Starting phenix.real_space_refine on Thu Jul 2 17:52:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xk0_33239/07_2026/7xk0_33239.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk0_33239/07_2026/7xk0_33239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xk0_33239/07_2026/7xk0_33239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk0_33239/07_2026/7xk0_33239.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk0_33239/07_2026/7xk0_33239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk0_33239/07_2026/7xk0_33239.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xk0_33239/07_2026/7xk0_33239.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xk0_33239/07_2026/7xk0_33239.cif" } resolution = 3.59 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= -0.001 sd= 0.088 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: 5 Type Number sf(0) Gaussians P 73 5.49 5 S 31 5.16 5 C 5581 2.51 5 N 1589 2.21 5 O 1934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 9208 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7688 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7683 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Conformer: "B" Number of residues, atoms: 983, 7683 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 bond proxies already assigned to first conformer: 7834 Chain: "B" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1520 Unusual residues: {'GTP': 1} Classifications: {'RNA': 70, 'undetermined': 1} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 60, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" C B 2 " Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 940 " occ=0.50 Time building chain proxies: 2.84, per 1000 atoms: 0.31 Number of scatterers: 9208 At special positions: 0 Unit cell: (126.5, 106.7, 106.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 73 15.00 O 1934 8.00 N 1589 7.00 C 5581 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 432.9 milliseconds 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 43.9% alpha, 9.6% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 73 through 89 removed outlier: 3.899A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.608A pdb=" N LEU A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.629A pdb=" N SER A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 256 through 273 removed outlier: 7.199A pdb=" N GLU A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.868A pdb=" N ASP A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 4.216A pdb=" N VAL A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 316 " --> pdb=" O HIS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.656A pdb=" N GLY A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 339 " --> pdb=" O MET A 335 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 removed outlier: 3.949A pdb=" N ILE A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 477 removed outlier: 3.717A pdb=" N GLY A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 520 removed outlier: 3.537A pdb=" N ASP A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Proline residue: A 516 - end of helix Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.649A pdb=" N LYS A 601 " --> pdb=" O MET A 597 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 removed outlier: 3.955A pdb=" N LEU A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 644 through 648 removed outlier: 3.794A pdb=" N PHE A 647 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 662 removed outlier: 4.193A pdb=" N THR A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 716 removed outlier: 3.727A pdb=" N PHE A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 729 removed outlier: 4.065A pdb=" N ARG A 724 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A 725 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A 726 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER A 728 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 748 removed outlier: 3.790A pdb=" N GLU A 747 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN A 748 " --> pdb=" O LYS A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 760 through 763 removed outlier: 3.567A pdb=" N MET A 763 " --> pdb=" O ASN A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 760 through 763' Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.793A pdb=" N LYS A 768 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP A 769 " --> pdb=" O PRO A 765 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 773 " --> pdb=" O ASP A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 779 Processing helix chain 'A' and resid 780 through 786 removed outlier: 3.589A pdb=" N THR A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 802 removed outlier: 3.592A pdb=" N ARG A 795 " --> pdb=" O GLY A 791 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR A 797 " --> pdb=" O MET A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 811 removed outlier: 3.594A pdb=" N ALA A 808 " --> pdb=" O SER A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 847 removed outlier: 3.760A pdb=" N ILE A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 874 removed outlier: 3.809A pdb=" N LEU A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 885 removed outlier: 3.696A pdb=" N LEU A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 918 removed outlier: 3.811A pdb=" N VAL A 904 " --> pdb=" O VAL A 900 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN A 906 " --> pdb=" O ASP A 902 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 911 " --> pdb=" O PHE A 907 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 918 " --> pdb=" O GLN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.666A pdb=" N SER A 941 " --> pdb=" O PRO A 937 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 963 removed outlier: 3.682A pdb=" N GLU A 961 " --> pdb=" O PRO A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 969 removed outlier: 3.569A pdb=" N ARG A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 964 through 969' Processing helix chain 'A' and resid 990 through 1003 removed outlier: 4.417A pdb=" N SER A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 removed outlier: 3.623A pdb=" N PHE A1014 " --> pdb=" O ASP A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1029 removed outlier: 3.595A pdb=" N LEU A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1055 removed outlier: 4.189A pdb=" N LEU A1049 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A1052 " --> pdb=" O LEU A1048 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 5.899A pdb=" N ALA A 91 " --> pdb=" O ALA A 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 121 through 123 current: chain 'A' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 144 through 152 current: chain 'A' and resid 193 through 202 removed outlier: 6.427A pdb=" N TRP A 194 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 208 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET A 202 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLU A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 216 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 249 through 251 removed outlier: 6.907A pdb=" N ILE A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 427 removed outlier: 4.044A pdb=" N ASN A 440 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG A 384 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP A 542 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 453 removed outlier: 3.575A pdb=" N LEU A 452 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 498 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR A 495 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ARG A 488 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 497 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 555 through 556 Processing sheet with id=AA6, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA7, first strand: chain 'A' and resid 617 through 619 removed outlier: 7.198A pdb=" N PHE A 666 " --> pdb=" O CYS A 679 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N CYS A 679 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL A 668 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET A 637 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 731 through 733 221 hydrogen bonds defined for protein. 618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1395 1.31 - 1.43: 2870 1.43 - 1.56: 5080 1.56 - 1.68: 145 1.68 - 1.81: 52 Bond restraints: 9542 Sorted by residual: bond pdb=" C8 GTP B 1 " pdb=" N9 GTP B 1 " ideal model delta sigma weight residual 1.370 1.197 0.173 2.00e-02 2.50e+03 7.44e+01 bond pdb=" C4 GTP B 1 " pdb=" N9 GTP B 1 " ideal model delta sigma weight residual 1.375 1.214 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O2G GTP B 1 " pdb=" PG GTP B 1 " ideal model delta sigma weight residual 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.450 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C1' GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sigma weight residual 1.410 1.508 -0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 9537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 13039 2.86 - 5.73: 216 5.73 - 8.59: 28 8.59 - 11.45: 4 11.45 - 14.32: 1 Bond angle restraints: 13288 Sorted by residual: angle pdb=" N GLY A 737 " pdb=" CA GLY A 737 " pdb=" C GLY A 737 " ideal model delta sigma weight residual 111.56 119.92 -8.36 1.01e+00 9.80e-01 6.85e+01 angle pdb=" C4 GTP B 1 " pdb=" N9 GTP B 1 " pdb=" C8 GTP B 1 " ideal model delta sigma weight residual 108.00 122.32 -14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" CA ARG A 965 " pdb=" C ARG A 965 " pdb=" N PRO A 966 " ideal model delta sigma weight residual 118.44 125.95 -7.51 1.59e+00 3.96e-01 2.23e+01 angle pdb=" C ARG A 529 " pdb=" N TRP A 530 " pdb=" CA TRP A 530 " ideal model delta sigma weight residual 122.58 113.93 8.65 2.07e+00 2.33e-01 1.75e+01 angle pdb=" N ILE A 945 " pdb=" CA ILE A 945 " pdb=" C ILE A 945 " ideal model delta sigma weight residual 111.00 106.83 4.17 1.09e+00 8.42e-01 1.46e+01 ... (remaining 13283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 5423 35.70 - 71.39: 154 71.39 - 107.09: 12 107.09 - 142.78: 3 142.78 - 178.48: 2 Dihedral angle restraints: 5594 sinusoidal: 2736 harmonic: 2858 Sorted by residual: dihedral pdb=" O4' U B 19 " pdb=" C1' U B 19 " pdb=" N1 U B 19 " pdb=" C2 U B 19 " ideal model delta sinusoidal sigma weight residual 232.00 60.17 171.83 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O5' GTP B 1 " pdb=" O3A GTP B 1 " pdb=" PA GTP B 1 " pdb=" PB GTP B 1 " ideal model delta sinusoidal sigma weight residual 274.12 95.64 178.48 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C4' GTP B 1 " pdb=" C5' GTP B 1 " pdb=" O5' GTP B 1 " pdb=" PA GTP B 1 " ideal model delta sinusoidal sigma weight residual 260.87 139.34 121.54 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 5591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1162 0.060 - 0.120: 351 0.120 - 0.180: 46 0.180 - 0.240: 4 0.240 - 0.300: 1 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CB ILE A 970 " pdb=" CA ILE A 970 " pdb=" CG1 ILE A 970 " pdb=" CG2 ILE A 970 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C1' U B 57 " pdb=" O4' U B 57 " pdb=" C2' U B 57 " pdb=" N1 U B 57 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ARG A 965 " pdb=" N ARG A 965 " pdb=" C ARG A 965 " pdb=" CB ARG A 965 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1561 not shown) Planarity restraints: 1455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 637 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO A 638 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 962 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ALA A 962 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA A 962 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 963 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 57 " -0.028 2.00e-02 2.50e+03 1.54e-02 5.32e+00 pdb=" N1 U B 57 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U B 57 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U B 57 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U B 57 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U B 57 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U B 57 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U B 57 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 57 " 0.006 2.00e-02 2.50e+03 ... (remaining 1452 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1534 2.75 - 3.28: 8621 3.28 - 3.82: 14776 3.82 - 4.36: 17529 4.36 - 4.90: 28787 Nonbonded interactions: 71247 Sorted by model distance: nonbonded pdb=" O LYS A1040 " pdb=" ND2 ASN A1043 " model vdw 2.206 3.120 nonbonded pdb=" NH1 ARG A 724 " pdb=" O ALA A 772 " model vdw 2.210 3.120 nonbonded pdb=" O VAL A1041 " pdb=" NH1 ARG A1045 " model vdw 2.230 3.120 nonbonded pdb=" OE2 GLU A 233 " pdb=" OH TYR A 256 " model vdw 2.237 3.040 nonbonded pdb=" O PRO A 481 " pdb=" OG SER A 484 " model vdw 2.246 3.040 ... (remaining 71242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.220 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.011 0.173 9543 Z= 0.477 Angle : 0.958 14.317 13288 Z= 0.532 Chirality : 0.055 0.300 1564 Planarity : 0.006 0.070 1455 Dihedral : 16.281 178.481 3746 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 5.36 % Allowed : 19.85 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -5.27 (0.20), residues: 982 helix: -3.73 (0.17), residues: 421 sheet: -2.22 (0.51), residues: 98 loop : -3.52 (0.23), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 432 TYR 0.019 0.003 TYR A 584 PHE 0.024 0.002 PHE A1014 TRP 0.012 0.002 TRP A 298 HIS 0.005 0.002 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.01058 / 0.48 ( 9542) covalent geometry : angle 0.95803 / 0.53 (13288) hydrogen bonds : bond 0.17272 / 11.47 ( 267) hydrogen bonds : angle 6.58390 / 4.52 ( 710) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 59 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 264 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: A 486 TYR cc_start: 0.7549 (p90) cc_final: 0.6956 (p90) REVERT: A 739 MET cc_start: 0.8116 (mmm) cc_final: 0.7799 (mmt) REVERT: A 743 MET cc_start: 0.8117 (mmm) cc_final: 0.7618 (mmm) outliers start: 44 outliers final: 22 residues processed: 98 average time/residue: 0.0922 time to fit residues: 12.7688 Evaluate side-chains 68 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 936 CYS Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1063 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 94 GLN A 106 ASN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 249 GLN A 598 GLN A 631 ASN A 856 ASN A1031 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.106959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084337 restraints weight = 18132.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.085464 restraints weight = 12333.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.085630 restraints weight = 9162.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.086065 restraints weight = 8591.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.086197 restraints weight = 7534.730| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9543 Z= 0.109 Angle : 0.607 8.091 13288 Z= 0.307 Chirality : 0.042 0.172 1564 Planarity : 0.005 0.052 1455 Dihedral : 13.036 176.845 1957 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.05 % Allowed : 20.22 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -4.01 (0.23), residues: 982 helix: -2.66 (0.22), residues: 433 sheet: -2.15 (0.49), residues: 108 loop : -2.69 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 292 TYR 0.012 0.001 TYR A 84 PHE 0.031 0.001 PHE A 322 TRP 0.016 0.001 TRP A 995 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 9542) covalent geometry : angle 0.60721 / 0.31 (13288) hydrogen bonds : bond 0.03664 / 2.39 ( 267) hydrogen bonds : angle 4.55119 / 3.20 ( 710) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 214 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: A 252 LYS cc_start: 0.8999 (tmmm) cc_final: 0.8649 (ttpp) REVERT: A 264 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: A 267 MET cc_start: 0.8592 (tpp) cc_final: 0.8194 (mmt) REVERT: A 743 MET cc_start: 0.8320 (mmm) cc_final: 0.7342 (mmm) REVERT: A 947 MET cc_start: 0.8675 (ttm) cc_final: 0.8409 (ttm) REVERT: A 1045 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7618 (mpp80) outliers start: 25 outliers final: 14 residues processed: 76 average time/residue: 0.0789 time to fit residues: 8.7746 Evaluate side-chains 64 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1045 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 79 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.086410 restraints weight = 18080.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.086925 restraints weight = 13498.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087475 restraints weight = 11259.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.087794 restraints weight = 9394.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.087904 restraints weight = 8890.900| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9543 Z= 0.104 Angle : 0.557 8.054 13288 Z= 0.279 Chirality : 0.041 0.169 1564 Planarity : 0.004 0.050 1455 Dihedral : 11.897 179.693 1940 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.56 % Allowed : 20.83 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -3.22 (0.25), residues: 982 helix: -1.97 (0.24), residues: 431 sheet: -1.99 (0.46), residues: 118 loop : -2.22 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 292 TYR 0.011 0.001 TYR A 84 PHE 0.010 0.001 PHE A 544 TRP 0.010 0.001 TRP A 995 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 9542) covalent geometry : angle 0.55705 / 0.28 (13288) hydrogen bonds : bond 0.03293 / 2.13 ( 267) hydrogen bonds : angle 4.07522 / 2.88 ( 710) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8959 (tmmm) cc_final: 0.8595 (ttpp) REVERT: A 947 MET cc_start: 0.8482 (ttm) cc_final: 0.8101 (ttm) REVERT: A 1045 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7402 (mpp80) outliers start: 21 outliers final: 12 residues processed: 72 average time/residue: 0.0871 time to fit residues: 9.1109 Evaluate side-chains 57 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1045 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 92 optimal weight: 0.0170 chunk 98 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 547 HIS A 631 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.105394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.082967 restraints weight = 18159.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.083531 restraints weight = 14414.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.083839 restraints weight = 11469.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084200 restraints weight = 10434.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.084424 restraints weight = 9138.287| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9543 Z= 0.158 Angle : 0.607 7.856 13288 Z= 0.303 Chirality : 0.044 0.163 1564 Planarity : 0.004 0.050 1455 Dihedral : 11.711 173.623 1933 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.92 % Allowed : 22.53 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -2.99 (0.25), residues: 982 helix: -1.78 (0.24), residues: 432 sheet: -1.20 (0.55), residues: 92 loop : -2.30 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.016 0.001 TYR A 643 PHE 0.012 0.001 PHE A 544 TRP 0.007 0.001 TRP A 194 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 9542) covalent geometry : angle 0.60729 / 0.30 (13288) hydrogen bonds : bond 0.03871 / 2.52 ( 267) hydrogen bonds : angle 4.31988 / 3.05 ( 710) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 159 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8696 (t) REVERT: A 214 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: A 252 LYS cc_start: 0.9006 (tmmm) cc_final: 0.8640 (ttpp) REVERT: A 264 GLU cc_start: 0.7962 (tp30) cc_final: 0.7192 (mm-30) REVERT: A 947 MET cc_start: 0.8567 (ttm) cc_final: 0.8156 (ttm) outliers start: 24 outliers final: 14 residues processed: 67 average time/residue: 0.0744 time to fit residues: 7.7975 Evaluate side-chains 60 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1068 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 84 optimal weight: 0.1980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086808 restraints weight = 18130.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087280 restraints weight = 14153.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.087955 restraints weight = 11662.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.088229 restraints weight = 9389.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.088379 restraints weight = 8949.838| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9543 Z= 0.093 Angle : 0.531 7.746 13288 Z= 0.264 Chirality : 0.040 0.156 1564 Planarity : 0.004 0.052 1455 Dihedral : 11.613 178.593 1933 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.58 % Allowed : 23.51 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -2.41 (0.26), residues: 982 helix: -1.34 (0.25), residues: 424 sheet: -1.52 (0.48), residues: 113 loop : -1.77 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.019 0.001 TYR A 486 PHE 0.010 0.001 PHE A 544 TRP 0.008 0.001 TRP A 995 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 ( 9542) covalent geometry : angle 0.53068 / 0.26 (13288) hydrogen bonds : bond 0.02868 / 1.87 ( 267) hydrogen bonds : angle 3.87974 / 2.75 ( 710) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8935 (tmmm) cc_final: 0.8565 (ttpp) REVERT: A 264 GLU cc_start: 0.7893 (tp30) cc_final: 0.7044 (mm-30) REVERT: A 947 MET cc_start: 0.8502 (ttm) cc_final: 0.8064 (ttm) outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.0701 time to fit residues: 6.9614 Evaluate side-chains 55 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 36 optimal weight: 0.0870 chunk 100 optimal weight: 10.0000 chunk 54 optimal weight: 0.2980 chunk 39 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.109545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.087172 restraints weight = 18208.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.087685 restraints weight = 14066.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088284 restraints weight = 11764.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.088554 restraints weight = 9476.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.088740 restraints weight = 8922.491| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9543 Z= 0.091 Angle : 0.517 7.608 13288 Z= 0.256 Chirality : 0.040 0.144 1564 Planarity : 0.004 0.050 1455 Dihedral : 11.410 178.432 1928 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.71 % Allowed : 24.12 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -2.09 (0.26), residues: 982 helix: -1.03 (0.26), residues: 426 sheet: -1.42 (0.48), residues: 113 loop : -1.63 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.010 0.001 TYR A 584 PHE 0.007 0.001 PHE A 544 TRP 0.005 0.001 TRP A 530 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 9542) covalent geometry : angle 0.51678 / 0.26 (13288) hydrogen bonds : bond 0.02762 / 1.80 ( 267) hydrogen bonds : angle 3.76966 / 2.67 ( 710) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7734 (tt0) REVERT: A 205 MET cc_start: 0.7545 (tpp) cc_final: 0.7170 (ttt) REVERT: A 252 LYS cc_start: 0.8949 (tmmm) cc_final: 0.8638 (ttpp) REVERT: A 947 MET cc_start: 0.8484 (ttm) cc_final: 0.8049 (ttm) outliers start: 14 outliers final: 10 residues processed: 64 average time/residue: 0.0765 time to fit residues: 7.6078 Evaluate side-chains 60 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1068 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 41 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN A 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.105401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.082057 restraints weight = 18256.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084288 restraints weight = 11672.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.084417 restraints weight = 7516.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.084603 restraints weight = 7427.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.084644 restraints weight = 6429.367| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9543 Z= 0.178 Angle : 0.612 10.267 13288 Z= 0.304 Chirality : 0.044 0.165 1564 Planarity : 0.004 0.048 1455 Dihedral : 11.525 172.783 1928 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.83 % Allowed : 24.48 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -2.12 (0.26), residues: 982 helix: -1.08 (0.26), residues: 422 sheet: -0.85 (0.57), residues: 92 loop : -1.78 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 487 TYR 0.018 0.002 TYR A 486 PHE 0.012 0.001 PHE A 461 TRP 0.007 0.001 TRP A 194 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 9542) covalent geometry : angle 0.61223 / 0.30 (13288) hydrogen bonds : bond 0.03852 / 2.50 ( 267) hydrogen bonds : angle 4.21494 / 2.98 ( 710) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.9021 (tmmm) cc_final: 0.8627 (ttpp) outliers start: 15 outliers final: 10 residues processed: 63 average time/residue: 0.0786 time to fit residues: 7.7337 Evaluate side-chains 59 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1068 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN A 149 GLN A 214 GLN A 547 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.108494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.084814 restraints weight = 18049.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.086420 restraints weight = 11686.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.087414 restraints weight = 8543.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088198 restraints weight = 6949.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088590 restraints weight = 5983.224| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9543 Z= 0.095 Angle : 0.534 7.882 13288 Z= 0.264 Chirality : 0.041 0.149 1564 Planarity : 0.004 0.052 1455 Dihedral : 11.430 179.248 1928 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.95 % Allowed : 24.73 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.83 (0.27), residues: 982 helix: -0.81 (0.26), residues: 433 sheet: -0.91 (0.53), residues: 101 loop : -1.61 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 487 TYR 0.011 0.001 TYR A 84 PHE 0.009 0.001 PHE A 544 TRP 0.006 0.001 TRP A 194 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.09 ( 9542) covalent geometry : angle 0.53388 / 0.26 (13288) hydrogen bonds : bond 0.02927 / 1.91 ( 267) hydrogen bonds : angle 3.82454 / 2.70 ( 710) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 214 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.9006 (mm-40) REVERT: A 252 LYS cc_start: 0.8992 (tmmm) cc_final: 0.8673 (ttpp) outliers start: 16 outliers final: 12 residues processed: 64 average time/residue: 0.0683 time to fit residues: 7.0155 Evaluate side-chains 61 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1068 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 0.1980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN A 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.106359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.082480 restraints weight = 18109.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.084021 restraints weight = 11812.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.085056 restraints weight = 8720.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.085645 restraints weight = 7063.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.086228 restraints weight = 6196.631| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9543 Z= 0.148 Angle : 0.582 8.476 13288 Z= 0.289 Chirality : 0.043 0.158 1564 Planarity : 0.004 0.048 1455 Dihedral : 11.426 176.373 1928 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.58 % Allowed : 24.73 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.88 (0.27), residues: 982 helix: -0.84 (0.26), residues: 433 sheet: -0.92 (0.54), residues: 101 loop : -1.65 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 487 TYR 0.018 0.002 TYR A 486 PHE 0.011 0.001 PHE A 544 TRP 0.007 0.001 TRP A 194 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 9542) covalent geometry : angle 0.58196 / 0.29 (13288) hydrogen bonds : bond 0.03506 / 2.29 ( 267) hydrogen bonds : angle 4.03324 / 2.85 ( 710) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.9002 (tmmm) cc_final: 0.8607 (ttpp) outliers start: 13 outliers final: 12 residues processed: 61 average time/residue: 0.0711 time to fit residues: 6.9884 Evaluate side-chains 62 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1068 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN A 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.107339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.083501 restraints weight = 18152.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.085105 restraints weight = 11740.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.086032 restraints weight = 8595.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.086847 restraints weight = 7023.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087343 restraints weight = 6043.726| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9543 Z= 0.116 Angle : 0.559 8.005 13288 Z= 0.277 Chirality : 0.042 0.154 1564 Planarity : 0.004 0.051 1455 Dihedral : 11.413 178.149 1928 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.95 % Allowed : 24.36 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.80 (0.27), residues: 982 helix: -0.78 (0.26), residues: 434 sheet: -0.91 (0.53), residues: 101 loop : -1.61 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 487 TYR 0.010 0.001 TYR A 212 PHE 0.010 0.001 PHE A 544 TRP 0.006 0.001 TRP A 194 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9542) covalent geometry : angle 0.55870 / 0.28 (13288) hydrogen bonds : bond 0.03246 / 2.12 ( 267) hydrogen bonds : angle 3.92422 / 2.76 ( 710) Misc. bond : bond 0.00012 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.9002 (tmmm) cc_final: 0.8616 (ttpp) outliers start: 16 outliers final: 13 residues processed: 63 average time/residue: 0.0707 time to fit residues: 7.2012 Evaluate side-chains 61 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1068 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 91 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 60 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN A 214 GLN A 547 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.108544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085754 restraints weight = 17917.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087017 restraints weight = 13141.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087155 restraints weight = 10159.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.087385 restraints weight = 9470.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087478 restraints weight = 8401.158| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9543 Z= 0.096 Angle : 0.535 7.671 13288 Z= 0.265 Chirality : 0.041 0.150 1564 Planarity : 0.004 0.052 1455 Dihedral : 11.351 178.678 1928 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.19 % Allowed : 24.24 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.71 (0.27), residues: 982 helix: -0.69 (0.26), residues: 439 sheet: -0.88 (0.53), residues: 101 loop : -1.57 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 487 TYR 0.019 0.001 TYR A 486 PHE 0.009 0.001 PHE A 544 TRP 0.007 0.001 TRP A 194 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 9542) covalent geometry : angle 0.53533 / 0.26 (13288) hydrogen bonds : bond 0.02940 / 1.92 ( 267) hydrogen bonds : angle 3.76638 / 2.65 ( 710) Misc. bond : bond 0.00002 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1619.78 seconds wall clock time: 28 minutes 38.04 seconds (1718.04 seconds total)