Starting phenix.real_space_refine on Fri Sep 11 13:24:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xk0_33239/09_2026/7xk0_33239.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk0_33239/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xk0_33239/09_2026/7xk0_33239.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xk0_33239/09_2026/7xk0_33239.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xk0_33239/09_2026/7xk0_33239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk0_33239/09_2026/7xk0_33239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xk0_33239/09_2026/7xk0_33239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk0_33239/09_2026/7xk0_33239.map" } 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-2.2.1-6174/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: {'RNAv2': 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: 3.36, per 1000 atoms: 0.36 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: 0.77 Conformation dependent library (CDL) restraints added in 550.5 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: 1.19 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: 1.90 Time building geometry restraints manager: 1.07 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: 12964 2.86 - 5.73: 290 5.73 - 8.59: 29 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=" C3' G B 18 " pdb=" O3' G B 18 " pdb=" P U B 19 " ideal model delta sigma weight residual 119.70 125.00 -5.30 1.20e+00 6.94e-01 1.95e+01 angle pdb=" C3' C B 34 " pdb=" O3' C B 34 " pdb=" P C B 35 " ideal model delta sigma weight residual 119.70 124.81 -5.11 1.20e+00 6.94e-01 1.81e+01 ... (remaining 13283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 5348 35.70 - 71.39: 229 71.39 - 107.09: 13 107.09 - 142.78: 3 142.78 - 178.48: 1 Dihedral angle restraints: 5594 sinusoidal: 2736 harmonic: 2858 Sorted by residual: dihedral pdb=" C4' U B 31 " pdb=" C3' U B 31 " pdb=" C2' U B 31 " pdb=" C1' U B 31 " ideal model delta sinusoidal sigma weight residual 36.34 -38.08 74.43 1 3.10e+00 1.04e-01 7.31e+02 dihedral pdb=" C4' A B 56 " pdb=" C3' A B 56 " pdb=" C2' A B 56 " pdb=" C1' A B 56 " ideal model delta sinusoidal sigma weight residual 36.34 -36.99 73.33 1 3.10e+00 1.04e-01 7.12e+02 dihedral pdb=" C4' U B 32 " pdb=" C3' U B 32 " pdb=" C2' U B 32 " pdb=" C1' U B 32 " ideal model delta sinusoidal sigma weight residual 36.35 -36.05 72.40 1 3.10e+00 1.04e-01 6.97e+02 ... (remaining 5591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1168 0.068 - 0.137: 278 0.137 - 0.205: 37 0.205 - 0.273: 73 0.273 - 0.342: 8 Chirality restraints: 1564 Sorted by residual: chirality pdb=" P U B 57 " pdb=" OP1 U B 57 " pdb=" OP2 U B 57 " pdb=" O5' U B 57 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" P A B 9 " pdb=" OP1 A B 9 " pdb=" OP2 A B 9 " pdb=" O5' A B 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" P C B 30 " pdb=" OP1 C B 30 " pdb=" OP2 C B 30 " pdb=" O5' C B 30 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.51e+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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.860 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- 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= 0.479 Angle : 1.025 14.317 13288 Z= 0.540 Chirality : 0.079 0.342 1564 Planarity : 0.006 0.070 1455 Dihedral : 17.944 178.481 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 0.01063 / 0.48 ( 9542) covalent geometry : angle 1.02515 / 0.54 (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 : 0.302 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: 0.0852 time to fit residues: 12.0542 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 : 0.245 ------------------------------------------------------------------------------- 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: 8.9990 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 856 ASN A1031 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.085172 restraints weight = 18071.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.085979 restraints weight = 13237.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.086343 restraints weight = 10474.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.086497 restraints weight = 9500.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.086640 restraints weight = 8674.530| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 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 = 0.3159 r_free = 0.3159 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: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9543 Z= 0.136 Angle : 0.856 17.977 13288 Z= 0.375 Chirality : 0.073 1.184 1564 Planarity : 0.005 0.053 1455 Dihedral : 14.694 159.752 1957 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.05 % Allowed : 20.46 % Favored : 76.49 % 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: -4.07 (0.23), residues: 982 helix: -2.70 (0.21), residues: 432 sheet: -2.15 (0.49), residues: 108 loop : -2.75 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 292 TYR 0.013 0.001 TYR A 84 PHE 0.028 0.001 PHE A 322 TRP 0.016 0.001 TRP A 995 HIS 0.005 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 9542) covalent geometry : angle 0.85591 / 0.37 (13288) hydrogen bonds : bond 0.03884 / 2.53 ( 267) hydrogen bonds : angle 4.60128 / 3.24 ( 710) Misc. bond : bond 0.00007 / 0.00 ( 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 : 0.319 Fit side-chains revert: symmetry clash REVERT: A 159 SER cc_start: 0.8896 (OUTLIER) cc_final: 0.8642 (t) REVERT: A 214 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: A 252 LYS cc_start: 0.9020 (tmmm) cc_final: 0.8676 (ttpp) REVERT: A 264 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: A 267 MET cc_start: 0.8600 (tpp) cc_final: 0.8160 (mmt) REVERT: A 743 MET cc_start: 0.8324 (mmm) cc_final: 0.7336 (mmm) REVERT: A 947 MET cc_start: 0.8613 (ttm) cc_final: 0.8354 (ttm) REVERT: A 1045 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7586 (mpp80) outliers start: 25 outliers final: 14 residues processed: 76 average time/residue: 0.0774 time to fit residues: 8.7713 Evaluate side-chains 64 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 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 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 964 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 79 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 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 = 0.3551 r_free = 0.3551 target = 0.110073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.087655 restraints weight = 18040.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088202 restraints weight = 13870.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.088581 restraints weight = 10889.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088893 restraints weight = 10343.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.089105 restraints weight = 8948.337| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 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 = 0.3206 r_free = 0.3206 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: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9543 Z= 0.114 Angle : 0.711 12.178 13288 Z= 0.320 Chirality : 0.056 0.509 1564 Planarity : 0.004 0.050 1455 Dihedral : 13.785 139.704 1940 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.56 % Allowed : 20.95 % Favored : 76.49 % 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: -3.21 (0.25), residues: 982 helix: -1.95 (0.24), residues: 431 sheet: -1.89 (0.47), residues: 116 loop : -2.27 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 292 TYR 0.012 0.001 TYR A 84 PHE 0.022 0.001 PHE A 322 TRP 0.007 0.001 TRP A 995 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 9542) covalent geometry : angle 0.71142 / 0.32 (13288) hydrogen bonds : bond 0.03210 / 2.09 ( 267) hydrogen bonds : angle 4.04281 / 2.86 ( 710) Misc. bond : bond 0.00079 / 0.04 ( 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 74 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 237 MET cc_start: 0.8789 (mtp) cc_final: 0.8497 (mtt) REVERT: A 252 LYS cc_start: 0.8999 (tmmm) cc_final: 0.8645 (ttpp) REVERT: A 947 MET cc_start: 0.8450 (ttm) cc_final: 0.8083 (ttm) REVERT: A 1045 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7427 (mpp80) outliers start: 21 outliers final: 11 residues processed: 73 average time/residue: 0.0849 time to fit residues: 9.1043 Evaluate side-chains 56 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 A 631 ASN A1043 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.082258 restraints weight = 18235.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.083457 restraints weight = 12046.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.083443 restraints weight = 9287.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.083895 restraints weight = 8594.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084037 restraints weight = 7252.580| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9543 Z= 0.181 Angle : 0.777 10.716 13288 Z= 0.351 Chirality : 0.061 0.417 1564 Planarity : 0.004 0.049 1455 Dihedral : 13.772 155.177 1933 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.92 % Allowed : 22.29 % 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: -2.99 (0.25), residues: 982 helix: -1.74 (0.24), residues: 427 sheet: -1.45 (0.54), residues: 96 loop : -2.28 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.018 0.002 TYR A 643 PHE 0.012 0.001 PHE A 544 TRP 0.008 0.001 TRP A 194 HIS 0.003 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 9542) covalent geometry : angle 0.77725 / 0.35 (13288) hydrogen bonds : bond 0.04075 / 2.66 ( 267) hydrogen bonds : angle 4.37953 / 3.09 ( 710) Misc. bond : bond 0.00001 / 0.00 ( 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 71 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 159 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8696 (t) REVERT: A 252 LYS cc_start: 0.9009 (tmmm) cc_final: 0.8635 (ttpp) REVERT: A 264 GLU cc_start: 0.7940 (tp30) cc_final: 0.7167 (mm-30) REVERT: A 947 MET cc_start: 0.8644 (ttm) cc_final: 0.8244 (ttm) outliers start: 24 outliers final: 14 residues processed: 69 average time/residue: 0.0668 time to fit residues: 7.2187 Evaluate side-chains 60 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 296 SER 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 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: 0.8980 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 0.0670 chunk 8 optimal weight: 0.0030 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.5128 ------------------------------------------------------------------------------- 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 A 631 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.110451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.087884 restraints weight = 18172.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088542 restraints weight = 14363.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088857 restraints weight = 11138.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089278 restraints weight = 10000.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.089411 restraints weight = 8670.229| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3030 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= 0.099 Angle : 0.669 11.330 13288 Z= 0.298 Chirality : 0.054 0.367 1564 Planarity : 0.004 0.050 1455 Dihedral : 13.520 161.565 1933 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.95 % Allowed : 23.39 % Favored : 74.67 % 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: -2.43 (0.26), residues: 982 helix: -1.36 (0.25), residues: 427 sheet: -1.65 (0.48), residues: 117 loop : -1.73 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 292 TYR 0.015 0.001 TYR A 486 PHE 0.010 0.001 PHE A 544 TRP 0.008 0.001 TRP A 194 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9542) covalent geometry : angle 0.66935 / 0.30 (13288) hydrogen bonds : bond 0.02848 / 1.88 ( 267) hydrogen bonds : angle 3.86603 / 2.74 ( 710) Misc. bond : bond 0.00042 / 0.02 ( 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 66 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8958 (tmmm) cc_final: 0.8588 (ttpp) REVERT: A 947 MET cc_start: 0.8482 (ttm) cc_final: 0.8063 (ttm) REVERT: A 1045 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7420 (mpp80) outliers start: 16 outliers final: 10 residues processed: 63 average time/residue: 0.0656 time to fit residues: 6.6420 Evaluate side-chains 59 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 1045 ARG Chi-restraints excluded: chain A residue 1068 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 36 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.108318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.081584 restraints weight = 18671.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.084095 restraints weight = 9388.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.085786 restraints weight = 5956.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.086892 restraints weight = 4371.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087624 restraints weight = 3554.529| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 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 = 0.3188 r_free = 0.3188 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: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9543 Z= 0.108 Angle : 0.668 10.199 13288 Z= 0.299 Chirality : 0.054 0.352 1564 Planarity : 0.004 0.050 1455 Dihedral : 13.386 164.452 1928 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.95 % Allowed : 23.75 % Favored : 74.30 % 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 (0.27), residues: 982 helix: -1.06 (0.25), residues: 430 sheet: -1.60 (0.48), residues: 117 loop : -1.57 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.010 0.001 TYR A 212 PHE 0.010 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 0.00251 / 0.11 ( 9542) covalent geometry : angle 0.66797 / 0.30 (13288) hydrogen bonds : bond 0.03028 / 1.99 ( 267) hydrogen bonds : angle 3.83162 / 2.71 ( 710) Misc. bond : bond 0.00030 / 0.02 ( 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 63 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 205 MET cc_start: 0.7670 (tpp) cc_final: 0.7390 (ttt) REVERT: A 252 LYS cc_start: 0.9181 (tmmm) cc_final: 0.8830 (ttpp) REVERT: A 461 PHE cc_start: 0.7323 (t80) cc_final: 0.7055 (t80) REVERT: A 947 MET cc_start: 0.8174 (ttm) cc_final: 0.7768 (ttm) outliers start: 16 outliers final: 10 residues processed: 61 average time/residue: 0.0691 time to fit residues: 6.6775 Evaluate side-chains 57 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL 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 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: 10.0000 chunk 76 optimal weight: 9.9990 chunk 14 optimal weight: 0.0970 chunk 101 optimal weight: 8.9990 chunk 6 optimal weight: 0.0970 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.109164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082485 restraints weight = 18630.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.084985 restraints weight = 9455.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.086668 restraints weight = 5997.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087690 restraints weight = 4415.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.088430 restraints weight = 3638.582| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 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 = 0.3205 r_free = 0.3205 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: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9543 Z= 0.103 Angle : 0.653 10.099 13288 Z= 0.292 Chirality : 0.053 0.333 1564 Planarity : 0.004 0.050 1455 Dihedral : 13.281 168.853 1928 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.07 % Allowed : 23.39 % 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: -1.84 (0.27), residues: 982 helix: -0.82 (0.26), residues: 437 sheet: -0.89 (0.53), residues: 101 loop : -1.62 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.015 0.001 TYR A 486 PHE 0.010 0.001 PHE A 544 TRP 0.007 0.001 TRP A 194 HIS 0.003 0.000 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 9542) covalent geometry : angle 0.65279 / 0.29 (13288) hydrogen bonds : bond 0.02883 / 1.89 ( 267) hydrogen bonds : angle 3.73040 / 2.63 ( 710) Misc. bond : bond 0.00030 / 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: 17 poor density : 49 time to evaluate : 0.223 Fit side-chains REVERT: A 79 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7916 (tt0) REVERT: A 205 MET cc_start: 0.7456 (tpp) cc_final: 0.7149 (ttt) REVERT: A 252 LYS cc_start: 0.9181 (tmmm) cc_final: 0.8876 (ttpp) REVERT: A 461 PHE cc_start: 0.7363 (t80) cc_final: 0.7155 (t80) REVERT: A 947 MET cc_start: 0.8099 (ttm) cc_final: 0.7674 (ttm) outliers start: 17 outliers final: 11 residues processed: 64 average time/residue: 0.0791 time to fit residues: 7.8735 Evaluate side-chains 57 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 225 SER 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: 0.0980 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 55 optimal weight: 0.0170 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 0.0030 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 0.3428 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.111877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085138 restraints weight = 18430.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087726 restraints weight = 9304.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.089419 restraints weight = 5862.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090503 restraints weight = 4294.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.091223 restraints weight = 3497.870| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3670 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= 0.092 Angle : 0.629 9.890 13288 Z= 0.280 Chirality : 0.051 0.348 1564 Planarity : 0.004 0.052 1455 Dihedral : 13.210 171.066 1928 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.34 % Allowed : 24.24 % Favored : 74.42 % 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: -1.64 (0.27), residues: 982 helix: -0.60 (0.26), residues: 440 sheet: -0.95 (0.53), residues: 105 loop : -1.53 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.011 0.001 TYR A 84 PHE 0.007 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 0.00204 / 0.09 ( 9542) covalent geometry : angle 0.62884 / 0.28 (13288) hydrogen bonds : bond 0.02534 / 1.68 ( 267) hydrogen bonds : angle 3.52169 / 2.48 ( 710) Misc. bond : bond 0.00035 / 0.02 ( 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 74 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.323 Fit side-chains REVERT: A 79 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7990 (tt0) REVERT: A 205 MET cc_start: 0.7320 (tpp) cc_final: 0.7050 (ttt) REVERT: A 252 LYS cc_start: 0.9126 (tmmm) cc_final: 0.8822 (ttpp) REVERT: A 947 MET cc_start: 0.8136 (ttm) cc_final: 0.7687 (ttm) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.0812 time to fit residues: 8.8211 Evaluate side-chains 59 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 225 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 0.0020 chunk 66 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.111459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.084637 restraints weight = 18438.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.087187 restraints weight = 9374.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.088859 restraints weight = 5931.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089965 restraints weight = 4351.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.090623 restraints weight = 3539.508| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9543 Z= 0.097 Angle : 0.641 9.643 13288 Z= 0.287 Chirality : 0.052 0.332 1564 Planarity : 0.004 0.050 1455 Dihedral : 13.146 171.732 1927 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.22 % Allowed : 24.48 % Favored : 74.30 % 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: -1.48 (0.27), residues: 982 helix: -0.49 (0.26), residues: 440 sheet: -0.66 (0.54), residues: 101 loop : -1.49 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.017 0.001 TYR A 486 PHE 0.011 0.001 PHE A1033 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 0.00220 / 0.10 ( 9542) covalent geometry : angle 0.64055 / 0.29 (13288) hydrogen bonds : bond 0.02768 / 1.81 ( 267) hydrogen bonds : angle 3.59265 / 2.52 ( 710) Misc. bond : bond 0.00026 / 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: 10 poor density : 53 time to evaluate : 0.317 Fit side-chains REVERT: A 79 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7938 (tt0) REVERT: A 205 MET cc_start: 0.7315 (tpp) cc_final: 0.7075 (ttt) REVERT: A 252 LYS cc_start: 0.9140 (tmmm) cc_final: 0.8853 (ttpp) REVERT: A 947 MET cc_start: 0.8072 (ttm) cc_final: 0.7639 (ttm) outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 0.0671 time to fit residues: 6.4190 Evaluate side-chains 57 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 736 LEU 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: 1.9990 chunk 61 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.0040 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 A 781 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.111705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.084694 restraints weight = 18530.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.087258 restraints weight = 9400.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.088940 restraints weight = 5937.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090046 restraints weight = 4357.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.090764 restraints weight = 3542.519| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9543 Z= 0.099 Angle : 0.639 9.786 13288 Z= 0.285 Chirality : 0.052 0.341 1564 Planarity : 0.004 0.051 1455 Dihedral : 13.052 174.008 1923 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.10 % Allowed : 24.73 % 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: -1.35 (0.27), residues: 982 helix: -0.35 (0.26), residues: 435 sheet: -0.58 (0.54), residues: 101 loop : -1.46 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.009 0.001 TYR A 84 PHE 0.008 0.001 PHE A 544 TRP 0.004 0.000 TRP A 530 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 9542) covalent geometry : angle 0.63905 / 0.28 (13288) hydrogen bonds : bond 0.02743 / 1.80 ( 267) hydrogen bonds : angle 3.56894 / 2.51 ( 710) Misc. bond : bond 0.00023 / 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 60 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.325 Fit side-chains REVERT: A 79 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7929 (tt0) REVERT: A 205 MET cc_start: 0.7285 (tpp) cc_final: 0.7032 (ttt) REVERT: A 252 LYS cc_start: 0.9121 (tmmm) cc_final: 0.8828 (ttpp) REVERT: A 1068 PHE cc_start: 0.5930 (OUTLIER) cc_final: 0.5395 (m-80) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.0680 time to fit residues: 6.3512 Evaluate side-chains 57 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 736 LEU 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: 0.8980 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 45 optimal weight: 0.0370 chunk 5 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 overall best weight: 0.3058 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.113886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.086909 restraints weight = 18290.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089463 restraints weight = 9287.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091160 restraints weight = 5865.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.092248 restraints weight = 4297.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.092952 restraints weight = 3503.817| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4099 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= 0.092 Angle : 0.623 9.726 13288 Z= 0.277 Chirality : 0.051 0.350 1564 Planarity : 0.004 0.053 1455 Dihedral : 12.993 176.757 1923 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.22 % Allowed : 24.73 % Favored : 74.06 % 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: -1.17 (0.27), residues: 982 helix: -0.19 (0.27), residues: 433 sheet: -0.40 (0.54), residues: 101 loop : -1.39 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.014 0.001 TYR A 486 PHE 0.007 0.001 PHE A 544 TRP 0.004 0.001 TRP A 85 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 9542) covalent geometry : angle 0.62326 / 0.28 (13288) hydrogen bonds : bond 0.02505 / 1.65 ( 267) hydrogen bonds : angle 3.44533 / 2.43 ( 710) Misc. bond : bond 0.00027 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1607.20 seconds wall clock time: 28 minutes 20.70 seconds (1700.70 seconds total)