Starting phenix.real_space_refine on Fri Jul 3 11:06:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ga5_51174/07_2026/9ga5_51174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ga5_51174/07_2026/9ga5_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_51174/07_2026/9ga5_51174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ga5_51174/07_2026/9ga5_51174_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ga5_51174/07_2026/9ga5_51174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ga5_51174/07_2026/9ga5_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 2.60, per 1000 atoms: 0.19 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: 1.16 Conformation dependent library (CDL) restraints added in 481.9 milliseconds 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: 1.93 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: 3.04 Time building geometry restraints manager: 1.57 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=" C3' DG D -19 " pdb=" C2' DG D -19 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC C 36 " pdb=" C2' DC C 36 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DA C 4 " pdb=" C2' DA C 4 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.80e+00 bond pdb=" C3' DA C 29 " pdb=" C2' DA C 29 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.97e+00 bond pdb=" C3' DG C 38 " pdb=" C2' DG C 38 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.48e+00 ... (remaining 14099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 19250 3.31 - 6.61: 142 6.61 - 9.92: 31 9.92 - 13.22: 1 13.22 - 16.53: 2 Bond angle restraints: 19426 Sorted by residual: angle pdb=" O4' DA D -25 " pdb=" C4' DA D -25 " pdb=" C3' DA D -25 " ideal model delta sigma weight residual 106.00 102.29 3.71 6.00e-01 2.78e+00 3.83e+01 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=" C3' DT D -28 " pdb=" C2' DT D -28 " pdb=" C1' DT D -28 " ideal model delta sigma weight residual 102.50 95.21 7.29 1.20e+00 6.94e-01 3.69e+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 ... (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 - 0.129: 2179 0.129 - 0.257: 17 0.257 - 0.386: 1 0.386 - 0.515: 3 0.515 - 0.643: 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 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+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 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.74e+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 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.90e+00 ... (remaining 2201 not shown) Planarity restraints: 2295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 362 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C VAL A 362 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL A 362 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS A 363 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT D -28 " -0.011 2.00e-02 2.50e+03 1.33e-02 4.40e+00 pdb=" N1 DT D -28 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DT D -28 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT D -28 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DT D -28 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT D -28 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT D -28 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DT D -28 " 0.011 2.00e-02 2.50e+03 pdb=" C7 DT D -28 " -0.027 2.00e-02 2.50e+03 pdb=" C6 DT D -28 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 44 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" CG ASP A 44 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP A 44 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 44 " 0.009 2.00e-02 2.50e+03 ... (remaining 2292 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 16 2.46 - 3.07: 9724 3.07 - 3.68: 22767 3.68 - 4.29: 32504 4.29 - 4.90: 50946 Nonbonded interactions: 115957 Sorted by model distance: nonbonded pdb=" NE2 HIS A 319 " pdb=" OP2 DA C 26 " model vdw 1.844 3.120 nonbonded pdb=" NE ARG B 860 " pdb=" OP2 DA C 8 " model vdw 1.963 3.120 nonbonded pdb=" CG MET A 399 " pdb=" N6 DA D -25 " model vdw 2.062 3.520 nonbonded pdb=" O4' DT D -27 " pdb=" O5' DT D -26 " model vdw 2.280 3.040 nonbonded pdb=" N6 DA C 14 " pdb=" O4 DT D -15 " model vdw 2.287 3.120 ... (remaining 115952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 16.370 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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 : 0.005 0.040 14120 Z= 0.307 Angle : 0.866 19.262 19450 Z= 0.513 Chirality : 0.056 0.643 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 are 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/Z covalent geometry : bond 0.00483 / 0.31 (14104) covalent geometry : angle 0.80665 / 0.51 (19426) hydrogen bonds : bond 0.15735 / 10.16 ( 568) hydrogen bonds : angle 6.85747 / 4.88 ( 1519) metal coordination : bond 0.00919 / 0.68 ( 16) metal coordination : angle 9.02757 / 6.08 ( 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 : 0.331 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: 0.1066 time to fit residues: 6.1753 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 : 0.416 ------------------------------------------------------------------------------- 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... 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 = 0.3606 r_free = 0.3606 target = 0.064180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.042036 restraints weight = 65297.849| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 4.10 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14120 Z= 0.200 Angle : 0.741 17.375 19450 Z= 0.357 Chirality : 0.047 0.341 2204 Planarity : 0.004 0.035 2295 Dihedral : 21.096 178.358 2591 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.37 % Allowed : 17.41 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.22), residues: 1582 helix: 0.53 (0.21), residues: 597 sheet: 0.86 (0.36), residues: 197 loop : -0.46 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.014 0.001 TYR B 403 PHE 0.012 0.001 PHE B 406 TRP 0.007 0.001 TRP B 913 HIS 0.004 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (14104) covalent geometry : angle 0.67963 / 0.35 (19426) hydrogen bonds : bond 0.05117 / 3.38 ( 568) hydrogen bonds : angle 5.46104 / 3.85 ( 1519) metal coordination : bond 0.00870 / 0.62 ( 16) metal coordination : angle 8.44757 / 5.77 ( 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 78 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 34 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.9319 (mmm) cc_final: 0.8309 (mmm) REVERT: B 528 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7640 (tm-30) REVERT: B 531 ILE cc_start: 0.9584 (OUTLIER) cc_final: 0.9047 (pt) REVERT: B 597 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8571 (t0) REVERT: B 856 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8427 (mp0) outliers start: 44 outliers final: 17 residues processed: 76 average time/residue: 0.0855 time to fit residues: 10.5776 Evaluate side-chains 55 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR 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: 0.7980 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 18 optimal weight: 40.0000 chunk 122 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 101 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 30.0000 chunk 13 optimal weight: 0.0980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.064413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.042519 restraints weight = 65207.390| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.08 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14120 Z= 0.161 Angle : 0.715 19.418 19450 Z= 0.341 Chirality : 0.046 0.321 2204 Planarity : 0.004 0.034 2295 Dihedral : 21.159 177.715 2591 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.30 % Allowed : 17.64 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1582 helix: 0.57 (0.21), residues: 597 sheet: 0.88 (0.36), residues: 196 loop : -0.43 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.008 0.001 TYR B 108 PHE 0.015 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/Z covalent geometry : bond 0.00341 / 0.16 (14104) covalent geometry : angle 0.65783 / 0.34 (19426) hydrogen bonds : bond 0.04810 / 3.21 ( 568) hydrogen bonds : angle 5.25152 / 3.69 ( 1519) metal coordination : bond 0.01074 / 0.84 ( 16) metal coordination : angle 8.02851 / 5.94 ( 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 79 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 36 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7711 (pp20) REVERT: A 407 MET cc_start: 0.9277 (mmm) cc_final: 0.8373 (mmm) REVERT: B 849 GLN cc_start: 0.9095 (tp40) cc_final: 0.8603 (tp40) REVERT: B 856 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8393 (mp0) outliers start: 43 outliers final: 21 residues processed: 77 average time/residue: 0.0855 time to fit residues: 10.8796 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 : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 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 401 GLU Chi-restraints excluded: chain B residue 404 GLU 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 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: 2.9990 chunk 89 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 124 optimal weight: 0.0070 chunk 95 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.063769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.041745 restraints weight = 66049.764| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 4.10 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14120 Z= 0.209 Angle : 0.732 17.825 19450 Z= 0.348 Chirality : 0.047 0.306 2204 Planarity : 0.004 0.034 2295 Dihedral : 21.220 177.400 2591 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.83 % Allowed : 17.56 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1582 helix: 0.55 (0.21), residues: 603 sheet: 0.69 (0.36), residues: 199 loop : -0.45 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.011 0.001 TYR B 403 PHE 0.014 0.001 PHE B 386 TRP 0.006 0.001 TRP A 570 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (14104) covalent geometry : angle 0.67194 / 0.34 (19426) hydrogen bonds : bond 0.04989 / 3.35 ( 568) hydrogen bonds : angle 5.19616 / 3.65 ( 1519) metal coordination : bond 0.00996 / 0.68 ( 16) metal coordination : angle 8.29428 / 5.79 ( 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: 50 poor density : 34 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7651 (pp20) REVERT: A 407 MET cc_start: 0.9294 (mmm) cc_final: 0.8433 (mmm) REVERT: A 802 LEU cc_start: 0.9364 (tp) cc_final: 0.9074 (pp) REVERT: B 111 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9125 (tt) REVERT: B 528 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: B 701 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7662 (t) REVERT: B 849 GLN cc_start: 0.9114 (tp40) cc_final: 0.8455 (tp40) outliers start: 50 outliers final: 29 residues processed: 82 average time/residue: 0.0892 time to fit residues: 12.0918 Evaluate side-chains 67 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 34 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 404 GLU 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 572 VAL Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 64 optimal weight: 0.2980 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 144 optimal weight: 0.1980 chunk 69 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 101 optimal weight: 30.0000 chunk 72 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 467 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.064868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.043112 restraints weight = 64715.577| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 4.10 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14120 Z= 0.121 Angle : 0.699 22.747 19450 Z= 0.329 Chirality : 0.046 0.299 2204 Planarity : 0.003 0.033 2295 Dihedral : 21.227 176.580 2591 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.84 % Allowed : 18.94 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.22), residues: 1582 helix: 0.67 (0.22), residues: 598 sheet: 0.81 (0.36), residues: 197 loop : -0.40 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.007 0.001 TYR B 323 PHE 0.014 0.001 PHE A 386 TRP 0.006 0.001 TRP B 913 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (14104) covalent geometry : angle 0.63902 / 0.32 (19426) hydrogen bonds : bond 0.04628 / 3.11 ( 568) hydrogen bonds : angle 4.97407 / 3.48 ( 1519) metal coordination : bond 0.00782 / 0.59 ( 16) metal coordination : angle 8.07300 / 5.44 ( 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 74 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 37 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 MET cc_start: 0.8014 (mpp) cc_final: 0.7787 (mpp) REVERT: A 333 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7587 (pp20) REVERT: A 407 MET cc_start: 0.9323 (mmm) cc_final: 0.8520 (mmm) REVERT: A 802 LEU cc_start: 0.9361 (tp) cc_final: 0.9070 (pp) REVERT: B 528 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: B 701 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7538 (t) REVERT: B 849 GLN cc_start: 0.9097 (tp40) cc_final: 0.8447 (tp40) outliers start: 37 outliers final: 23 residues processed: 71 average time/residue: 0.0789 time to fit residues: 9.4743 Evaluate side-chains 60 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 34 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 698 LEU 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 401 GLU Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 701 VAL 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: 2.9990 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 101 optimal weight: 40.0000 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.063993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.042136 restraints weight = 65164.856| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.10 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14120 Z= 0.180 Angle : 0.700 18.534 19450 Z= 0.335 Chirality : 0.046 0.283 2204 Planarity : 0.003 0.032 2295 Dihedral : 21.260 176.896 2591 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.37 % Allowed : 18.94 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.22), residues: 1582 helix: 0.70 (0.22), residues: 604 sheet: 0.63 (0.36), residues: 201 loop : -0.37 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.009 0.001 TYR B 403 PHE 0.012 0.001 PHE B 337 TRP 0.006 0.001 TRP A 570 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (14104) covalent geometry : angle 0.65047 / 0.33 (19426) hydrogen bonds : bond 0.04982 / 3.37 ( 568) hydrogen bonds : angle 4.95458 / 3.48 ( 1519) metal coordination : bond 0.01037 / 0.79 ( 16) metal coordination : angle 7.39778 / 5.17 ( 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 79 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 35 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7601 (pp20) REVERT: A 407 MET cc_start: 0.9370 (mmm) cc_final: 0.8610 (mmm) REVERT: A 802 LEU cc_start: 0.9369 (tp) cc_final: 0.9092 (pp) REVERT: B 328 MET cc_start: 0.8205 (ppp) cc_final: 0.7907 (ppp) REVERT: B 528 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: B 701 VAL cc_start: 0.7901 (OUTLIER) cc_final: 0.7569 (t) REVERT: B 849 GLN cc_start: 0.9126 (tp40) cc_final: 0.8457 (tp40) outliers start: 44 outliers final: 30 residues processed: 76 average time/residue: 0.0901 time to fit residues: 11.0968 Evaluate side-chains 68 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 35 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 800 GLU 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 401 GLU Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 842 THR 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: 2.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 163 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 162 optimal weight: 30.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** 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 = 0.3608 r_free = 0.3608 target = 0.064288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.042424 restraints weight = 64938.032| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 4.12 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1299 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= 0.153 Angle : 0.695 17.538 19450 Z= 0.332 Chirality : 0.046 0.287 2204 Planarity : 0.003 0.034 2295 Dihedral : 21.287 176.981 2591 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.45 % Allowed : 19.63 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.22), residues: 1582 helix: 0.75 (0.22), residues: 598 sheet: 0.71 (0.36), residues: 199 loop : -0.37 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 326 TYR 0.007 0.001 TYR B 403 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/Z covalent geometry : bond 0.00324 / 0.15 (14104) covalent geometry : angle 0.64834 / 0.33 (19426) hydrogen bonds : bond 0.04900 / 3.30 ( 568) hydrogen bonds : angle 4.92322 / 3.44 ( 1519) metal coordination : bond 0.00767 / 0.58 ( 16) metal coordination : angle 7.14003 / 5.05 ( 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 80 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 35 time to evaluate : 0.419 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: 0.7999 (OUTLIER) cc_final: 0.7501 (pp20) REVERT: A 800 GLU cc_start: 0.9429 (OUTLIER) cc_final: 0.9216 (tm-30) REVERT: A 802 LEU cc_start: 0.9358 (tp) cc_final: 0.9096 (pp) REVERT: B 328 MET cc_start: 0.8238 (ppp) cc_final: 0.7891 (ppp) REVERT: B 528 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: B 701 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7518 (t) REVERT: B 849 GLN cc_start: 0.9136 (tp40) cc_final: 0.8459 (tp40) outliers start: 45 outliers final: 28 residues processed: 78 average time/residue: 0.0958 time to fit residues: 12.1895 Evaluate side-chains 67 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 35 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 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 901 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 76 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 7 optimal weight: 0.0470 chunk 62 optimal weight: 5.9990 chunk 22 optimal weight: 0.0570 chunk 9 optimal weight: 0.2980 chunk 70 optimal weight: 8.9990 chunk 53 optimal weight: 0.4980 chunk 97 optimal weight: 6.9990 chunk 145 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3637 r_free = 0.3637 target = 0.065356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.043674 restraints weight = 63595.563| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.11 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14120 Z= 0.111 Angle : 0.702 16.329 19450 Z= 0.327 Chirality : 0.046 0.291 2204 Planarity : 0.003 0.036 2295 Dihedral : 21.206 176.392 2591 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.14 % Allowed : 19.86 % Favored : 76.99 % 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 are not related in a simple way. whole: 0.22 (0.22), residues: 1582 helix: 0.70 (0.21), residues: 611 sheet: 0.81 (0.36), residues: 200 loop : -0.41 (0.24), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.008 0.001 TYR B 403 PHE 0.012 0.001 PHE A 386 TRP 0.007 0.001 TRP B 913 HIS 0.003 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (14104) covalent geometry : angle 0.65253 / 0.32 (19426) hydrogen bonds : bond 0.04783 / 3.23 ( 568) hydrogen bonds : angle 4.80192 / 3.35 ( 1519) metal coordination : bond 0.00412 / 0.28 ( 16) metal coordination : angle 7.43278 / 4.80 ( 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 : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7453 (pp20) REVERT: A 800 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.9201 (tm-30) REVERT: A 802 LEU cc_start: 0.9351 (tp) cc_final: 0.9093 (pp) REVERT: B 328 MET cc_start: 0.8206 (ppp) cc_final: 0.7880 (ppp) REVERT: B 407 MET cc_start: 0.8706 (mmm) cc_final: 0.8463 (mmm) REVERT: B 528 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: B 541 LEU cc_start: 0.9322 (tp) cc_final: 0.9105 (tt) REVERT: B 597 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8573 (t0) REVERT: B 701 VAL cc_start: 0.7686 (OUTLIER) cc_final: 0.7388 (t) REVERT: B 849 GLN cc_start: 0.9126 (tp40) cc_final: 0.8512 (tp40) outliers start: 41 outliers final: 27 residues processed: 75 average time/residue: 0.0970 time to fit residues: 11.5627 Evaluate side-chains 69 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 37 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 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 401 GLU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 39 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 140 optimal weight: 0.0770 chunk 151 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.064858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.043141 restraints weight = 64810.590| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.13 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14120 Z= 0.140 Angle : 0.713 16.476 19450 Z= 0.338 Chirality : 0.046 0.292 2204 Planarity : 0.003 0.037 2295 Dihedral : 21.180 176.686 2591 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.91 % Allowed : 20.32 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.22), residues: 1582 helix: 0.72 (0.22), residues: 612 sheet: 0.86 (0.36), residues: 198 loop : -0.34 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.009 0.001 TYR A 323 PHE 0.011 0.001 PHE B 337 TRP 0.008 0.001 TRP A 315 HIS 0.002 0.000 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (14104) covalent geometry : angle 0.66637 / 0.33 (19426) hydrogen bonds : bond 0.04912 / 3.32 ( 568) hydrogen bonds : angle 4.84465 / 3.37 ( 1519) metal coordination : bond 0.00756 / 0.58 ( 16) metal coordination : angle 7.28127 / 4.77 ( 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 76 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 38 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7459 (pp20) REVERT: A 407 MET cc_start: 0.9376 (mmm) cc_final: 0.8362 (mmm) REVERT: A 802 LEU cc_start: 0.9360 (tp) cc_final: 0.9108 (pp) REVERT: B 328 MET cc_start: 0.8116 (ppp) cc_final: 0.7721 (ppp) REVERT: B 407 MET cc_start: 0.8738 (mmm) cc_final: 0.8471 (mmm) REVERT: B 528 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: B 541 LEU cc_start: 0.9348 (tp) cc_final: 0.9125 (tt) REVERT: B 597 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8647 (t0) REVERT: B 701 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.7368 (t) REVERT: B 849 GLN cc_start: 0.9090 (tp40) cc_final: 0.8451 (tp40) outliers start: 38 outliers final: 28 residues processed: 73 average time/residue: 0.0863 time to fit residues: 10.3169 Evaluate side-chains 70 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 38 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 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 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 907 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 66 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.0980 chunk 102 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 161 optimal weight: 30.0000 chunk 95 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3632 r_free = 0.3632 target = 0.065194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.043130 restraints weight = 65881.582| |-----------------------------------------------------------------------------| 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: 0.8636 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14120 Z= 0.127 Angle : 0.711 16.385 19450 Z= 0.337 Chirality : 0.046 0.297 2204 Planarity : 0.003 0.037 2295 Dihedral : 21.152 176.912 2591 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.68 % Allowed : 20.63 % 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 are not related in a simple way. whole: 0.24 (0.22), residues: 1582 helix: 0.68 (0.22), residues: 611 sheet: 0.89 (0.36), residues: 198 loop : -0.38 (0.24), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 596 TYR 0.007 0.001 TYR A 323 PHE 0.012 0.001 PHE A 386 TRP 0.005 0.001 TRP A 315 HIS 0.002 0.000 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (14104) covalent geometry : angle 0.66770 / 0.33 (19426) hydrogen bonds : bond 0.04959 / 3.34 ( 568) hydrogen bonds : angle 4.83721 / 3.37 ( 1519) metal coordination : bond 0.00666 / 0.51 ( 16) metal coordination : angle 7.02385 / 4.67 ( 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 73 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 38 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7486 (pp20) REVERT: A 407 MET cc_start: 0.9400 (mmm) cc_final: 0.8423 (mmm) REVERT: A 797 THR cc_start: 0.9497 (OUTLIER) cc_final: 0.9278 (t) REVERT: B 328 MET cc_start: 0.8117 (ppp) cc_final: 0.7721 (ppp) REVERT: B 407 MET cc_start: 0.8818 (mmm) cc_final: 0.8546 (mmm) REVERT: B 528 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: B 541 LEU cc_start: 0.9360 (tp) cc_final: 0.9132 (tt) REVERT: B 597 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8432 (t0) REVERT: B 701 VAL cc_start: 0.7710 (OUTLIER) cc_final: 0.7378 (t) REVERT: B 849 GLN cc_start: 0.9104 (tp40) cc_final: 0.8494 (tp40) outliers start: 35 outliers final: 27 residues processed: 70 average time/residue: 0.0914 time to fit residues: 10.4208 Evaluate side-chains 70 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 38 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 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 462 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 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: 5.9990 chunk 148 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 0.0670 chunk 144 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3606 r_free = 0.3606 target = 0.064119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.041954 restraints weight = 67007.232| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.14 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14120 Z= 0.210 Angle : 0.744 16.894 19450 Z= 0.354 Chirality : 0.046 0.299 2204 Planarity : 0.004 0.036 2295 Dihedral : 21.191 177.480 2591 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.61 % Allowed : 20.94 % 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 are not related in a simple way. whole: 0.23 (0.22), residues: 1582 helix: 0.69 (0.22), residues: 614 sheet: 0.75 (0.36), residues: 200 loop : -0.37 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 596 TYR 0.010 0.001 TYR A 717 PHE 0.011 0.001 PHE B 337 TRP 0.006 0.001 TRP A 570 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (14104) covalent geometry : angle 0.69679 / 0.35 (19426) hydrogen bonds : bond 0.05260 / 3.55 ( 568) hydrogen bonds : angle 4.91049 / 3.42 ( 1519) metal coordination : bond 0.01091 / 0.81 ( 16) metal coordination : angle 7.41799 / 5.02 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2072.95 seconds wall clock time: 36 minutes 45.79 seconds (2205.79 seconds total)