Starting phenix.real_space_refine on Wed Mar 4 13:22:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6npl_0473/03_2026/6npl_0473.cif Found real_map, /net/cci-nas-00/data/ceres_data/6npl_0473/03_2026/6npl_0473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6npl_0473/03_2026/6npl_0473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6npl_0473/03_2026/6npl_0473.map" model { file = "/net/cci-nas-00/data/ceres_data/6npl_0473/03_2026/6npl_0473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6npl_0473/03_2026/6npl_0473.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.010 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 7 5.49 5 S 76 5.16 5 Cl 4 4.86 5 C 9002 2.51 5 N 2235 2.21 5 O 2448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13774 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6702 Classifications: {'peptide': 861} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 834} Chain breaks: 1 Chain: "B" Number of atoms: 6702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6702 Classifications: {'peptide': 861} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 834} Chain breaks: 1 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 159 Unusual residues: {' K': 1, ' CL': 2, 'POV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 211 Unusual residues: {' K': 1, ' CL': 2, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 2.86, per 1000 atoms: 0.21 Number of scatterers: 13774 At special positions: 0 Unit cell: (118.16, 88.62, 161.415, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 76 16.00 P 7 15.00 O 2448 8.00 N 2235 7.00 C 9002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 507 " distance=2.04 Simple disulfide: pdb=" SG CYS B 496 " - pdb=" SG CYS B 507 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 476.2 milliseconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 2 sheets defined 56.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.639A pdb=" N ILE A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 265 Processing helix chain 'A' and resid 273 through 282 removed outlier: 4.180A pdb=" N LEU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 319 removed outlier: 4.038A pdb=" N SER A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 349 removed outlier: 3.868A pdb=" N ARG A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 375 removed outlier: 4.096A pdb=" N GLU A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA A 354 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 398 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.697A pdb=" N ALA A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY A 425 " --> pdb=" O ILE A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 421 through 425' Processing helix chain 'A' and resid 434 through 463 Proline residue: A 440 - end of helix removed outlier: 3.599A pdb=" N LEU A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.728A pdb=" N VAL A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 545 removed outlier: 3.842A pdb=" N LEU A 537 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 removed outlier: 3.524A pdb=" N VAL A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 removed outlier: 4.144A pdb=" N ALA A 564 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE A 565 " --> pdb=" O GLY A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 592 removed outlier: 3.646A pdb=" N LEU A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 625 removed outlier: 3.511A pdb=" N ILE A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Proline residue: A 601 - end of helix removed outlier: 3.540A pdb=" N ASN A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 656 removed outlier: 3.577A pdb=" N ASN A 656 " --> pdb=" O MET A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 676 removed outlier: 3.583A pdb=" N VAL A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 removed outlier: 3.653A pdb=" N TYR A 692 " --> pdb=" O GLN A 688 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 736 removed outlier: 3.850A pdb=" N LEU A 730 " --> pdb=" O ARG A 726 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 774 Processing helix chain 'A' and resid 787 through 797 removed outlier: 3.979A pdb=" N TYR A 794 " --> pdb=" O GLN A 790 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET A 795 " --> pdb=" O GLY A 791 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A 797 " --> pdb=" O GLN A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 836 removed outlier: 3.758A pdb=" N ASN A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 832 " --> pdb=" O TYR A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 936 Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.954A pdb=" N LEU A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) Proline residue: A 964 - end of helix Processing helix chain 'A' and resid 991 through 1003 removed outlier: 3.841A pdb=" N LEU A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1030 removed outlier: 3.750A pdb=" N GLU A1027 " --> pdb=" O GLU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1049 removed outlier: 3.865A pdb=" N LYS A1049 " --> pdb=" O GLU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1084 removed outlier: 3.682A pdb=" N GLY A1070 " --> pdb=" O TYR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1115 removed outlier: 3.569A pdb=" N SER A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 5.144A pdb=" N VAL B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ARG B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 238 through 265 Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.722A pdb=" N ILE B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 319 removed outlier: 3.850A pdb=" N SER B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 349 removed outlier: 4.030A pdb=" N ARG B 332 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 375 removed outlier: 3.575A pdb=" N GLN B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 398 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 421 through 425 removed outlier: 3.673A pdb=" N ALA B 424 " --> pdb=" O GLY B 421 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY B 425 " --> pdb=" O ILE B 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 421 through 425' Processing helix chain 'B' and resid 434 through 463 Proline residue: B 440 - end of helix removed outlier: 3.974A pdb=" N LEU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 522 removed outlier: 3.711A pdb=" N VAL B 520 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 545 removed outlier: 3.682A pdb=" N LEU B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 removed outlier: 3.513A pdb=" N VAL B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 removed outlier: 4.084A pdb=" N ALA B 564 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE B 565 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 592 removed outlier: 3.586A pdb=" N PHE B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 Proline residue: B 601 - end of helix Processing helix chain 'B' and resid 637 through 656 removed outlier: 3.537A pdb=" N ASN B 656 " --> pdb=" O MET B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 676 removed outlier: 3.536A pdb=" N VAL B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 704 Processing helix chain 'B' and resid 726 through 736 removed outlier: 3.677A pdb=" N LEU B 730 " --> pdb=" O ARG B 726 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 774 removed outlier: 3.607A pdb=" N ARG B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 774 " --> pdb=" O TRP B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.658A pdb=" N MET B 795 " --> pdb=" O GLY B 791 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN B 797 " --> pdb=" O GLN B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 824 through 836 removed outlier: 3.767A pdb=" N LEU B 831 " --> pdb=" O THR B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 839 No H-bonds generated for 'chain 'B' and resid 837 through 839' Processing helix chain 'B' and resid 927 through 937 removed outlier: 3.633A pdb=" N ASP B 935 " --> pdb=" O GLN B 931 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 937 " --> pdb=" O LEU B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 969 removed outlier: 3.514A pdb=" N LEU B 962 " --> pdb=" O GLY B 958 " (cutoff:3.500A) Proline residue: B 964 - end of helix removed outlier: 3.533A pdb=" N ASN B 969 " --> pdb=" O TYR B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1003 removed outlier: 3.721A pdb=" N LEU B 999 " --> pdb=" O ALA B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1032 removed outlier: 3.644A pdb=" N PHE B1028 " --> pdb=" O GLY B1024 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B1032 " --> pdb=" O PHE B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1036 removed outlier: 3.789A pdb=" N LYS B1036 " --> pdb=" O GLU B1033 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1033 through 1036' Processing helix chain 'B' and resid 1041 through 1052 removed outlier: 3.585A pdb=" N GLU B1045 " --> pdb=" O ASP B1041 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B1050 " --> pdb=" O ALA B1046 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B1052 " --> pdb=" O GLU B1048 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1084 removed outlier: 3.522A pdb=" N GLY B1070 " --> pdb=" O TYR B1066 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B1078 " --> pdb=" O ILE B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1114 removed outlier: 3.614A pdb=" N THR B1113 " --> pdb=" O ALA B1109 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B1114 " --> pdb=" O TRP B1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 778 through 784 removed outlier: 6.216A pdb=" N LEU A 717 " --> pdb=" O VAL A 810 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLY A 812 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N MET A 719 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A1093 " --> pdb=" O TRP A 951 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 950 " --> pdb=" O PHE A 981 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N GLY A 983 " --> pdb=" O VAL A 950 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TRP A 952 " --> pdb=" O GLY A 983 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 778 through 784 removed outlier: 6.932A pdb=" N MET B 743 " --> pdb=" O PHE B 779 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N THR B 781 " --> pdb=" O MET B 743 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS B 745 " --> pdb=" O THR B 781 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 783 " --> pdb=" O CYS B 745 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N HIS B 747 " --> pdb=" O VAL B 783 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN B 715 " --> pdb=" O THR B 808 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL B 810 " --> pdb=" O GLN B 715 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU B 717 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLY B 812 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N MET B 719 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 809 " --> pdb=" O VAL B 843 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU B 845 " --> pdb=" O LEU B 809 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 811 " --> pdb=" O LEU B 845 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 846 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B1121 " --> pdb=" O ARG B 846 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE B1090 " --> pdb=" O LEU B1122 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL B1124 " --> pdb=" O ILE B1090 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N MET B1092 " --> pdb=" O VAL B1124 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N LEU B1089 " --> pdb=" O LYS B 945 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR B 947 " --> pdb=" O LEU B1089 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL B1091 " --> pdb=" O THR B 947 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP B 949 " --> pdb=" O VAL B1091 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N SER B1093 " --> pdb=" O ASP B 949 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N TRP B 951 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 983 " --> pdb=" O TRP B 952 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N THR B1011 " --> pdb=" O ILE B 978 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL B 980 " --> pdb=" O THR B1011 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU B1013 " --> pdb=" O VAL B 980 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 982 " --> pdb=" O LEU B1013 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.64 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: 2141 1.31 - 1.44: 3806 1.44 - 1.57: 7952 1.57 - 1.70: 42 1.70 - 1.83: 120 Bond restraints: 14061 Sorted by residual: bond pdb=" C31 POV A1205 " pdb=" O31 POV A1205 " ideal model delta sigma weight residual 1.327 1.438 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C31 POV B1205 " pdb=" O31 POV B1205 " ideal model delta sigma weight residual 1.327 1.433 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C31 POV B1204 " pdb=" O31 POV B1204 " ideal model delta sigma weight residual 1.327 1.432 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C31 POV A1204 " pdb=" O31 POV A1204 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C21 POV A1206 " pdb=" O21 POV A1206 " ideal model delta sigma weight residual 1.330 1.434 -0.104 2.00e-02 2.50e+03 2.68e+01 ... (remaining 14056 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.24: 18919 6.24 - 12.48: 71 12.48 - 18.72: 2 18.72 - 24.96: 3 24.96 - 31.20: 4 Bond angle restraints: 18999 Sorted by residual: angle pdb=" C12 POV A1206 " pdb=" N POV A1206 " pdb=" C15 POV A1206 " ideal model delta sigma weight residual 112.10 80.90 31.20 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C13 POV A1206 " pdb=" N POV A1206 " pdb=" C14 POV A1206 " ideal model delta sigma weight residual 108.80 79.65 29.15 3.00e+00 1.11e-01 9.44e+01 angle pdb=" C13 POV A1206 " pdb=" N POV A1206 " pdb=" C15 POV A1206 " ideal model delta sigma weight residual 109.35 80.50 28.85 3.00e+00 1.11e-01 9.25e+01 angle pdb=" C12 POV A1206 " pdb=" N POV A1206 " pdb=" C14 POV A1206 " ideal model delta sigma weight residual 107.13 80.33 26.80 3.00e+00 1.11e-01 7.98e+01 angle pdb=" C14 POV A1206 " pdb=" N POV A1206 " pdb=" C15 POV A1206 " ideal model delta sigma weight residual 108.02 132.28 -24.26 3.00e+00 1.11e-01 6.54e+01 ... (remaining 18994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.83: 7830 27.83 - 55.67: 443 55.67 - 83.50: 60 83.50 - 111.34: 8 111.34 - 139.17: 6 Dihedral angle restraints: 8347 sinusoidal: 3399 harmonic: 4948 Sorted by residual: dihedral pdb=" CA SER B 525 " pdb=" C SER B 525 " pdb=" N PRO B 526 " pdb=" CA PRO B 526 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA SER A 525 " pdb=" C SER A 525 " pdb=" N PRO A 526 " pdb=" CA PRO A 526 " ideal model delta harmonic sigma weight residual -180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA LEU B1037 " pdb=" C LEU B1037 " pdb=" N ARG B1038 " pdb=" CA ARG B1038 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 8344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1716 0.064 - 0.128: 379 0.128 - 0.192: 38 0.192 - 0.256: 4 0.256 - 0.320: 2 Chirality restraints: 2139 Sorted by residual: chirality pdb=" CB VAL B 339 " pdb=" CA VAL B 339 " pdb=" CG1 VAL B 339 " pdb=" CG2 VAL B 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB VAL A 339 " pdb=" CA VAL A 339 " pdb=" CG1 VAL A 339 " pdb=" CG2 VAL A 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE B1058 " pdb=" CA ILE B1058 " pdb=" CG1 ILE B1058 " pdb=" CG2 ILE B1058 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2136 not shown) Planarity restraints: 2349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B1119 " 0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO B1120 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO B1120 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B1120 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1119 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO A1120 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A1120 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A1120 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 416 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO A 417 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 417 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 417 " 0.042 5.00e-02 4.00e+02 ... (remaining 2346 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 4482 2.84 - 3.41: 13940 3.41 - 3.99: 25027 3.99 - 4.56: 35425 4.56 - 5.14: 52233 Nonbonded interactions: 131107 Sorted by model distance: nonbonded pdb=" O LEU A 771 " pdb=" OG SER A 776 " model vdw 2.264 3.040 nonbonded pdb=" O CYS A 496 " pdb=" OG SER A 505 " model vdw 2.294 3.040 nonbonded pdb=" OE1 GLN B 406 " pdb=" OG SER B 410 " model vdw 2.300 3.040 nonbonded pdb=" O GLU B 824 " pdb=" OG1 THR B 827 " model vdw 2.308 3.040 nonbonded pdb=" OD2 ASP A 391 " pdb=" OH TYR A 489 " model vdw 2.314 3.040 ... (remaining 131102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 206 through 1206) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.660 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 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 : 0.009 0.111 14063 Z= 0.412 Angle : 1.182 31.197 19003 Z= 0.542 Chirality : 0.053 0.320 2139 Planarity : 0.007 0.082 2349 Dihedral : 17.241 139.172 5169 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.46 % Favored : 91.48 % Rotamer: Outliers : 7.67 % Allowed : 12.55 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.62 (0.15), residues: 1714 helix: -2.57 (0.12), residues: 927 sheet: -2.45 (0.41), residues: 130 loop : -3.80 (0.18), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 404 TYR 0.025 0.002 TYR A 676 PHE 0.033 0.003 PHE B 606 TRP 0.039 0.002 TRP B 639 HIS 0.007 0.001 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.00869 (14061) covalent geometry : angle 1.18040 (18999) SS BOND : bond 0.00477 ( 2) SS BOND : angle 4.84549 ( 4) hydrogen bonds : bond 0.15948 ( 633) hydrogen bonds : angle 6.88900 ( 1893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 358 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 829 ILE cc_start: 0.6776 (mm) cc_final: 0.6489 (mm) REVERT: A 852 ASP cc_start: -0.0087 (OUTLIER) cc_final: -0.0400 (m-30) REVERT: B 384 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7630 (pttm) REVERT: B 1057 ARG cc_start: 0.4119 (OUTLIER) cc_final: 0.3007 (mmt180) outliers start: 110 outliers final: 19 residues processed: 437 average time/residue: 0.4300 time to fit residues: 210.5377 Evaluate side-chains 236 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1057 ARG Chi-restraints excluded: chain B residue 1124 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 436 GLN A 573 ASN A 664 ASN A 739 ASN A 768 GLN A 815 ASN A1061 ASN B 298 ASN B 327 GLN B 427 ASN B 436 GLN B 664 ASN B 701 GLN B 724 ASN B 938 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.119882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.084553 restraints weight = 24373.875| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.96 r_work: 0.3140 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14063 Z= 0.141 Angle : 0.835 31.959 19003 Z= 0.377 Chirality : 0.044 0.232 2139 Planarity : 0.005 0.075 2349 Dihedral : 14.661 119.600 2188 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.23 % Favored : 92.71 % Rotamer: Outliers : 5.65 % Allowed : 20.15 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.19), residues: 1714 helix: -0.55 (0.16), residues: 928 sheet: -1.60 (0.42), residues: 140 loop : -3.32 (0.20), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 713 TYR 0.019 0.001 TYR A 965 PHE 0.025 0.002 PHE B 369 TRP 0.021 0.001 TRP A 770 HIS 0.004 0.001 HIS B 620 Details of bonding type rmsd covalent geometry : bond 0.00298 (14061) covalent geometry : angle 0.83493 (18999) SS BOND : bond 0.00321 ( 2) SS BOND : angle 0.66958 ( 4) hydrogen bonds : bond 0.04062 ( 633) hydrogen bonds : angle 4.34366 ( 1893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 271 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7985 (ttmm) REVERT: A 577 LEU cc_start: 0.7742 (mm) cc_final: 0.7525 (mp) REVERT: A 662 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7565 (tp) REVERT: A 795 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8173 (mtm) REVERT: A 796 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8366 (tm) REVERT: A 829 ILE cc_start: 0.7325 (mm) cc_final: 0.6998 (mm) REVERT: A 836 PHE cc_start: 0.7790 (m-10) cc_final: 0.7452 (m-10) REVERT: A 844 ILE cc_start: 0.7721 (mm) cc_final: 0.7467 (mm) REVERT: A 956 ASP cc_start: 0.6746 (m-30) cc_final: 0.6505 (m-30) REVERT: A 975 ASP cc_start: 0.5689 (OUTLIER) cc_final: 0.4465 (t70) REVERT: A 1031 MET cc_start: 0.7568 (tmm) cc_final: 0.7205 (ppp) REVERT: A 1112 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8362 (t0) REVERT: A 1118 LEU cc_start: 0.8513 (tt) cc_final: 0.8029 (tm) REVERT: B 304 MET cc_start: 0.8487 (ttp) cc_final: 0.8276 (ttm) REVERT: B 345 ILE cc_start: 0.8743 (mt) cc_final: 0.8492 (mp) REVERT: B 483 THR cc_start: 0.8270 (p) cc_final: 0.8016 (m) REVERT: B 719 MET cc_start: 0.7277 (mmm) cc_final: 0.5379 (tmt) REVERT: B 934 LEU cc_start: 0.8803 (mt) cc_final: 0.8543 (mt) REVERT: B 949 ASP cc_start: 0.8041 (p0) cc_final: 0.7468 (t0) REVERT: B 977 LYS cc_start: 0.8367 (mmtm) cc_final: 0.7986 (ptpp) REVERT: B 1031 MET cc_start: 0.8256 (ttp) cc_final: 0.7669 (ttt) REVERT: B 1036 LYS cc_start: 0.8340 (mttt) cc_final: 0.8045 (mmtp) REVERT: B 1038 ARG cc_start: 0.5611 (tpt90) cc_final: 0.5227 (tpm-80) REVERT: B 1124 VAL cc_start: 0.7944 (OUTLIER) cc_final: 0.7696 (m) outliers start: 81 outliers final: 16 residues processed: 327 average time/residue: 0.4117 time to fit residues: 152.3661 Evaluate side-chains 232 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 693 HIS Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1124 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 20 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 109 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 HIS A 797 GLN A1073 GLN B 266 ASN B 329 ASN B 734 HIS B 833 HIS B1017 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.117151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.080777 restraints weight = 24752.041| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.96 r_work: 0.3062 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14063 Z= 0.230 Angle : 0.889 31.874 19003 Z= 0.406 Chirality : 0.048 0.265 2139 Planarity : 0.005 0.078 2349 Dihedral : 14.235 111.733 2152 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 5.23 % Allowed : 21.83 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.20), residues: 1714 helix: 0.04 (0.17), residues: 936 sheet: -1.46 (0.42), residues: 143 loop : -3.16 (0.21), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1098 TYR 0.020 0.002 TYR B 676 PHE 0.028 0.002 PHE A 606 TRP 0.025 0.002 TRP B 209 HIS 0.021 0.001 HIS B 734 Details of bonding type rmsd covalent geometry : bond 0.00552 (14061) covalent geometry : angle 0.88892 (18999) SS BOND : bond 0.01757 ( 2) SS BOND : angle 1.35362 ( 4) hydrogen bonds : bond 0.04714 ( 633) hydrogen bonds : angle 4.32655 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 243 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 LEU cc_start: 0.8139 (mm) cc_final: 0.7937 (mp) REVERT: A 700 LEU cc_start: 0.8768 (tm) cc_final: 0.8509 (tp) REVERT: A 719 MET cc_start: 0.8127 (mmm) cc_final: 0.5900 (tmt) REVERT: A 750 ILE cc_start: 0.8678 (mm) cc_final: 0.8458 (mm) REVERT: A 760 LEU cc_start: 0.8405 (mp) cc_final: 0.8110 (mm) REVERT: A 795 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8792 (mtm) REVERT: A 951 TRP cc_start: 0.8840 (m100) cc_final: 0.8489 (m100) REVERT: A 956 ASP cc_start: 0.6801 (m-30) cc_final: 0.6598 (m-30) REVERT: A 1009 ASP cc_start: 0.7943 (m-30) cc_final: 0.7650 (t0) REVERT: A 1025 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7462 (mp) REVERT: A 1086 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8038 (p) REVERT: A 1092 MET cc_start: 0.7698 (tpt) cc_final: 0.7390 (tpt) REVERT: B 214 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8599 (tp) REVERT: B 229 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8425 (mmt-90) REVERT: B 304 MET cc_start: 0.9059 (ttp) cc_final: 0.8855 (ttt) REVERT: B 324 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7661 (ptp) REVERT: B 325 ILE cc_start: 0.6235 (OUTLIER) cc_final: 0.5841 (mt) REVERT: B 353 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: B 483 THR cc_start: 0.8285 (p) cc_final: 0.8025 (m) REVERT: B 719 MET cc_start: 0.7760 (mmm) cc_final: 0.5694 (tmt) REVERT: B 793 GLN cc_start: 0.7978 (mp10) cc_final: 0.7610 (mp10) REVERT: B 834 ASP cc_start: 0.7536 (t0) cc_final: 0.6786 (t0) REVERT: B 977 LYS cc_start: 0.8362 (mmtm) cc_final: 0.8085 (mtmm) REVERT: B 982 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8344 (tp) REVERT: B 1031 MET cc_start: 0.8235 (ttp) cc_final: 0.7863 (ttm) REVERT: B 1037 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6378 (tm) REVERT: B 1079 LEU cc_start: 0.9255 (mt) cc_final: 0.8837 (tm) REVERT: B 1121 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8637 (pp) outliers start: 75 outliers final: 22 residues processed: 296 average time/residue: 0.4013 time to fit residues: 135.1461 Evaluate side-chains 235 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1121 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 49 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 693 HIS A 768 GLN A 938 GLN A1073 GLN B 698 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.118413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.082411 restraints weight = 24477.092| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.03 r_work: 0.3112 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.6296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14063 Z= 0.140 Angle : 0.820 32.630 19003 Z= 0.361 Chirality : 0.045 0.264 2139 Planarity : 0.005 0.075 2349 Dihedral : 13.580 111.501 2151 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.53 % Allowed : 24.55 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.20), residues: 1714 helix: 0.59 (0.17), residues: 935 sheet: -1.27 (0.42), residues: 143 loop : -3.12 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 713 TYR 0.015 0.001 TYR B 828 PHE 0.022 0.002 PHE B 813 TRP 0.025 0.002 TRP A 770 HIS 0.004 0.001 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00321 (14061) covalent geometry : angle 0.81957 (18999) SS BOND : bond 0.00349 ( 2) SS BOND : angle 0.83150 ( 4) hydrogen bonds : bond 0.03845 ( 633) hydrogen bonds : angle 4.00750 ( 1893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: A 700 LEU cc_start: 0.8762 (tm) cc_final: 0.8499 (tp) REVERT: A 719 MET cc_start: 0.8119 (mmm) cc_final: 0.6112 (tmt) REVERT: A 732 LEU cc_start: 0.8507 (tm) cc_final: 0.8239 (tt) REVERT: A 750 ILE cc_start: 0.8681 (mm) cc_final: 0.8450 (mm) REVERT: A 760 LEU cc_start: 0.8526 (mp) cc_final: 0.8287 (mm) REVERT: A 767 TYR cc_start: 0.7972 (m-80) cc_final: 0.7766 (m-80) REVERT: A 1009 ASP cc_start: 0.7771 (m-30) cc_final: 0.7482 (t0) REVERT: A 1025 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7352 (mp) REVERT: A 1075 ARG cc_start: 0.8365 (tpp-160) cc_final: 0.7663 (tpp-160) REVERT: A 1076 LEU cc_start: 0.8792 (pp) cc_final: 0.8577 (pp) REVERT: A 1078 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: A 1086 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8077 (p) REVERT: A 1121 ILE cc_start: 0.8582 (tt) cc_final: 0.8298 (tp) REVERT: B 229 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8495 (mmt-90) REVERT: B 248 MET cc_start: 0.8596 (ttm) cc_final: 0.8270 (mtp) REVERT: B 315 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7599 (mt-10) REVERT: B 324 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7659 (ptp) REVERT: B 353 GLU cc_start: 0.8009 (mp0) cc_final: 0.7694 (mp0) REVERT: B 427 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8512 (m-40) REVERT: B 483 THR cc_start: 0.8387 (p) cc_final: 0.8091 (m) REVERT: B 719 MET cc_start: 0.7571 (mmm) cc_final: 0.5517 (tmt) REVERT: B 949 ASP cc_start: 0.8039 (p0) cc_final: 0.7627 (t0) REVERT: B 952 TRP cc_start: 0.8332 (OUTLIER) cc_final: 0.8099 (t60) REVERT: B 954 PHE cc_start: 0.8038 (t80) cc_final: 0.7485 (t80) REVERT: B 981 PHE cc_start: 0.7678 (m-10) cc_final: 0.6856 (m-10) REVERT: B 1079 LEU cc_start: 0.9134 (mt) cc_final: 0.8841 (tm) REVERT: B 1121 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8697 (pp) outliers start: 65 outliers final: 21 residues processed: 271 average time/residue: 0.4438 time to fit residues: 136.0379 Evaluate side-chains 228 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1078 GLU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 427 ASN Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 952 TRP Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1040 ASP Chi-restraints excluded: chain B residue 1094 MET Chi-restraints excluded: chain B residue 1121 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 97 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 163 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 698 HIS A1073 GLN B1073 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.118651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082535 restraints weight = 24566.498| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.03 r_work: 0.3114 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14063 Z= 0.123 Angle : 0.809 33.222 19003 Z= 0.352 Chirality : 0.045 0.320 2139 Planarity : 0.005 0.072 2349 Dihedral : 13.206 110.071 2151 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.46 % Allowed : 25.52 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.20), residues: 1714 helix: 0.90 (0.18), residues: 931 sheet: -1.14 (0.42), residues: 143 loop : -3.04 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 988 TYR 0.012 0.001 TYR B 676 PHE 0.019 0.001 PHE A 954 TRP 0.027 0.002 TRP A 770 HIS 0.003 0.001 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.00280 (14061) covalent geometry : angle 0.80950 (18999) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.65905 ( 4) hydrogen bonds : bond 0.03671 ( 633) hydrogen bonds : angle 3.88491 ( 1893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 209 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: A 478 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.6064 (mt) REVERT: A 700 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8595 (tp) REVERT: A 719 MET cc_start: 0.8056 (mmm) cc_final: 0.6124 (tmt) REVERT: A 732 LEU cc_start: 0.8508 (tm) cc_final: 0.8200 (tt) REVERT: A 750 ILE cc_start: 0.8645 (mm) cc_final: 0.8418 (mm) REVERT: A 760 LEU cc_start: 0.8587 (mp) cc_final: 0.8355 (mm) REVERT: A 767 TYR cc_start: 0.7903 (m-80) cc_final: 0.7671 (m-80) REVERT: A 1009 ASP cc_start: 0.7915 (m-30) cc_final: 0.7672 (t0) REVERT: A 1025 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7318 (mp) REVERT: A 1086 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8112 (p) REVERT: A 1121 ILE cc_start: 0.8608 (tt) cc_final: 0.8362 (tp) REVERT: B 229 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8544 (mmt-90) REVERT: B 248 MET cc_start: 0.8578 (ttm) cc_final: 0.8306 (mtp) REVERT: B 315 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7612 (mt-10) REVERT: B 324 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7869 (ptp) REVERT: B 353 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: B 427 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8391 (m110) REVERT: B 483 THR cc_start: 0.8386 (p) cc_final: 0.8044 (m) REVERT: B 506 SER cc_start: 0.8935 (t) cc_final: 0.8694 (t) REVERT: B 719 MET cc_start: 0.7530 (mmm) cc_final: 0.5399 (tmt) REVERT: B 949 ASP cc_start: 0.8010 (p0) cc_final: 0.7626 (t0) REVERT: B 954 PHE cc_start: 0.8062 (t80) cc_final: 0.7424 (t80) REVERT: B 981 PHE cc_start: 0.7639 (m-10) cc_final: 0.7364 (m-10) REVERT: B 1032 ILE cc_start: 0.8868 (pt) cc_final: 0.8637 (pp) REVERT: B 1121 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8714 (pp) outliers start: 64 outliers final: 25 residues processed: 251 average time/residue: 0.4292 time to fit residues: 122.2378 Evaluate side-chains 223 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1078 GLU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 427 ASN Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1040 ASP Chi-restraints excluded: chain B residue 1094 MET Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 43 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 693 HIS A 731 HIS A1073 GLN A1128 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.117073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.080668 restraints weight = 24552.819| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.02 r_work: 0.3055 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14063 Z= 0.167 Angle : 0.832 34.842 19003 Z= 0.365 Chirality : 0.046 0.355 2139 Planarity : 0.005 0.070 2349 Dihedral : 13.109 110.101 2151 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.60 % Allowed : 25.80 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.21), residues: 1714 helix: 0.95 (0.18), residues: 931 sheet: -1.05 (0.43), residues: 143 loop : -2.96 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 988 TYR 0.020 0.001 TYR A 692 PHE 0.018 0.002 PHE A 954 TRP 0.028 0.002 TRP A 770 HIS 0.011 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00398 (14061) covalent geometry : angle 0.83154 (18999) SS BOND : bond 0.00214 ( 2) SS BOND : angle 0.82423 ( 4) hydrogen bonds : bond 0.04005 ( 633) hydrogen bonds : angle 3.92813 ( 1893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 200 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: A 326 ASP cc_start: 0.6200 (m-30) cc_final: 0.5962 (m-30) REVERT: A 700 LEU cc_start: 0.8795 (tm) cc_final: 0.8552 (tp) REVERT: A 719 MET cc_start: 0.8081 (mmm) cc_final: 0.6285 (tmt) REVERT: A 732 LEU cc_start: 0.8529 (tm) cc_final: 0.8207 (tt) REVERT: A 750 ILE cc_start: 0.8717 (mm) cc_final: 0.8508 (mm) REVERT: A 760 LEU cc_start: 0.8682 (mp) cc_final: 0.8472 (mm) REVERT: A 795 MET cc_start: 0.9197 (mtm) cc_final: 0.8889 (mtm) REVERT: A 1009 ASP cc_start: 0.7989 (m-30) cc_final: 0.7735 (t0) REVERT: A 1025 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7387 (mp) REVERT: A 1121 ILE cc_start: 0.8632 (tt) cc_final: 0.8383 (tp) REVERT: B 229 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8596 (mmt-90) REVERT: B 248 MET cc_start: 0.8659 (ttm) cc_final: 0.8387 (mtp) REVERT: B 315 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7681 (mt-10) REVERT: B 324 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7917 (ptp) REVERT: B 427 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8575 (m-40) REVERT: B 719 MET cc_start: 0.7709 (mmm) cc_final: 0.5627 (tmt) REVERT: B 724 ASN cc_start: 0.8390 (t160) cc_final: 0.8138 (m-40) REVERT: B 949 ASP cc_start: 0.7984 (p0) cc_final: 0.7609 (t0) REVERT: B 954 PHE cc_start: 0.8097 (t80) cc_final: 0.7383 (t80) REVERT: B 981 PHE cc_start: 0.7747 (m-10) cc_final: 0.7492 (m-10) REVERT: B 1038 ARG cc_start: 0.5839 (tpm170) cc_final: 0.4827 (tmt-80) REVERT: B 1094 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7720 (mtm) REVERT: B 1108 MET cc_start: 0.9085 (mmm) cc_final: 0.8768 (tmm) REVERT: B 1121 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8725 (pp) outliers start: 66 outliers final: 31 residues processed: 250 average time/residue: 0.3815 time to fit residues: 109.5888 Evaluate side-chains 224 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 427 ASN Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 960 THR Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1040 ASP Chi-restraints excluded: chain B residue 1094 MET Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 84 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 161 optimal weight: 0.1980 chunk 115 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 ASN B 830 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.119086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082953 restraints weight = 24421.153| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.06 r_work: 0.3084 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.7263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14063 Z= 0.116 Angle : 0.673 15.216 19003 Z= 0.318 Chirality : 0.045 0.366 2139 Planarity : 0.004 0.070 2349 Dihedral : 12.672 108.130 2151 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.11 % Allowed : 26.50 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.21), residues: 1714 helix: 1.20 (0.18), residues: 926 sheet: -0.90 (0.43), residues: 143 loop : -2.90 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 932 TYR 0.015 0.001 TYR A 692 PHE 0.014 0.001 PHE A 387 TRP 0.031 0.002 TRP A 770 HIS 0.003 0.001 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00259 (14061) covalent geometry : angle 0.67344 (18999) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.55430 ( 4) hydrogen bonds : bond 0.03625 ( 633) hydrogen bonds : angle 3.84002 ( 1893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: A 326 ASP cc_start: 0.6208 (m-30) cc_final: 0.5975 (m-30) REVERT: A 478 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.6030 (mt) REVERT: A 593 ILE cc_start: 0.8260 (tt) cc_final: 0.7992 (pt) REVERT: A 700 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8575 (tp) REVERT: A 719 MET cc_start: 0.7803 (mmm) cc_final: 0.6239 (tmt) REVERT: A 732 LEU cc_start: 0.8534 (tm) cc_final: 0.8192 (tt) REVERT: A 750 ILE cc_start: 0.8695 (mm) cc_final: 0.8480 (mm) REVERT: A 760 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8484 (mm) REVERT: A 795 MET cc_start: 0.9174 (mtm) cc_final: 0.8964 (mtm) REVERT: A 830 ASN cc_start: 0.8223 (m-40) cc_final: 0.7986 (m-40) REVERT: A 975 ASP cc_start: 0.5914 (OUTLIER) cc_final: 0.4688 (t70) REVERT: A 1009 ASP cc_start: 0.7997 (m-30) cc_final: 0.7731 (t0) REVERT: A 1025 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7307 (mp) REVERT: A 1086 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8140 (p) REVERT: A 1106 LEU cc_start: 0.8982 (tt) cc_final: 0.8668 (tm) REVERT: A 1121 ILE cc_start: 0.8628 (tt) cc_final: 0.8386 (tp) REVERT: B 229 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8561 (mmt-90) REVERT: B 248 MET cc_start: 0.8630 (ttm) cc_final: 0.8421 (mtp) REVERT: B 315 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7711 (mt-10) REVERT: B 324 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7752 (ptp) REVERT: B 427 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8447 (m110) REVERT: B 719 MET cc_start: 0.7570 (mmm) cc_final: 0.5447 (tmt) REVERT: B 733 VAL cc_start: 0.8347 (t) cc_final: 0.8057 (p) REVERT: B 949 ASP cc_start: 0.7954 (p0) cc_final: 0.7590 (t0) REVERT: B 954 PHE cc_start: 0.8100 (t80) cc_final: 0.7420 (t80) REVERT: B 1000 LEU cc_start: 0.8897 (tt) cc_final: 0.8671 (tm) REVERT: B 1032 ILE cc_start: 0.8936 (pt) cc_final: 0.8660 (pp) REVERT: B 1038 ARG cc_start: 0.5886 (tpm170) cc_final: 0.4798 (tmt-80) REVERT: B 1108 MET cc_start: 0.9068 (mmm) cc_final: 0.8757 (tmm) REVERT: B 1121 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8730 (pp) outliers start: 59 outliers final: 27 residues processed: 234 average time/residue: 0.4022 time to fit residues: 106.8811 Evaluate side-chains 219 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 427 ASN Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1040 ASP Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN A1088 ASN B 830 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.118106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.082005 restraints weight = 24341.981| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.05 r_work: 0.3063 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.7496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14063 Z= 0.143 Angle : 0.680 15.160 19003 Z= 0.326 Chirality : 0.045 0.329 2139 Planarity : 0.005 0.071 2349 Dihedral : 12.467 110.472 2150 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.63 % Allowed : 26.71 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.21), residues: 1714 helix: 1.26 (0.18), residues: 926 sheet: -0.88 (0.43), residues: 143 loop : -2.88 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 932 TYR 0.013 0.001 TYR A 692 PHE 0.021 0.002 PHE B 981 TRP 0.037 0.002 TRP A 770 HIS 0.004 0.001 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.00336 (14061) covalent geometry : angle 0.67965 (18999) SS BOND : bond 0.00626 ( 2) SS BOND : angle 1.99161 ( 4) hydrogen bonds : bond 0.03776 ( 633) hydrogen bonds : angle 3.84005 ( 1893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: A 326 ASP cc_start: 0.6303 (m-30) cc_final: 0.6093 (m-30) REVERT: A 478 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6000 (mt) REVERT: A 593 ILE cc_start: 0.8307 (tt) cc_final: 0.8010 (pt) REVERT: A 700 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8585 (tp) REVERT: A 719 MET cc_start: 0.7903 (mmm) cc_final: 0.6367 (tmt) REVERT: A 732 LEU cc_start: 0.8548 (tm) cc_final: 0.8325 (tp) REVERT: A 750 ILE cc_start: 0.8739 (mm) cc_final: 0.8511 (mm) REVERT: A 795 MET cc_start: 0.9220 (mtm) cc_final: 0.8951 (mtm) REVERT: A 932 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7929 (tmm-80) REVERT: A 975 ASP cc_start: 0.5913 (OUTLIER) cc_final: 0.4795 (t70) REVERT: A 1009 ASP cc_start: 0.7988 (m-30) cc_final: 0.7784 (t0) REVERT: A 1025 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7343 (mp) REVERT: A 1040 ASP cc_start: 0.7551 (t0) cc_final: 0.7096 (t0) REVERT: A 1106 LEU cc_start: 0.9040 (tt) cc_final: 0.8788 (tm) REVERT: A 1121 ILE cc_start: 0.8663 (tt) cc_final: 0.8399 (tp) REVERT: B 229 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8610 (mmt-90) REVERT: B 248 MET cc_start: 0.8676 (ttm) cc_final: 0.8464 (mtp) REVERT: B 315 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7761 (mt-10) REVERT: B 324 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7768 (ptp) REVERT: B 353 GLU cc_start: 0.8048 (mp0) cc_final: 0.7839 (mp0) REVERT: B 427 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8469 (m110) REVERT: B 719 MET cc_start: 0.7432 (mmm) cc_final: 0.5457 (tmt) REVERT: B 733 VAL cc_start: 0.8310 (t) cc_final: 0.8045 (p) REVERT: B 807 ASN cc_start: 0.8514 (p0) cc_final: 0.8307 (p0) REVERT: B 954 PHE cc_start: 0.8073 (t80) cc_final: 0.7369 (t80) REVERT: B 996 MET cc_start: 0.9016 (tpt) cc_final: 0.8285 (tmm) REVERT: B 1000 LEU cc_start: 0.8842 (tt) cc_final: 0.8276 (mm) REVERT: B 1004 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7713 (mmm-85) REVERT: B 1032 ILE cc_start: 0.8945 (pt) cc_final: 0.8674 (pp) REVERT: B 1038 ARG cc_start: 0.5935 (tpm170) cc_final: 0.4881 (tmt-80) REVERT: B 1108 MET cc_start: 0.9072 (mmm) cc_final: 0.8706 (tmm) REVERT: B 1121 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8728 (pp) outliers start: 52 outliers final: 27 residues processed: 232 average time/residue: 0.3676 time to fit residues: 97.0826 Evaluate side-chains 220 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 427 ASN Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1004 ARG Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1040 ASP Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 6 optimal weight: 9.9990 chunk 162 optimal weight: 0.0060 chunk 45 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 ASN A1073 GLN A1128 HIS B 830 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.119157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.083018 restraints weight = 24651.737| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.07 r_work: 0.3113 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.7650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14063 Z= 0.111 Angle : 0.662 15.698 19003 Z= 0.312 Chirality : 0.045 0.314 2139 Planarity : 0.004 0.072 2349 Dihedral : 11.994 108.588 2150 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.14 % Allowed : 27.48 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1714 helix: 1.47 (0.18), residues: 925 sheet: -0.94 (0.43), residues: 143 loop : -2.78 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 932 TYR 0.012 0.001 TYR A 692 PHE 0.025 0.001 PHE B 712 TRP 0.036 0.002 TRP A 770 HIS 0.013 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00244 (14061) covalent geometry : angle 0.66090 (18999) SS BOND : bond 0.00215 ( 2) SS BOND : angle 2.15531 ( 4) hydrogen bonds : bond 0.03400 ( 633) hydrogen bonds : angle 3.75486 ( 1893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: A 478 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.6031 (mt) REVERT: A 593 ILE cc_start: 0.8167 (tt) cc_final: 0.7960 (pt) REVERT: A 700 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8550 (tp) REVERT: A 719 MET cc_start: 0.7865 (mmm) cc_final: 0.6340 (tmt) REVERT: A 732 LEU cc_start: 0.8490 (tm) cc_final: 0.8257 (tp) REVERT: A 750 ILE cc_start: 0.8764 (mm) cc_final: 0.8499 (mm) REVERT: A 823 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8713 (mppt) REVERT: A 830 ASN cc_start: 0.8040 (m-40) cc_final: 0.7466 (m-40) REVERT: A 932 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7915 (tmm-80) REVERT: A 975 ASP cc_start: 0.5979 (OUTLIER) cc_final: 0.4907 (t70) REVERT: A 1025 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7343 (mp) REVERT: A 1031 MET cc_start: 0.8310 (ppp) cc_final: 0.7905 (ppp) REVERT: A 1086 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8220 (p) REVERT: A 1106 LEU cc_start: 0.9028 (tt) cc_final: 0.8760 (tm) REVERT: A 1121 ILE cc_start: 0.8608 (tt) cc_final: 0.8337 (tp) REVERT: B 229 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8620 (mmt-90) REVERT: B 315 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7767 (mt-10) REVERT: B 324 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7723 (ptp) REVERT: B 719 MET cc_start: 0.7348 (mmm) cc_final: 0.5351 (tmt) REVERT: B 733 VAL cc_start: 0.8308 (t) cc_final: 0.8008 (p) REVERT: B 829 ILE cc_start: 0.7188 (mm) cc_final: 0.6819 (tp) REVERT: B 830 ASN cc_start: 0.8381 (m-40) cc_final: 0.8127 (m110) REVERT: B 954 PHE cc_start: 0.8020 (t80) cc_final: 0.7309 (t80) REVERT: B 961 LEU cc_start: 0.8900 (mt) cc_final: 0.8691 (mt) REVERT: B 996 MET cc_start: 0.8974 (tpt) cc_final: 0.8228 (tmm) REVERT: B 1000 LEU cc_start: 0.8857 (tt) cc_final: 0.8411 (mm) REVERT: B 1032 ILE cc_start: 0.8915 (pt) cc_final: 0.8447 (pp) REVERT: B 1036 LYS cc_start: 0.8907 (mttt) cc_final: 0.8691 (mttt) REVERT: B 1108 MET cc_start: 0.9016 (mmm) cc_final: 0.7459 (tmm) outliers start: 45 outliers final: 23 residues processed: 226 average time/residue: 0.4220 time to fit residues: 108.4985 Evaluate side-chains 212 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 59 optimal weight: 0.0570 chunk 77 optimal weight: 0.9990 chunk 166 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 78 optimal weight: 0.0070 chunk 38 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.120048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.084172 restraints weight = 24508.976| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.06 r_work: 0.3135 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.7764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14063 Z= 0.110 Angle : 0.682 16.275 19003 Z= 0.318 Chirality : 0.045 0.352 2139 Planarity : 0.004 0.072 2349 Dihedral : 11.634 107.119 2150 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.23 % Allowed : 29.22 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.21), residues: 1714 helix: 1.60 (0.18), residues: 924 sheet: -0.76 (0.43), residues: 142 loop : -2.70 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 932 TYR 0.013 0.001 TYR A 692 PHE 0.026 0.001 PHE B 712 TRP 0.042 0.002 TRP A 770 HIS 0.002 0.001 HIS A 620 Details of bonding type rmsd covalent geometry : bond 0.00238 (14061) covalent geometry : angle 0.68131 (18999) SS BOND : bond 0.00196 ( 2) SS BOND : angle 1.62184 ( 4) hydrogen bonds : bond 0.03305 ( 633) hydrogen bonds : angle 3.74119 ( 1893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.6004 (mt) REVERT: A 700 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8543 (tp) REVERT: A 719 MET cc_start: 0.7774 (mmm) cc_final: 0.6274 (tmt) REVERT: A 750 ILE cc_start: 0.8746 (mm) cc_final: 0.8462 (mm) REVERT: A 823 LYS cc_start: 0.8947 (tmtt) cc_final: 0.8631 (mppt) REVERT: A 830 ASN cc_start: 0.8066 (m-40) cc_final: 0.7491 (m-40) REVERT: A 1025 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7284 (mp) REVERT: A 1086 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 1106 LEU cc_start: 0.9007 (tt) cc_final: 0.8725 (tm) REVERT: B 229 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8614 (mmt-90) REVERT: B 315 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7742 (mt-10) REVERT: B 324 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7651 (pmm) REVERT: B 330 ASP cc_start: 0.7740 (m-30) cc_final: 0.7523 (m-30) REVERT: B 719 MET cc_start: 0.7211 (mmm) cc_final: 0.5308 (tmt) REVERT: B 733 VAL cc_start: 0.8253 (t) cc_final: 0.7983 (p) REVERT: B 807 ASN cc_start: 0.8432 (p0) cc_final: 0.8065 (p0) REVERT: B 829 ILE cc_start: 0.6883 (mm) cc_final: 0.6502 (tp) REVERT: B 830 ASN cc_start: 0.8330 (m-40) cc_final: 0.8079 (m110) REVERT: B 954 PHE cc_start: 0.7935 (t80) cc_final: 0.7213 (t80) REVERT: B 996 MET cc_start: 0.8989 (tpt) cc_final: 0.8542 (tmm) REVERT: B 1032 ILE cc_start: 0.8893 (pt) cc_final: 0.8412 (pp) REVERT: B 1038 ARG cc_start: 0.5909 (tpm170) cc_final: 0.5005 (tmt-80) REVERT: B 1108 MET cc_start: 0.8976 (mmm) cc_final: 0.8427 (tmm) outliers start: 32 outliers final: 17 residues processed: 209 average time/residue: 0.4079 time to fit residues: 96.6671 Evaluate side-chains 197 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 ASN B 724 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.118761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082550 restraints weight = 24590.858| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.05 r_work: 0.3089 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.7883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14063 Z= 0.132 Angle : 0.704 17.718 19003 Z= 0.331 Chirality : 0.045 0.350 2139 Planarity : 0.004 0.073 2349 Dihedral : 11.706 108.027 2150 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.51 % Allowed : 29.36 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1714 helix: 1.50 (0.18), residues: 930 sheet: -0.72 (0.43), residues: 142 loop : -2.77 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 766 TYR 0.022 0.001 TYR B 965 PHE 0.018 0.001 PHE A1134 TRP 0.042 0.002 TRP A 770 HIS 0.003 0.001 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.00307 (14061) covalent geometry : angle 0.70322 (18999) SS BOND : bond 0.00167 ( 2) SS BOND : angle 1.77141 ( 4) hydrogen bonds : bond 0.03529 ( 633) hydrogen bonds : angle 3.78706 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5255.04 seconds wall clock time: 90 minutes 7.58 seconds (5407.58 seconds total)