Starting phenix.real_space_refine on Fri Mar 14 04:35:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk0_33239/03_2025/7xk0_33239.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk0_33239/03_2025/7xk0_33239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xk0_33239/03_2025/7xk0_33239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk0_33239/03_2025/7xk0_33239.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk0_33239/03_2025/7xk0_33239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk0_33239/03_2025/7xk0_33239.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 bond proxies already assigned to first conformer: 7834 Chain: "B" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1520 Unusual residues: {'GTP': 1} Classifications: {'RNA': 70, 'undetermined': 1} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 60, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" C B 2 " Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 940 " occ=0.50 Time building chain proxies: 9.19, per 1000 atoms: 1.00 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: 2.15 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 3.12 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: 3.64 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1395 1.31 - 1.43: 2870 1.43 - 1.56: 5080 1.56 - 1.68: 145 1.68 - 1.81: 52 Bond restraints: 9542 Sorted by residual: bond pdb=" C8 GTP B 1 " pdb=" N9 GTP B 1 " ideal model delta sigma weight residual 1.370 1.197 0.173 2.00e-02 2.50e+03 7.44e+01 bond pdb=" C4 GTP B 1 " pdb=" N9 GTP B 1 " ideal model delta sigma weight residual 1.375 1.214 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O2G GTP B 1 " pdb=" PG GTP B 1 " ideal model delta sigma weight residual 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.450 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C1' GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sigma weight residual 1.410 1.508 -0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 9537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 13039 2.86 - 5.73: 216 5.73 - 8.59: 28 8.59 - 11.45: 4 11.45 - 14.32: 1 Bond angle restraints: 13288 Sorted by residual: angle pdb=" N GLY A 737 " pdb=" CA GLY A 737 " pdb=" C GLY A 737 " ideal model delta sigma weight residual 111.56 119.92 -8.36 1.01e+00 9.80e-01 6.85e+01 angle pdb=" C4 GTP B 1 " pdb=" N9 GTP B 1 " pdb=" C8 GTP B 1 " ideal model delta sigma weight residual 108.00 122.32 -14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" CA ARG A 965 " pdb=" C ARG A 965 " pdb=" N PRO A 966 " ideal model delta sigma weight residual 118.44 125.95 -7.51 1.59e+00 3.96e-01 2.23e+01 angle pdb=" C ARG A 529 " pdb=" N TRP A 530 " pdb=" CA TRP A 530 " ideal model delta sigma weight residual 122.58 113.93 8.65 2.07e+00 2.33e-01 1.75e+01 angle pdb=" N ILE A 945 " pdb=" CA ILE A 945 " pdb=" C ILE A 945 " ideal model delta sigma weight residual 111.00 106.83 4.17 1.09e+00 8.42e-01 1.46e+01 ... (remaining 13283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 5550 35.70 - 71.39: 255 71.39 - 107.09: 32 107.09 - 142.78: 3 142.78 - 178.48: 2 Dihedral angle restraints: 5842 sinusoidal: 2984 harmonic: 2858 Sorted by residual: dihedral pdb=" O4' U B 19 " pdb=" C1' U B 19 " pdb=" N1 U B 19 " pdb=" C2 U B 19 " ideal model delta sinusoidal sigma weight residual 232.00 60.17 171.83 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O5' GTP B 1 " pdb=" O3A GTP B 1 " pdb=" PA GTP B 1 " pdb=" PB GTP B 1 " ideal model delta sinusoidal sigma weight residual 274.12 95.64 178.48 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C4' GTP B 1 " pdb=" C5' GTP B 1 " pdb=" O5' GTP B 1 " pdb=" PA GTP B 1 " ideal model delta sinusoidal sigma weight residual 260.87 139.34 121.54 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 5839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1162 0.060 - 0.120: 351 0.120 - 0.180: 46 0.180 - 0.240: 4 0.240 - 0.300: 1 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CB ILE A 970 " pdb=" CA ILE A 970 " pdb=" CG1 ILE A 970 " pdb=" CG2 ILE A 970 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C1' U B 57 " pdb=" O4' U B 57 " pdb=" C2' U B 57 " pdb=" N1 U B 57 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ARG A 965 " pdb=" N ARG A 965 " pdb=" C ARG A 965 " pdb=" CB ARG A 965 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1561 not shown) Planarity restraints: 1455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 637 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO A 638 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 962 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ALA A 962 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA A 962 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 963 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 57 " -0.028 2.00e-02 2.50e+03 1.54e-02 5.32e+00 pdb=" N1 U B 57 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U B 57 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U B 57 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U B 57 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U B 57 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U B 57 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U B 57 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 57 " 0.006 2.00e-02 2.50e+03 ... (remaining 1452 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1534 2.75 - 3.28: 8621 3.28 - 3.82: 14776 3.82 - 4.36: 17529 4.36 - 4.90: 28787 Nonbonded interactions: 71247 Sorted by model distance: nonbonded pdb=" O LYS A1040 " pdb=" ND2 ASN A1043 " model vdw 2.206 3.120 nonbonded pdb=" NH1 ARG A 724 " pdb=" O ALA A 772 " model vdw 2.210 3.120 nonbonded pdb=" O VAL A1041 " pdb=" NH1 ARG A1045 " model vdw 2.230 3.120 nonbonded pdb=" OE2 GLU A 233 " pdb=" OH TYR A 256 " model vdw 2.237 3.040 nonbonded pdb=" O PRO A 481 " pdb=" OG SER A 484 " model vdw 2.246 3.040 ... (remaining 71242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 30.930 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 9542 Z= 0.695 Angle : 0.958 14.317 13288 Z= 0.532 Chirality : 0.055 0.300 1564 Planarity : 0.006 0.070 1455 Dihedral : 19.034 178.481 3994 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.002 TRP A 298 HIS 0.005 0.002 HIS A 586 PHE 0.024 0.002 PHE A1014 TYR 0.019 0.003 TYR A 584 ARG 0.006 0.001 ARG A 432 *********************** 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 : 0.868 Fit side-chains revert: symmetry clash REVERT: A 264 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7191 (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: 0.7797 (mmt) REVERT: A 743 MET cc_start: 0.8116 (mmm) cc_final: 0.7620 (mmm) outliers start: 44 outliers final: 22 residues processed: 98 average time/residue: 0.2179 time to fit residues: 30.5452 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 : 0.995 ------------------------------------------------------------------------------- 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 88 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 94 GLN ** A 106 ASN ** 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 781 ASN A 856 ASN A1031 ASN A1043 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.104325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.081428 restraints weight = 18206.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.082686 restraints weight = 12749.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.082884 restraints weight = 9157.468| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9542 Z= 0.257 Angle : 0.654 7.593 13288 Z= 0.332 Chirality : 0.045 0.179 1564 Planarity : 0.005 0.054 1455 Dihedral : 18.716 170.639 2205 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.41 % Allowed : 20.46 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.23), residues: 982 helix: -2.75 (0.21), residues: 432 sheet: -1.94 (0.53), residues: 98 loop : -2.92 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 995 HIS 0.004 0.001 HIS A 244 PHE 0.030 0.002 PHE A 322 TYR 0.015 0.001 TYR A 643 ARG 0.006 0.000 ARG A 292 *********************** 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 78 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 159 SER cc_start: 0.8957 (OUTLIER) cc_final: 0.8743 (t) REVERT: A 214 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8264 (mt0) REVERT: A 264 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6227 (mp0) REVERT: A 486 TYR cc_start: 0.7823 (p90) cc_final: 0.7438 (p90) REVERT: A 743 MET cc_start: 0.8355 (mmm) cc_final: 0.7401 (mmm) REVERT: A 947 MET cc_start: 0.8634 (ttm) cc_final: 0.8333 (ttm) REVERT: A 1045 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7654 (mpp80) outliers start: 28 outliers final: 15 residues processed: 77 average time/residue: 0.2393 time to fit residues: 26.9401 Evaluate side-chains 62 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 677 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1045 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 84 optimal weight: 0.6980 chunk 39 optimal weight: 0.0670 chunk 22 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 214 GLN A 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.108378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.086207 restraints weight = 18082.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087555 restraints weight = 12749.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087615 restraints weight = 9652.538| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 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 = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9542 Z= 0.147 Angle : 0.565 8.490 13288 Z= 0.282 Chirality : 0.041 0.169 1564 Planarity : 0.004 0.051 1455 Dihedral : 18.056 178.038 2186 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.44 % Allowed : 21.92 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.25), residues: 982 helix: -2.06 (0.23), residues: 437 sheet: -1.84 (0.47), residues: 114 loop : -2.26 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 995 HIS 0.003 0.001 HIS A 244 PHE 0.022 0.001 PHE A 322 TYR 0.013 0.001 TYR A 212 ARG 0.004 0.000 ARG A 292 *********************** 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 75 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8983 (tmmm) cc_final: 0.8640 (ttpp) REVERT: A 264 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: A 947 MET cc_start: 0.8506 (ttm) cc_final: 0.8147 (ttm) REVERT: A 964 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8157 (m) REVERT: A 1045 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7533 (mpp80) outliers start: 20 outliers final: 12 residues processed: 74 average time/residue: 0.2099 time to fit residues: 22.6077 Evaluate side-chains 57 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 32 optimal weight: 0.9990 chunk 81 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3524 r_free = 0.3524 target = 0.108078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.085736 restraints weight = 18012.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087057 restraints weight = 12863.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.087012 restraints weight = 9936.248| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 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 = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9542 Z= 0.152 Angle : 0.555 8.341 13288 Z= 0.273 Chirality : 0.041 0.147 1564 Planarity : 0.004 0.050 1455 Dihedral : 17.899 179.789 2185 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.44 % Allowed : 23.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.26), residues: 982 helix: -1.58 (0.25), residues: 424 sheet: -1.61 (0.48), residues: 112 loop : -1.93 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 995 HIS 0.003 0.001 HIS A 244 PHE 0.010 0.001 PHE A 544 TYR 0.011 0.001 TYR A 486 ARG 0.004 0.000 ARG A 292 *********************** 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 65 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.9027 (tmmm) cc_final: 0.8665 (ttpp) REVERT: A 267 MET cc_start: 0.8664 (tpp) cc_final: 0.8420 (tpt) REVERT: A 947 MET cc_start: 0.8581 (ttm) cc_final: 0.8164 (ttm) REVERT: A 1045 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7423 (mpp80) outliers start: 20 outliers final: 10 residues processed: 64 average time/residue: 0.1797 time to fit residues: 17.9340 Evaluate side-chains 56 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 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 1045 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 47 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 38 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN A 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085755 restraints weight = 18017.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087113 restraints weight = 12783.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.087074 restraints weight = 9789.126| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 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 = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9542 Z= 0.155 Angle : 0.544 7.810 13288 Z= 0.267 Chirality : 0.041 0.154 1564 Planarity : 0.004 0.051 1455 Dihedral : 17.762 178.426 2181 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.07 % Allowed : 23.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.26), residues: 982 helix: -1.30 (0.25), residues: 427 sheet: -1.48 (0.48), residues: 113 loop : -1.75 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 194 HIS 0.003 0.001 HIS A 244 PHE 0.010 0.001 PHE A 544 TYR 0.009 0.001 TYR A 84 ARG 0.004 0.000 ARG A 292 *********************** 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 65 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8982 (tmmm) cc_final: 0.8621 (ttpp) REVERT: A 264 GLU cc_start: 0.7894 (tp30) cc_final: 0.7258 (mm-30) REVERT: A 461 PHE cc_start: 0.7325 (t80) cc_final: 0.7062 (t80) REVERT: A 947 MET cc_start: 0.8528 (ttm) cc_final: 0.8109 (ttm) outliers start: 17 outliers final: 11 residues processed: 64 average time/residue: 0.1593 time to fit residues: 16.3283 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 : 0.873 ------------------------------------------------------------------------------- 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 450 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3531 r_free = 0.3531 target = 0.108597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.086278 restraints weight = 17981.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.086895 restraints weight = 14486.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087187 restraints weight = 11253.557| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9542 Z= 0.154 Angle : 0.539 7.701 13288 Z= 0.265 Chirality : 0.041 0.149 1564 Planarity : 0.004 0.051 1455 Dihedral : 17.696 177.639 2178 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.83 % Allowed : 23.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.26), residues: 982 helix: -1.06 (0.25), residues: 430 sheet: -1.35 (0.49), residues: 113 loop : -1.60 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 194 HIS 0.003 0.000 HIS A 244 PHE 0.008 0.001 PHE A 544 TYR 0.018 0.001 TYR A 486 ARG 0.003 0.000 ARG A 292 *********************** 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 65 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7732 (tt0) REVERT: A 159 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8717 (t) REVERT: A 205 MET cc_start: 0.7531 (tpp) cc_final: 0.7105 (ttt) REVERT: A 252 LYS cc_start: 0.8957 (tmmm) cc_final: 0.8610 (ttpp) REVERT: A 461 PHE cc_start: 0.7261 (t80) cc_final: 0.7006 (t80) REVERT: A 947 MET cc_start: 0.8541 (ttm) cc_final: 0.8101 (ttm) outliers start: 15 outliers final: 11 residues processed: 63 average time/residue: 0.1774 time to fit residues: 17.9813 Evaluate side-chains 60 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 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 500 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3547 r_free = 0.3547 target = 0.109659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.087360 restraints weight = 18097.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.087860 restraints weight = 14107.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088529 restraints weight = 11508.039| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9542 Z= 0.139 Angle : 0.530 7.623 13288 Z= 0.261 Chirality : 0.040 0.151 1564 Planarity : 0.004 0.051 1455 Dihedral : 17.662 176.981 2178 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.27), residues: 982 helix: -0.83 (0.26), residues: 437 sheet: -0.82 (0.53), residues: 101 loop : -1.63 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 194 HIS 0.003 0.001 HIS A 244 PHE 0.009 0.001 PHE A 544 TYR 0.010 0.001 TYR A 84 ARG 0.004 0.000 ARG A 745 *********************** 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 63 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7817 (tt0) REVERT: A 252 LYS cc_start: 0.8947 (tmmm) cc_final: 0.8649 (ttpp) REVERT: A 947 MET cc_start: 0.8495 (ttm) cc_final: 0.8055 (ttm) outliers start: 10 outliers final: 8 residues processed: 60 average time/residue: 0.1763 time to fit residues: 16.5832 Evaluate side-chains 57 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 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 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3514 r_free = 0.3514 target = 0.107285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.083452 restraints weight = 18358.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.085032 restraints weight = 11834.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.086121 restraints weight = 8677.250| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9542 Z= 0.206 Angle : 0.561 7.607 13288 Z= 0.277 Chirality : 0.042 0.151 1564 Planarity : 0.004 0.049 1455 Dihedral : 17.677 176.468 2176 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.07 % Allowed : 24.00 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.27), residues: 982 helix: -0.83 (0.26), residues: 434 sheet: -0.81 (0.53), residues: 101 loop : -1.56 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 194 HIS 0.002 0.001 HIS A 244 PHE 0.010 0.001 PHE A 544 TYR 0.018 0.001 TYR A 486 ARG 0.004 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7775 (tt0) REVERT: A 205 MET cc_start: 0.7490 (tpp) cc_final: 0.7091 (ttt) REVERT: A 252 LYS cc_start: 0.8958 (tmmm) cc_final: 0.8580 (ttpp) REVERT: A 947 MET cc_start: 0.8572 (ttm) cc_final: 0.8128 (ttm) outliers start: 17 outliers final: 12 residues processed: 64 average time/residue: 0.1808 time to fit residues: 18.0691 Evaluate side-chains 61 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 500 VAL 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 81 optimal weight: 7.9990 chunk 49 optimal weight: 0.0970 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 3 optimal weight: 0.0050 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.110324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.087665 restraints weight = 17976.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089071 restraints weight = 12990.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.089100 restraints weight = 9944.852| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 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 = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9542 Z= 0.132 Angle : 0.518 7.525 13288 Z= 0.255 Chirality : 0.040 0.149 1564 Planarity : 0.004 0.052 1455 Dihedral : 17.660 177.555 2176 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.71 % Allowed : 24.36 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.27), residues: 982 helix: -0.61 (0.26), residues: 438 sheet: -0.82 (0.53), residues: 103 loop : -1.53 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 194 HIS 0.003 0.001 HIS A 244 PHE 0.011 0.001 PHE A 461 TYR 0.011 0.001 TYR A 84 ARG 0.004 0.000 ARG A 487 *********************** 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 68 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7694 (tt0) REVERT: A 205 MET cc_start: 0.7291 (tpp) cc_final: 0.6901 (ttt) REVERT: A 252 LYS cc_start: 0.8932 (tmmm) cc_final: 0.8613 (ttpp) REVERT: A 947 MET cc_start: 0.8416 (ttm) cc_final: 0.7956 (ttm) outliers start: 14 outliers final: 13 residues processed: 66 average time/residue: 0.1722 time to fit residues: 17.9253 Evaluate side-chains 61 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 500 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1068 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 68 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.0050 chunk 75 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 83 optimal weight: 0.0270 chunk 84 optimal weight: 0.6980 chunk 81 optimal weight: 0.0670 overall best weight: 0.1748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3596 r_free = 0.3596 target = 0.112850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090374 restraints weight = 18174.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.091203 restraints weight = 13925.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.091786 restraints weight = 11165.888| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 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 = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9542 Z= 0.123 Angle : 0.507 7.446 13288 Z= 0.248 Chirality : 0.039 0.151 1564 Planarity : 0.004 0.053 1455 Dihedral : 17.619 176.367 2176 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.58 % Allowed : 24.73 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.27), residues: 982 helix: -0.31 (0.27), residues: 432 sheet: -0.65 (0.54), residues: 103 loop : -1.51 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 194 HIS 0.004 0.001 HIS A 244 PHE 0.007 0.001 PHE A 544 TYR 0.012 0.001 TYR A 643 ARG 0.004 0.000 ARG A 487 ********************** 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 70 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 205 MET cc_start: 0.7123 (tpp) cc_final: 0.6829 (ttt) REVERT: A 252 LYS cc_start: 0.8900 (tmmm) cc_final: 0.8604 (ttpp) REVERT: A 947 MET cc_start: 0.8383 (ttm) cc_final: 0.7930 (ttm) REVERT: A 1068 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.5870 (m-80) outliers start: 13 outliers final: 11 residues processed: 68 average time/residue: 0.1616 time to fit residues: 17.3114 Evaluate side-chains 63 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 500 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 840 ASP 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 36 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 34 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3538 r_free = 0.3538 target = 0.108911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.084963 restraints weight = 18077.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.086550 restraints weight = 11688.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.087608 restraints weight = 8589.349| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9542 Z= 0.203 Angle : 0.562 8.545 13288 Z= 0.276 Chirality : 0.042 0.149 1564 Planarity : 0.004 0.050 1455 Dihedral : 17.582 175.982 2174 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.71 % Allowed : 24.48 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.27), residues: 982 helix: -0.40 (0.26), residues: 436 sheet: -0.65 (0.53), residues: 101 loop : -1.44 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 530 HIS 0.003 0.001 HIS A 306 PHE 0.010 0.001 PHE A 544 TYR 0.013 0.001 TYR A 212 ARG 0.004 0.000 ARG A 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3177.01 seconds wall clock time: 56 minutes 10.40 seconds (3370.40 seconds total)