pdb=" N TYR B 822 " --> pdb=" O GLY B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 843 Processing helix chain 'B' and resid 844 through 858 removed outlier: 3.789A pdb=" N GLN B 858 " --> pdb=" O ALA B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 894 removed outlier: 3.506A pdb=" N LYS B 894 " --> pdb=" O GLY B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 911 Processing helix chain 'B' and resid 921 through 925 removed outlier: 3.806A pdb=" N GLY B 924 " --> pdb=" O GLY B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 943 through 950 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 23 removed outlier: 5.686A pdb=" N VAL A 18 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 9 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86 removed outlier: 6.104A pdb=" N VAL A 84 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU A 27 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL A 572 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL A 29 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE A 574 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR A 31 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 294 Processing sheet with id=AA4, first strand: chain 'A' and resid 640 through 645 removed outlier: 5.723A pdb=" N ILE A 640 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 698 through 701 removed outlier: 6.248A pdb=" N TYR A 867 " --> pdb=" O ILE A 899 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE A 901 " --> pdb=" O TYR A 867 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU A 869 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 930 " --> pdb=" O ASP A 916 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 761 through 764 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 removed outlier: 5.351A pdb=" N VAL B 18 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 86 removed outlier: 6.025A pdb=" N VAL B 84 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE B 28 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU B 27 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL B 572 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B 29 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE B 574 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR B 31 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 571 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER B 588 " --> pdb=" O ILE B 571 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP B 573 " --> pdb=" O VAL B 586 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 290 through 293 Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 361 removed outlier: 3.773A pdb=" N PHE B 380 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 640 through 645 removed outlier: 5.457A pdb=" N ILE B 640 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 631 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 697 through 701 removed outlier: 3.906A pdb=" N ALA B 930 " --> pdb=" O ASP B 916 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 761 through 764 508 hydrogen bonds defined for protein. 1401 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 4.13 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: 4314 1.34 - 1.46: 2689 1.46 - 1.58: 6898 1.58 - 1.70: 145 1.70 - 1.82: 58 Bond restraints: 14104 Sorted by residual: bond pdb=" CA LEU A 462 " pdb=" C LEU A 462 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.34e-02 5.57e+03 5.74e+00 bond pdb=" P DG D -23 " pdb=" OP1 DG D -23 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 2.99e+00 bond pdb=" CG HIS A 363 " pdb=" CD2 HIS A 363 " ideal model delta sigma weight residual 1.354 1.336 0.018 1.10e-02 8.26e+03 2.75e+00 bond pdb=" N TYR A 377 " pdb=" CA TYR A 377 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.42e+00 bond pdb=" N HIS A 363 " pdb=" CA HIS A 363 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.35e+00 ... (remaining 14099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 19256 3.31 - 6.61: 137 6.61 - 9.92: 30 9.92 - 13.22: 1 13.22 - 16.53: 2 Bond angle restraints: 19426 Sorted by residual: angle pdb=" C HIS B 635 " pdb=" CA HIS B 635 " pdb=" CB HIS B 635 " ideal model delta sigma weight residual 116.54 109.49 7.05 1.15e+00 7.56e-01 3.76e+01 angle pdb=" O3' DT D -28 " pdb=" C3' DT D -28 " pdb=" C2' DT D -28 " ideal model delta sigma weight residual 111.50 102.62 8.88 1.50e+00 4.44e-01 3.51e+01 angle pdb=" C3' DT D -29 " pdb=" O3' DT D -29 " pdb=" P DT D -28 " ideal model delta sigma weight residual 120.20 111.47 8.73 1.50e+00 4.44e-01 3.39e+01 angle pdb=" CA MET A 391 " pdb=" CB MET A 391 " pdb=" CG MET A 391 " ideal model delta sigma weight residual 114.10 125.31 -11.21 2.00e+00 2.50e-01 3.14e+01 angle pdb=" N MET A 391 " pdb=" CA MET A 391 " pdb=" CB MET A 391 " ideal model delta sigma weight residual 110.41 119.75 -9.34 1.68e+00 3.54e-01 3.09e+01 ... (remaining 19421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 7847 35.78 - 71.55: 452 71.55 - 107.33: 17 107.33 - 143.10: 5 143.10 - 178.88: 6 Dihedral angle restraints: 8327 sinusoidal: 3825 harmonic: 4502 Sorted by residual: dihedral pdb=" CA CYS B 756 " pdb=" C CYS B 756 " pdb=" N THR B 757 " pdb=" CA THR B 757 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DT D -26 " pdb=" C3' DT D -26 " pdb=" O3' DT D -26 " pdb=" P DA D -25 " ideal model delta sinusoidal sigma weight residual 220.00 41.12 178.88 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC C 36 " pdb=" C3' DC C 36 " pdb=" O3' DC C 36 " pdb=" P DT C 37 " ideal model delta sinusoidal sigma weight residual 220.00 41.79 178.21 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2188 0.127 - 0.253: 7 0.253 - 0.380: 3 0.380 - 0.507: 2 0.507 - 0.633: 4 Chirality restraints: 2204 Sorted by residual: chirality pdb=" P DT D -28 " pdb=" OP1 DT D -28 " pdb=" OP2 DT D -28 " pdb=" O5' DT D -28 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DC D -22 " pdb=" OP1 DC D -22 " pdb=" OP2 DC D -22 " pdb=" O5' DC D -22 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.44e+00 chirality pdb=" P DT D -27 " pdb=" OP1 DT D -27 " pdb=" OP2 DT D -27 " pdb=" O5' DT D -27 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.62e+00 ... (remaining 2201 not shown) Planarity restraints: 2295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 362 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C VAL A 362 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL A 362 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS A 363 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT D -28 " -0.011 2.00e-02 2.50e+03 1.33e-02 4.40e+00 pdb=" N1 DT D -28 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DT D -28 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT D -28 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DT D -28 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT D -28 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT D -28 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DT D -28 " 0.011 2.00e-02 2.50e+03 pdb=" C7 DT D -28 " -0.027 2.00e-02 2.50e+03 pdb=" C6 DT D -28 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 44 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" CG ASP A 44 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP A 44 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 44 " 0.009 2.00e-02 2.50e+03 ... (remaining 2292 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 16 2.46 - 3.07: 9724 3.07 - 3.68: 22767 3.68 - 4.29: 32504 4.29 - 4.90: 50946 Nonbonded interactions: 115957 Sorted by model distance: nonbonded pdb=" NE2 HIS A 319 " pdb=" OP2 DA C 26 " model vdw 1.844 3.120 nonbonded pdb=" NE ARG B 860 " pdb=" OP2 DA C 8 " model vdw 1.963 3.120 nonbonded pdb=" CG MET A 399 " pdb=" N6 DA D -25 " model vdw 2.062 3.520 nonbonded pdb=" O4' DT D -27 " pdb=" O5' DT D -26 " model vdw 2.280 3.040 nonbonded pdb=" N6 DA C 14 " pdb=" O4 DT D -15 " model vdw 2.287 3.120 ... (remaining 115952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.570 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: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 41.140 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14120 Z= 0.210 Angle : 0.836 19.262 19450 Z= 0.416 Chirality : 0.053 0.633 2204 Planarity : 0.004 0.036 2295 Dihedral : 20.062 178.879 5459 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.23 % Allowed : 17.94 % Favored : 81.83 % Cbeta Deviations : 0.07 % 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 (0.22), residues: 1582 helix: 0.38 (0.22), residues: 590 sheet: 0.78 (0.36), residues: 198 loop : -0.47 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 315 HIS 0.008 0.001 HIS A 363 PHE 0.016 0.001 PHE A 386 TYR 0.014 0.001 TYR A 739 ARG 0.003 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.15735 ( 568) hydrogen bonds : angle 6.85747 ( 1519) metal coordination : bond 0.00919 ( 16) metal coordination : angle 9.02757 ( 24) covalent geometry : bond 0.00448 (14104) covalent geometry : angle 0.77453 (19426) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 1.505 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.9120 (mmm) cc_final: 0.7914 (mmm) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.2700 time to fit residues: 16.2292 Evaluate side-chains 35 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 92 ASN A 538 ASN ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN B 467 GLN B 514 GLN B 535 GLN B 538 ASN B 597 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.064474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.042521 restraints weight = 65060.336| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.11 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14120 Z= 0.173 Angle : 0.705 17.100 19450 Z= 0.332 Chirality : 0.043 0.159 2204 Planarity : 0.004 0.036 2295 Dihedral : 21.018 179.792 2591 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.68 % Allowed : 16.26 % Favored : 80.06 % 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: 0.15 (0.22), residues: 1582 helix: 0.59 (0.22), residues: 597 sheet: 0.83 (0.35), residues: 197 loop : -0.40 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 913 HIS 0.004 0.001 HIS A 587 PHE 0.010 0.001 PHE B 337 TYR 0.016 0.001 TYR B 403 ARG 0.003 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 568) hydrogen bonds : angle 5.26912 ( 1519) metal coordination : bond 0.00784 ( 16) metal coordination : angle 8.34484 ( 24) covalent geometry : bond 0.00392 (14104) covalent geometry : angle 0.64200 (19426) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 36 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7733 (pp20) REVERT: A 407 MET cc_start: 0.9348 (mmm) cc_final: 0.8289 (mmm) REVERT: A 802 LEU cc_start: 0.9303 (tp) cc_final: 0.9089 (pp) REVERT: B 597 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8565 (t0) REVERT: B 849 GLN cc_start: 0.9121 (tp40) cc_final: 0.8651 (tp40) REVERT: B 856 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8391 (mp0) outliers start: 48 outliers final: 18 residues processed: 82 average time/residue: 0.2214 time to fit residues: 29.2905 Evaluate side-chains 56 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 35 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 351 ARG Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 121 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 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 = 0.3582 r_free = 0.3582 target = 0.063108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.040959 restraints weight = 66123.996| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 4.10 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 14120 Z= 0.262 Angle : 0.756 18.929 19450 Z= 0.358 Chirality : 0.045 0.169 2204 Planarity : 0.004 0.035 2295 Dihedral : 21.172 179.468 2591 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.91 % Allowed : 17.48 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1582 helix: 0.48 (0.21), residues: 597 sheet: 0.65 (0.36), residues: 199 loop : -0.46 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 570 HIS 0.005 0.001 HIS A 587 PHE 0.013 0.002 PHE A 324 TYR 0.010 0.002 TYR A 717 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.05114 ( 568) hydrogen bonds : angle 5.23252 ( 1519) metal coordination : bond 0.01351 ( 16) metal coordination : angle 8.47406 ( 24) covalent geometry : bond 0.00583 (14104) covalent geometry : angle 0.69527 (19426) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 35 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 MET cc_start: 0.8043 (mpp) cc_final: 0.7755 (mpp) REVERT: A 333 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7896 (pp20) REVERT: A 407 MET cc_start: 0.9332 (mmm) cc_final: 0.8451 (mmm) REVERT: B 282 CYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6824 (p) REVERT: B 528 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: B 701 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7740 (t) REVERT: B 849 GLN cc_start: 0.9145 (tp40) cc_final: 0.8496 (tp40) outliers start: 51 outliers final: 23 residues processed: 83 average time/residue: 0.2110 time to fit residues: 28.8136 Evaluate side-chains 63 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 36 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 351 ARG Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 104 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 92 ASN ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.064238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.042282 restraints weight = 64865.108| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.10 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14120 Z= 0.148 Angle : 0.679 19.867 19450 Z= 0.320 Chirality : 0.043 0.152 2204 Planarity : 0.003 0.034 2295 Dihedral : 21.140 178.451 2591 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.45 % Allowed : 18.56 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.22), residues: 1582 helix: 0.58 (0.22), residues: 603 sheet: 0.81 (0.36), residues: 197 loop : -0.41 (0.24), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 913 HIS 0.004 0.001 HIS A 363 PHE 0.012 0.001 PHE B 337 TYR 0.006 0.001 TYR B 108 ARG 0.003 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 568) hydrogen bonds : angle 4.92598 ( 1519) metal coordination : bond 0.01112 ( 16) metal coordination : angle 7.64065 ( 24) covalent geometry : bond 0.00339 (14104) covalent geometry : angle 0.62424 (19426) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 37 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7591 (pp20) REVERT: A 802 LEU cc_start: 0.9315 (tp) cc_final: 0.9092 (pp) REVERT: B 528 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: B 701 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7500 (t) REVERT: B 849 GLN cc_start: 0.9117 (tp40) cc_final: 0.8433 (tp40) outliers start: 45 outliers final: 25 residues processed: 79 average time/residue: 0.2156 time to fit residues: 27.8997 Evaluate side-chains 63 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 35 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 17 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 157 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.063921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.042042 restraints weight = 65079.821| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.09 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14120 Z= 0.174 Angle : 0.697 19.035 19450 Z= 0.328 Chirality : 0.043 0.171 2204 Planarity : 0.003 0.036 2295 Dihedral : 21.182 179.444 2591 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.60 % Allowed : 18.33 % Favored : 78.07 % 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 (0.22), residues: 1582 helix: 0.65 (0.22), residues: 603 sheet: 0.78 (0.36), residues: 197 loop : -0.39 (0.24), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 570 HIS 0.003 0.001 HIS A 587 PHE 0.012 0.001 PHE B 337 TYR 0.008 0.001 TYR A 323 ARG 0.004 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04985 ( 568) hydrogen bonds : angle 4.89977 ( 1519) metal coordination : bond 0.00982 ( 16) metal coordination : angle 7.96064 ( 24) covalent geometry : bond 0.00394 (14104) covalent geometry : angle 0.63924 (19426) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 37 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7434 (pp20) REVERT: A 800 GLU cc_start: 0.9425 (OUTLIER) cc_final: 0.9184 (tm-30) REVERT: B 328 MET cc_start: 0.8227 (ppp) cc_final: 0.7920 (ppp) REVERT: B 528 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: B 701 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7520 (t) REVERT: B 849 GLN cc_start: 0.9099 (tp40) cc_final: 0.8417 (tp40) outliers start: 47 outliers final: 28 residues processed: 80 average time/residue: 0.2149 time to fit residues: 28.2288 Evaluate side-chains 68 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 36 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 66 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 78 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.063004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040512 restraints weight = 67990.979| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 4.14 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 14120 Z= 0.251 Angle : 0.754 22.120 19450 Z= 0.354 Chirality : 0.045 0.226 2204 Planarity : 0.004 0.036 2295 Dihedral : 21.331 179.847 2591 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.37 % Allowed : 18.56 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1582 helix: 0.40 (0.21), residues: 613 sheet: 0.63 (0.37), residues: 189 loop : -0.50 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 570 HIS 0.004 0.001 HIS A 587 PHE 0.013 0.002 PHE A 324 TYR 0.010 0.002 TYR B 108 ARG 0.004 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.05442 ( 568) hydrogen bonds : angle 5.04514 ( 1519) metal coordination : bond 0.01316 ( 16) metal coordination : angle 8.77474 ( 24) covalent geometry : bond 0.00559 (14104) covalent geometry : angle 0.68811 (19426) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 36 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7519 (pp20) REVERT: B 68 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7935 (mm-40) REVERT: B 528 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: B 597 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8678 (t0) REVERT: B 701 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7689 (t) REVERT: B 849 GLN cc_start: 0.9098 (tp40) cc_final: 0.8437 (tp40) outliers start: 57 outliers final: 34 residues processed: 88 average time/residue: 0.2051 time to fit residues: 29.4951 Evaluate side-chains 73 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 34 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 917 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 137 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.063157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.040733 restraints weight = 67598.680| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 4.14 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14120 Z= 0.226 Angle : 0.744 20.047 19450 Z= 0.350 Chirality : 0.044 0.213 2204 Planarity : 0.004 0.036 2295 Dihedral : 21.357 179.426 2591 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.37 % Allowed : 20.32 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.22), residues: 1582 helix: 0.41 (0.21), residues: 607 sheet: 0.58 (0.37), residues: 189 loop : -0.53 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 570 HIS 0.003 0.001 HIS A 587 PHE 0.019 0.001 PHE A 386 TYR 0.009 0.001 TYR B 108 ARG 0.005 0.000 ARG B 596 Details of bonding type rmsd hydrogen bonds : bond 0.05339 ( 568) hydrogen bonds : angle 5.04064 ( 1519) metal coordination : bond 0.01123 ( 16) metal coordination : angle 8.36793 ( 24) covalent geometry : bond 0.00504 (14104) covalent geometry : angle 0.68368 (19426) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 36 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7501 (pp20) REVERT: A 802 LEU cc_start: 0.9238 (tp) cc_final: 0.8998 (pp) REVERT: B 328 MET cc_start: 0.8242 (ppp) cc_final: 0.7770 (ppp) REVERT: B 528 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: B 701 VAL cc_start: 0.8033 (OUTLIER) cc_final: 0.7631 (t) REVERT: B 849 GLN cc_start: 0.9096 (tp40) cc_final: 0.8444 (tp40) outliers start: 44 outliers final: 33 residues processed: 77 average time/residue: 0.2090 time to fit residues: 26.4786 Evaluate side-chains 72 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 36 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 917 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 131 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.064902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.042767 restraints weight = 65716.444| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 4.15 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14120 Z= 0.126 Angle : 0.685 16.090 19450 Z= 0.325 Chirality : 0.043 0.229 2204 Planarity : 0.003 0.037 2295 Dihedral : 21.236 178.525 2591 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.99 % Allowed : 20.63 % Favored : 76.38 % 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: 0.09 (0.22), residues: 1582 helix: 0.58 (0.22), residues: 615 sheet: 0.71 (0.36), residues: 199 loop : -0.47 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 343 HIS 0.002 0.000 HIS B 635 PHE 0.014 0.001 PHE A 386 TYR 0.008 0.001 TYR B 61 ARG 0.005 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04980 ( 568) hydrogen bonds : angle 4.81023 ( 1519) metal coordination : bond 0.00537 ( 16) metal coordination : angle 6.53176 ( 24) covalent geometry : bond 0.00286 (14104) covalent geometry : angle 0.64536 (19426) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 38 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8192 (t0) cc_final: 0.7522 (t0) REVERT: A 802 LEU cc_start: 0.9257 (tp) cc_final: 0.9007 (pp) REVERT: B 58 LEU cc_start: 0.9175 (mm) cc_final: 0.8904 (pp) REVERT: B 327 MET cc_start: 0.8990 (mpp) cc_final: 0.8753 (mpp) REVERT: B 328 MET cc_start: 0.8052 (ppp) cc_final: 0.7565 (ppp) REVERT: B 528 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: B 541 LEU cc_start: 0.9316 (tp) cc_final: 0.9055 (tt) REVERT: B 701 VAL cc_start: 0.7710 (OUTLIER) cc_final: 0.7495 (t) outliers start: 39 outliers final: 28 residues processed: 74 average time/residue: 0.2430 time to fit residues: 28.5275 Evaluate side-chains 67 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 37 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 61 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.062455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.040044 restraints weight = 67686.881| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.09 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 14120 Z= 0.308 Angle : 0.808 22.613 19450 Z= 0.380 Chirality : 0.046 0.217 2204 Planarity : 0.004 0.036 2295 Dihedral : 21.406 178.249 2591 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.76 % Allowed : 21.32 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.22), residues: 1582 helix: 0.33 (0.21), residues: 613 sheet: 0.50 (0.36), residues: 189 loop : -0.56 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 570 HIS 0.005 0.001 HIS B 820 PHE 0.014 0.002 PHE A 386 TYR 0.011 0.002 TYR B 944 ARG 0.004 0.000 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.05982 ( 568) hydrogen bonds : angle 5.13447 ( 1519) metal coordination : bond 0.01547 ( 16) metal coordination : angle 9.01943 ( 24) covalent geometry : bond 0.00679 (14104) covalent geometry : angle 0.74326 (19426) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 35 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 528 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8178 (tm-30) outliers start: 36 outliers final: 31 residues processed: 68 average time/residue: 0.2661 time to fit residues: 29.7468 Evaluate side-chains 66 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 34 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 917 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 129 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.064179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.042093 restraints weight = 65336.494| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.15 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14120 Z= 0.142 Angle : 0.705 16.429 19450 Z= 0.333 Chirality : 0.043 0.217 2204 Planarity : 0.003 0.037 2295 Dihedral : 21.314 178.774 2591 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.22 % Allowed : 21.93 % Favored : 75.84 % 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: 0.04 (0.22), residues: 1582 helix: 0.59 (0.22), residues: 608 sheet: 0.63 (0.36), residues: 199 loop : -0.52 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 343 HIS 0.002 0.001 HIS B 635 PHE 0.014 0.001 PHE A 386 TYR 0.010 0.001 TYR A 739 ARG 0.005 0.000 ARG B 326 Details of bonding type rmsd hydrogen bonds : bond 0.05165 ( 568) hydrogen bonds : angle 4.89139 ( 1519) metal coordination : bond 0.00643 ( 16) metal coordination : angle 7.06113 ( 24) covalent geometry : bond 0.00324 (14104) covalent geometry : angle 0.66061 (19426) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 39 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8210 (t0) cc_final: 0.7514 (t0) REVERT: A 802 LEU cc_start: 0.9264 (tp) cc_final: 0.8931 (pp) REVERT: B 328 MET cc_start: 0.8030 (ppp) cc_final: 0.7561 (ppp) REVERT: B 528 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7872 (tm-30) outliers start: 29 outliers final: 26 residues processed: 65 average time/residue: 0.2583 time to fit residues: 29.4000 Evaluate side-chains 66 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 39 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.063564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.041091 restraints weight = 67206.938| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 4.18 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14120 Z= 0.195 Angle : 0.731 17.872 19450 Z= 0.344 Chirality : 0.044 0.210 2204 Planarity : 0.004 0.037 2295 Dihedral : 21.334 179.335 2591 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.15 % Allowed : 21.86 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1582 helix: 0.55 (0.22), residues: 608 sheet: 0.55 (0.36), residues: 199 loop : -0.48 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 570 HIS 0.003 0.001 HIS B 587 PHE 0.014 0.001 PHE A 386 TYR 0.007 0.001 TYR B 108 ARG 0.004 0.000 ARG B 326 Details of bonding type rmsd hydrogen bonds : bond 0.05431 ( 568) hydrogen bonds : angle 4.92588 ( 1519) metal coordination : bond 0.00987 ( 16) metal coordination : angle 7.57791 ( 24) covalent geometry : bond 0.00440 (14104) covalent geometry : angle 0.68093 (19426) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5601.42 seconds wall clock time: 100 minutes 7.29 seconds (6007.29 seconds total)