Starting phenix.real_space_refine on Thu Sep 18 03:55:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ga5_51174/09_2025/9ga5_51174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ga5_51174/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ga5_51174/09_2025/9ga5_51174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ga5_51174/09_2025/9ga5_51174_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ga5_51174/09_2025/9ga5_51174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ga5_51174/09_2025/9ga5_51174.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.63, per 1000 atoms: 0.26 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: 1.24 Conformation dependent library (CDL) restraints added in 590.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.88 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: 3.11 Time building geometry restraints manager: 1.60 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: 0.010 Normalize map: mean=0, sd=1: 4.350 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.830 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 305 TYR 0.014 0.001 TYR A 739 PHE 0.016 0.001 PHE A 386 TRP 0.006 0.001 TRP B 315 HIS 0.008 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00448 (14104) covalent geometry : angle 0.77453 (19426) hydrogen bonds : bond 0.15735 ( 568) hydrogen bonds : angle 6.85747 ( 1519) metal coordination : bond 0.00919 ( 16) metal coordination : angle 9.02757 ( 24) *********************** 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 : 0.554 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: 0.1356 time to fit residues: 7.9773 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 : 0.507 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 535 GLN B 538 ASN B 597 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.064063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.042022 restraints weight = 65465.406| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 4.11 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14120 Z= 0.204 Angle : 0.726 17.770 19450 Z= 0.342 Chirality : 0.044 0.157 2204 Planarity : 0.004 0.034 2295 Dihedral : 21.015 179.480 2591 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.68 % Allowed : 16.56 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.22), residues: 1582 helix: 0.50 (0.21), residues: 603 sheet: 0.79 (0.35), residues: 197 loop : -0.41 (0.24), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.014 0.001 TYR B 403 PHE 0.012 0.001 PHE B 337 TRP 0.007 0.001 TRP B 913 HIS 0.005 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00457 (14104) covalent geometry : angle 0.65848 (19426) hydrogen bonds : bond 0.04801 ( 568) hydrogen bonds : angle 5.32346 ( 1519) metal coordination : bond 0.00890 ( 16) metal coordination : angle 8.70752 ( 24) *********************** 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 83 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 35 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7687 (pp20) REVERT: A 407 MET cc_start: 0.9344 (mmm) cc_final: 0.8300 (mmm) REVERT: B 528 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: B 531 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9033 (pt) REVERT: B 597 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8571 (t0) REVERT: B 856 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8411 (mp0) outliers start: 48 outliers final: 18 residues processed: 81 average time/residue: 0.1158 time to fit residues: 14.8868 Evaluate side-chains 56 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 33 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 528 GLU Chi-restraints excluded: chain B residue 531 ILE 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 81 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 18 optimal weight: 40.0000 chunk 122 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 101 optimal weight: 30.0000 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 13 optimal weight: 0.3980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.064323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.042390 restraints weight = 65390.500| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.13 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14120 Z= 0.162 Angle : 0.681 16.508 19450 Z= 0.323 Chirality : 0.043 0.143 2204 Planarity : 0.004 0.035 2295 Dihedral : 21.092 179.354 2591 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.53 % Allowed : 17.48 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.22), residues: 1582 helix: 0.65 (0.22), residues: 591 sheet: 0.85 (0.36), residues: 197 loop : -0.40 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.007 0.001 TYR B 108 PHE 0.012 0.001 PHE B 406 TRP 0.005 0.001 TRP B 913 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00370 (14104) covalent geometry : angle 0.63084 (19426) hydrogen bonds : bond 0.04510 ( 568) hydrogen bonds : angle 5.02343 ( 1519) metal coordination : bond 0.00904 ( 16) metal coordination : angle 7.35243 ( 24) *********************** 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 82 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 36 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 MET cc_start: 0.7979 (mpp) cc_final: 0.7671 (mpp) REVERT: A 333 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7845 (pp20) REVERT: A 407 MET cc_start: 0.9349 (mmm) cc_final: 0.8391 (mmm) REVERT: A 802 LEU cc_start: 0.9333 (tp) cc_final: 0.9109 (pp) REVERT: B 282 CYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6871 (p) REVERT: B 701 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7546 (t) REVERT: B 849 GLN cc_start: 0.9119 (tp40) cc_final: 0.8467 (tp40) REVERT: B 856 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8353 (mp0) outliers start: 46 outliers final: 19 residues processed: 80 average time/residue: 0.1020 time to fit residues: 13.3042 Evaluate side-chains 57 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 34 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 282 CYS Chi-restraints excluded: chain B residue 456 PHE 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 701 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 102 optimal weight: 0.0010 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 chunk 46 optimal weight: 6.9990 overall best weight: 1.4792 ------------------------------------------------------------------------------- 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 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 = 0.3607 r_free = 0.3607 target = 0.064126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.042247 restraints weight = 65318.807| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 4.12 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14120 Z= 0.165 Angle : 0.674 19.360 19450 Z= 0.319 Chirality : 0.043 0.171 2204 Planarity : 0.003 0.035 2295 Dihedral : 21.116 179.518 2591 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.76 % Allowed : 17.41 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.22), residues: 1582 helix: 0.62 (0.22), residues: 603 sheet: 0.76 (0.36), residues: 199 loop : -0.35 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.007 0.001 TYR B 108 PHE 0.012 0.001 PHE B 337 TRP 0.005 0.001 TRP A 570 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00375 (14104) covalent geometry : angle 0.62113 (19426) hydrogen bonds : bond 0.04752 ( 568) hydrogen bonds : angle 4.87938 ( 1519) metal coordination : bond 0.00918 ( 16) metal coordination : angle 7.44954 ( 24) *********************** 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 84 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 35 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7535 (pp20) REVERT: A 407 MET cc_start: 0.9372 (mmm) cc_final: 0.8537 (mmm) REVERT: A 802 LEU cc_start: 0.9309 (tp) cc_final: 0.9086 (pp) REVERT: B 528 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: B 701 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7512 (t) REVERT: B 849 GLN cc_start: 0.9126 (tp40) cc_final: 0.8450 (tp40) outliers start: 49 outliers final: 27 residues processed: 79 average time/residue: 0.1055 time to fit residues: 13.5798 Evaluate side-chains 65 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 35 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 391 MET 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 901 ILE Chi-restraints excluded: chain A residue 929 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 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 856 GLU 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 64 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 144 optimal weight: 0.0980 chunk 69 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.064852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.043196 restraints weight = 64708.828| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.13 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1469 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= 0.128 Angle : 0.654 16.318 19450 Z= 0.309 Chirality : 0.043 0.165 2204 Planarity : 0.003 0.037 2295 Dihedral : 21.121 178.863 2591 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.53 % Allowed : 18.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1582 helix: 0.68 (0.22), residues: 609 sheet: 0.89 (0.36), residues: 199 loop : -0.41 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 402 TYR 0.007 0.001 TYR B 54 PHE 0.012 0.001 PHE A 324 TRP 0.005 0.001 TRP B 913 HIS 0.002 0.000 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00295 (14104) covalent geometry : angle 0.60552 (19426) hydrogen bonds : bond 0.04775 ( 568) hydrogen bonds : angle 4.73658 ( 1519) metal coordination : bond 0.00580 ( 16) metal coordination : angle 7.07709 ( 24) *********************** 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 83 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 37 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7428 (pp20) REVERT: A 800 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.9185 (tm-30) REVERT: B 528 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: B 541 LEU cc_start: 0.9337 (tp) cc_final: 0.9083 (tt) REVERT: B 597 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8632 (t0) REVERT: B 701 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7474 (t) REVERT: B 849 GLN cc_start: 0.9105 (tp40) cc_final: 0.8459 (tp40) outliers start: 46 outliers final: 27 residues processed: 79 average time/residue: 0.1049 time to fit residues: 13.4105 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 : 0.516 ------------------------------------------------------------------------------- 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 391 MET 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 621 VAL 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 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 326 ARG Chi-restraints excluded: chain B residue 456 PHE 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 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 856 GLU 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 59 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.064394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042620 restraints weight = 64970.140| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 4.12 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14120 Z= 0.153 Angle : 0.662 15.157 19450 Z= 0.316 Chirality : 0.043 0.201 2204 Planarity : 0.003 0.038 2295 Dihedral : 21.151 179.551 2591 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.45 % Allowed : 19.10 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.22), residues: 1582 helix: 0.63 (0.21), residues: 617 sheet: 0.83 (0.36), residues: 198 loop : -0.37 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.006 0.001 TYR A 524 PHE 0.012 0.001 PHE A 386 TRP 0.005 0.001 TRP A 570 HIS 0.002 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00349 (14104) covalent geometry : angle 0.61844 (19426) hydrogen bonds : bond 0.04925 ( 568) hydrogen bonds : angle 4.74167 ( 1519) metal coordination : bond 0.00787 ( 16) metal coordination : angle 6.72741 ( 24) *********************** 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 82 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 37 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7492 (pp20) REVERT: A 800 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.9204 (tm-30) REVERT: A 802 LEU cc_start: 0.9324 (tp) cc_final: 0.9039 (pp) REVERT: B 328 MET cc_start: 0.8200 (ppp) cc_final: 0.7884 (ppp) REVERT: B 528 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: B 541 LEU cc_start: 0.9348 (tp) cc_final: 0.9085 (tt) REVERT: B 597 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8838 (t0) REVERT: B 701 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7444 (t) REVERT: B 849 GLN cc_start: 0.9105 (tp40) cc_final: 0.8464 (tp40) outliers start: 45 outliers final: 29 residues processed: 78 average time/residue: 0.1054 time to fit residues: 13.2956 Evaluate side-chains 70 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 36 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 391 MET 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 621 VAL 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 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 A residue 949 LEU Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 456 PHE 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 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 806 ILE Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 87 optimal weight: 0.0070 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 overall best weight: 1.1000 ------------------------------------------------------------------------------- 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 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 = 0.3622 r_free = 0.3622 target = 0.064660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.043027 restraints weight = 64457.904| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.10 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14120 Z= 0.139 Angle : 0.653 14.168 19450 Z= 0.312 Chirality : 0.043 0.158 2204 Planarity : 0.003 0.039 2295 Dihedral : 21.163 179.518 2591 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.07 % Allowed : 19.79 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1582 helix: 0.62 (0.21), residues: 619 sheet: 0.85 (0.36), residues: 198 loop : -0.36 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 596 TYR 0.006 0.001 TYR A 524 PHE 0.012 0.001 PHE B 337 TRP 0.004 0.001 TRP B 913 HIS 0.002 0.000 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00318 (14104) covalent geometry : angle 0.61325 (19426) hydrogen bonds : bond 0.04901 ( 568) hydrogen bonds : angle 4.71670 ( 1519) metal coordination : bond 0.00676 ( 16) metal coordination : angle 6.41727 ( 24) *********************** 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 78 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 38 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7446 (pp20) REVERT: A 407 MET cc_start: 0.9425 (mmm) cc_final: 0.8414 (mmm) REVERT: A 800 GLU cc_start: 0.9424 (OUTLIER) cc_final: 0.9206 (tm-30) REVERT: A 802 LEU cc_start: 0.9335 (tp) cc_final: 0.9070 (pp) REVERT: B 328 MET cc_start: 0.8206 (ppp) cc_final: 0.7835 (ppp) REVERT: B 528 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: B 541 LEU cc_start: 0.9339 (tp) cc_final: 0.9084 (tt) REVERT: B 701 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7438 (t) REVERT: B 849 GLN cc_start: 0.9101 (tp40) cc_final: 0.8451 (tp40) outliers start: 40 outliers final: 30 residues processed: 75 average time/residue: 0.1037 time to fit residues: 12.6267 Evaluate side-chains 72 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 38 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN 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 391 MET 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 621 VAL 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 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 326 ARG Chi-restraints excluded: chain B residue 456 PHE 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 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 856 GLU Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 76 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 22 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 53 optimal weight: 0.4980 chunk 97 optimal weight: 30.0000 chunk 145 optimal weight: 0.4980 chunk 102 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.064656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.043010 restraints weight = 64193.734| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.10 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14120 Z= 0.142 Angle : 0.656 14.004 19450 Z= 0.314 Chirality : 0.043 0.230 2204 Planarity : 0.003 0.039 2295 Dihedral : 21.177 179.716 2591 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.14 % Allowed : 20.02 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.22), residues: 1582 helix: 0.65 (0.21), residues: 619 sheet: 0.85 (0.36), residues: 198 loop : -0.37 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.006 0.001 TYR B 108 PHE 0.011 0.001 PHE B 337 TRP 0.004 0.001 TRP A 570 HIS 0.002 0.000 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00324 (14104) covalent geometry : angle 0.61736 (19426) hydrogen bonds : bond 0.04956 ( 568) hydrogen bonds : angle 4.69442 ( 1519) metal coordination : bond 0.00701 ( 16) metal coordination : angle 6.34421 ( 24) *********************** 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 79 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 38 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7433 (pp20) REVERT: A 407 MET cc_start: 0.9423 (mmm) cc_final: 0.8536 (mmm) REVERT: A 800 GLU cc_start: 0.9426 (OUTLIER) cc_final: 0.9206 (tm-30) REVERT: A 802 LEU cc_start: 0.9331 (tp) cc_final: 0.9073 (pp) REVERT: B 68 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7834 (mm110) REVERT: B 328 MET cc_start: 0.8136 (ppp) cc_final: 0.7787 (ppp) REVERT: B 528 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: B 541 LEU cc_start: 0.9345 (tp) cc_final: 0.9091 (tt) REVERT: B 701 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7404 (t) REVERT: B 849 GLN cc_start: 0.9089 (tp40) cc_final: 0.8468 (tp40) outliers start: 41 outliers final: 28 residues processed: 75 average time/residue: 0.1053 time to fit residues: 12.8621 Evaluate side-chains 71 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 38 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 391 MET 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 621 VAL 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 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 68 GLN Chi-restraints excluded: chain B residue 456 PHE 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 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 856 GLU 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 39 optimal weight: 0.0870 chunk 86 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- 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 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 = 0.3583 r_free = 0.3583 target = 0.062893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.040456 restraints weight = 67851.077| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.12 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 14120 Z= 0.281 Angle : 0.778 21.399 19450 Z= 0.369 Chirality : 0.046 0.246 2204 Planarity : 0.004 0.038 2295 Dihedral : 21.343 178.474 2591 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.76 % Allowed : 20.55 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1582 helix: 0.41 (0.21), residues: 614 sheet: 0.59 (0.36), residues: 201 loop : -0.43 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 326 TYR 0.012 0.002 TYR A 717 PHE 0.013 0.002 PHE B 746 TRP 0.006 0.001 TRP A 570 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00622 (14104) covalent geometry : angle 0.71554 (19426) hydrogen bonds : bond 0.05888 ( 568) hydrogen bonds : angle 5.02576 ( 1519) metal coordination : bond 0.01463 ( 16) metal coordination : angle 8.71977 ( 24) *********************** 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 72 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 36 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.9388 (mmm) cc_final: 0.8456 (mmm) REVERT: A 800 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.8954 (mp0) REVERT: B 68 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7921 (mm-40) REVERT: B 528 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8049 (tm-30) outliers start: 36 outliers final: 27 residues processed: 70 average time/residue: 0.1016 time to fit residues: 11.7919 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 : 0.512 ------------------------------------------------------------------------------- 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 391 MET 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 621 VAL 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 885 LEU Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 456 PHE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 66 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.0470 chunk 102 optimal weight: 0.0030 chunk 59 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 95 optimal weight: 0.0060 chunk 13 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 overall best weight: 0.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 68 GLN B 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.065816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.043740 restraints weight = 65459.237| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.21 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14120 Z= 0.118 Angle : 0.666 12.663 19450 Z= 0.321 Chirality : 0.043 0.228 2204 Planarity : 0.003 0.039 2295 Dihedral : 21.174 177.879 2591 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.30 % Allowed : 21.24 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.22), residues: 1582 helix: 0.69 (0.22), residues: 618 sheet: 0.85 (0.36), residues: 200 loop : -0.45 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 624 TYR 0.010 0.001 TYR B 61 PHE 0.012 0.001 PHE B 337 TRP 0.009 0.001 TRP B 343 HIS 0.002 0.001 HIS B 635 Details of bonding type rmsd covalent geometry : bond 0.00266 (14104) covalent geometry : angle 0.63184 (19426) hydrogen bonds : bond 0.04977 ( 568) hydrogen bonds : angle 4.69691 ( 1519) metal coordination : bond 0.00470 ( 16) metal coordination : angle 6.03218 ( 24) ********************** 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 72 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 0.444 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: 0.8193 (t0) cc_final: 0.7510 (t0) REVERT: A 397 GLU cc_start: 0.9747 (mm-30) cc_final: 0.9344 (pm20) REVERT: A 407 MET cc_start: 0.9417 (mmm) cc_final: 0.8437 (mmm) REVERT: A 800 GLU cc_start: 0.9399 (OUTLIER) cc_final: 0.9186 (tm-30) REVERT: A 802 LEU cc_start: 0.9225 (tp) cc_final: 0.8956 (pp) REVERT: B 328 MET cc_start: 0.8075 (ppp) cc_final: 0.7615 (ppp) REVERT: B 528 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: B 541 LEU cc_start: 0.9334 (tp) cc_final: 0.9094 (tt) REVERT: B 597 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8724 (t0) outliers start: 30 outliers final: 24 residues processed: 69 average time/residue: 0.1008 time to fit residues: 11.4273 Evaluate side-chains 67 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 40 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 391 MET 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 621 VAL 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 885 LEU Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER 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 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 66 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 144 optimal weight: 0.0570 chunk 77 optimal weight: 0.8980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 68 GLN B 507 GLN B 597 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.065254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.043591 restraints weight = 65223.530| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.16 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1993 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= 0.121 Angle : 0.654 12.557 19450 Z= 0.315 Chirality : 0.043 0.227 2204 Planarity : 0.003 0.039 2295 Dihedral : 21.145 179.929 2591 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.30 % Allowed : 21.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.22), residues: 1582 helix: 0.71 (0.22), residues: 619 sheet: 0.89 (0.36), residues: 200 loop : -0.42 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 596 TYR 0.006 0.001 TYR B 323 PHE 0.011 0.001 PHE B 337 TRP 0.005 0.001 TRP B 913 HIS 0.002 0.000 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00279 (14104) covalent geometry : angle 0.62150 (19426) hydrogen bonds : bond 0.05104 ( 568) hydrogen bonds : angle 4.62105 ( 1519) metal coordination : bond 0.00543 ( 16) metal coordination : angle 5.82002 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2666.59 seconds wall clock time: 46 minutes 58.02 seconds (2818.02 seconds total)