Starting phenix.real_space_refine on Thu Jul 31 23:03:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6npl_0473/07_2025/6npl_0473.cif Found real_map, /net/cci-nas-00/data/ceres_data/6npl_0473/07_2025/6npl_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_0473/07_2025/6npl_0473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6npl_0473/07_2025/6npl_0473.map" model { file = "/net/cci-nas-00/data/ceres_data/6npl_0473/07_2025/6npl_0473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6npl_0473/07_2025/6npl_0473.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.67, per 1000 atoms: 0.56 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: 3.53 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.28 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: 4.25 Time building geometry restraints manager: 4.18 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 1136 or resid 1201 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.930 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:21.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (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 TRP 0.039 0.002 TRP B 639 HIS 0.007 0.001 HIS A 512 PHE 0.033 0.003 PHE B 606 TYR 0.025 0.002 TYR A 676 ARG 0.006 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.15948 ( 633) hydrogen bonds : angle 6.88900 ( 1893) SS BOND : bond 0.00477 ( 2) SS BOND : angle 4.84549 ( 4) covalent geometry : bond 0.00869 (14061) covalent geometry : angle 1.18040 (18999) *********************** 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 : 1.340 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: 0.9846 time to fit residues: 483.5650 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 : 1.404 ------------------------------------------------------------------------------- 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 145 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN A 436 GLN A 573 ASN A 664 ASN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 ASN A 768 GLN A 797 GLN A 815 ASN A1017 ASN A1061 ASN B 266 ASN B 298 ASN B 327 GLN B 427 ASN ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN B 938 GLN B1017 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.118582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.082248 restraints weight = 24387.182| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.08 r_work: 0.3085 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 14063 Z= 0.267 Angle : 0.848 21.422 19003 Z= 0.423 Chirality : 0.050 0.228 2139 Planarity : 0.006 0.087 2349 Dihedral : 14.760 114.731 2188 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.69 % Favored : 91.25 % Rotamer: Outliers : 6.00 % Allowed : 19.94 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.18), residues: 1714 helix: -0.81 (0.16), residues: 932 sheet: -1.73 (0.42), residues: 136 loop : -3.35 (0.20), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 770 HIS 0.006 0.001 HIS A 512 PHE 0.027 0.003 PHE A 388 TYR 0.023 0.002 TYR A 676 ARG 0.013 0.001 ARG B 932 Details of bonding type rmsd hydrogen bonds : bond 0.05001 ( 633) hydrogen bonds : angle 4.60482 ( 1893) SS BOND : bond 0.02268 ( 2) SS BOND : angle 1.84577 ( 4) covalent geometry : bond 0.00629 (14061) covalent geometry : angle 0.84742 (18999) *********************** 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 351 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 265 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7991 (tt0) REVERT: A 441 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8631 (ttpp) REVERT: A 719 MET cc_start: 0.8301 (mmm) cc_final: 0.6244 (tmt) REVERT: A 745 CYS cc_start: 0.8167 (m) cc_final: 0.7495 (p) REVERT: A 795 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8809 (mtm) REVERT: A 829 ILE cc_start: 0.7883 (mm) cc_final: 0.7600 (mm) REVERT: A 846 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.8020 (tmm-80) REVERT: A 960 THR cc_start: 0.8825 (p) cc_final: 0.8469 (t) REVERT: A 1025 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7623 (mp) REVERT: A 1118 LEU cc_start: 0.8692 (tt) cc_final: 0.8123 (tm) REVERT: A 1121 ILE cc_start: 0.8375 (tt) cc_final: 0.7830 (tt) REVERT: B 427 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8468 (m-40) REVERT: B 483 THR cc_start: 0.8089 (p) cc_final: 0.7793 (m) REVERT: B 701 GLN cc_start: 0.8801 (tt0) cc_final: 0.8505 (tp-100) REVERT: B 719 MET cc_start: 0.7681 (mmm) cc_final: 0.5687 (tmt) REVERT: B 977 LYS cc_start: 0.8375 (mmtm) cc_final: 0.8009 (ptpp) REVERT: B 982 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8225 (tp) REVERT: B 1004 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7340 (tpp80) REVERT: B 1076 LEU cc_start: 0.8858 (mt) cc_final: 0.8628 (mp) REVERT: B 1108 MET cc_start: 0.8930 (mmm) cc_final: 0.8644 (tmm) outliers start: 86 outliers final: 25 residues processed: 325 average time/residue: 0.8369 time to fit residues: 309.4127 Evaluate side-chains 248 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 718 VAL 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 846 ARG Chi-restraints excluded: chain A residue 947 THR 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 1011 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain B residue 427 ASN Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 982 ILE 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 1050 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 0.2980 chunk 80 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 0.0370 chunk 20 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 HIS A 734 HIS A1073 GLN B 220 ASN B 664 ASN B 701 GLN ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.119535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083809 restraints weight = 24504.071| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.04 r_work: 0.3111 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14063 Z= 0.120 Angle : 0.650 11.786 19003 Z= 0.320 Chirality : 0.044 0.213 2139 Planarity : 0.005 0.074 2349 Dihedral : 13.823 117.645 2156 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.74 % Allowed : 23.85 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.20), residues: 1714 helix: 0.14 (0.17), residues: 931 sheet: -1.55 (0.42), residues: 145 loop : -3.15 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 770 HIS 0.019 0.001 HIS B 734 PHE 0.018 0.001 PHE A 954 TYR 0.017 0.001 TYR A 767 ARG 0.008 0.001 ARG B 818 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 633) hydrogen bonds : angle 4.14535 ( 1893) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.77780 ( 4) covalent geometry : bond 0.00262 (14061) covalent geometry : angle 0.65007 (18999) *********************** 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 295 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 227 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: A 441 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8674 (ttpp) REVERT: A 700 LEU cc_start: 0.8765 (tm) cc_final: 0.8469 (tp) REVERT: A 719 MET cc_start: 0.8078 (mmm) cc_final: 0.5969 (tmt) REVERT: A 745 CYS cc_start: 0.8127 (m) cc_final: 0.7575 (p) REVERT: A 960 THR cc_start: 0.8725 (p) cc_final: 0.8397 (t) REVERT: A 1025 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7588 (mp) REVERT: A 1086 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8203 (p) REVERT: A 1118 LEU cc_start: 0.8755 (tt) cc_final: 0.8068 (tt) REVERT: A 1121 ILE cc_start: 0.8548 (tt) cc_final: 0.8077 (mt) REVERT: B 229 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8371 (mmt-90) REVERT: B 325 ILE cc_start: 0.6106 (OUTLIER) cc_final: 0.5886 (mt) REVERT: B 395 LEU cc_start: 0.8679 (tm) cc_final: 0.8468 (tp) REVERT: B 483 THR cc_start: 0.8261 (p) cc_final: 0.7977 (m) REVERT: B 701 GLN cc_start: 0.8912 (tt0) cc_final: 0.8511 (tp-100) REVERT: B 719 MET cc_start: 0.7499 (mmm) cc_final: 0.5525 (tmt) REVERT: B 748 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8475 (t) REVERT: B 844 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8449 (mt) REVERT: B 934 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8642 (mt) REVERT: B 977 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7924 (mtmm) REVERT: B 982 ILE cc_start: 0.8531 (tt) cc_final: 0.8324 (tp) REVERT: B 1045 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 1076 LEU cc_start: 0.8823 (mt) cc_final: 0.8581 (mp) REVERT: B 1079 LEU cc_start: 0.9234 (mt) cc_final: 0.8846 (tm) REVERT: B 1121 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8627 (pp) outliers start: 68 outliers final: 14 residues processed: 271 average time/residue: 0.9044 time to fit residues: 277.5440 Evaluate side-chains 221 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 772 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 1037 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 363 ILE 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 732 LEU Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 998 THR 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 148 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 0.0570 chunk 149 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 ASN A1073 GLN B 220 ASN ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.116496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080331 restraints weight = 24363.574| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.01 r_work: 0.3078 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14063 Z= 0.173 Angle : 0.678 15.608 19003 Z= 0.332 Chirality : 0.046 0.215 2139 Planarity : 0.005 0.071 2349 Dihedral : 13.608 114.853 2152 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 5.02 % Allowed : 23.57 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.20), residues: 1714 helix: 0.51 (0.17), residues: 933 sheet: -1.53 (0.42), residues: 143 loop : -3.08 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 770 HIS 0.013 0.001 HIS B 734 PHE 0.026 0.002 PHE A 388 TYR 0.012 0.002 TYR A 673 ARG 0.005 0.001 ARG B 497 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 633) hydrogen bonds : angle 4.06767 ( 1893) SS BOND : bond 0.00274 ( 2) SS BOND : angle 0.91689 ( 4) covalent geometry : bond 0.00411 (14061) covalent geometry : angle 0.67815 (18999) *********************** 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: 72 poor density : 220 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: A 441 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8750 (ttpp) REVERT: A 473 GLU cc_start: 0.8373 (tt0) cc_final: 0.8158 (tt0) REVERT: A 700 LEU cc_start: 0.8783 (tm) cc_final: 0.8526 (tp) REVERT: A 719 MET cc_start: 0.8304 (mmm) cc_final: 0.6280 (tmt) REVERT: A 745 CYS cc_start: 0.8107 (m) cc_final: 0.7400 (p) REVERT: A 795 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8870 (mtm) REVERT: A 824 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7889 (pp20) REVERT: A 846 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8181 (tmm-80) REVERT: A 975 ASP cc_start: 0.6009 (OUTLIER) cc_final: 0.4830 (t70) REVERT: A 1009 ASP cc_start: 0.7941 (m-30) cc_final: 0.7322 (t0) REVERT: A 1025 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7683 (mp) REVERT: A 1086 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8161 (p) REVERT: A 1106 LEU cc_start: 0.8698 (pp) cc_final: 0.8365 (tt) REVERT: B 229 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8570 (mmt-90) REVERT: B 248 MET cc_start: 0.8634 (ttm) cc_final: 0.8333 (mtp) REVERT: B 395 LEU cc_start: 0.8881 (tm) cc_final: 0.8680 (tp) REVERT: B 441 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8683 (ttpp) REVERT: B 483 THR cc_start: 0.8358 (p) cc_final: 0.8037 (m) REVERT: B 701 GLN cc_start: 0.8955 (tt0) cc_final: 0.8514 (tp-100) REVERT: B 748 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8566 (t) REVERT: B 977 LYS cc_start: 0.8246 (mmtm) cc_final: 0.8023 (mtmm) REVERT: B 1038 ARG cc_start: 0.5862 (tpm170) cc_final: 0.4689 (tmt-80) REVERT: B 1042 MET cc_start: 0.8260 (tpp) cc_final: 0.7992 (tpt) REVERT: B 1076 LEU cc_start: 0.8840 (mt) cc_final: 0.8590 (mp) REVERT: B 1108 MET cc_start: 0.9121 (mmm) cc_final: 0.7939 (tmm) REVERT: B 1121 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8679 (pp) outliers start: 72 outliers final: 23 residues processed: 270 average time/residue: 0.8901 time to fit residues: 271.9937 Evaluate side-chains 229 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 362 VAL Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 846 ARG 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 1037 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 363 ILE 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 729 ILE Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1040 ASP 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 127 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 HIS A 937 GLN ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.116904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.080891 restraints weight = 24664.138| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.97 r_work: 0.3039 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.7114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14063 Z= 0.159 Angle : 0.657 15.410 19003 Z= 0.322 Chirality : 0.045 0.213 2139 Planarity : 0.005 0.072 2349 Dihedral : 13.217 114.396 2152 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 5.65 % Allowed : 23.92 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1714 helix: 0.80 (0.17), residues: 934 sheet: -1.37 (0.42), residues: 143 loop : -2.97 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 770 HIS 0.011 0.001 HIS B 734 PHE 0.019 0.002 PHE A 954 TYR 0.011 0.001 TYR A 965 ARG 0.006 0.001 ARG B1098 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 633) hydrogen bonds : angle 3.95151 ( 1893) SS BOND : bond 0.00774 ( 2) SS BOND : angle 0.77338 ( 4) covalent geometry : bond 0.00379 (14061) covalent geometry : angle 0.65686 (18999) *********************** 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 284 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 203 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: A 441 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8744 (ttpp) REVERT: A 473 GLU cc_start: 0.8363 (tt0) cc_final: 0.8115 (tt0) REVERT: A 700 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8557 (tp) REVERT: A 719 MET cc_start: 0.8063 (mmm) cc_final: 0.6506 (tmt) REVERT: A 732 LEU cc_start: 0.8543 (tm) cc_final: 0.8223 (tt) REVERT: A 795 MET cc_start: 0.9202 (mtp) cc_final: 0.8967 (mtm) REVERT: A 1025 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7707 (mp) REVERT: B 229 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8500 (mmt-90) REVERT: B 248 MET cc_start: 0.8751 (ttm) cc_final: 0.8497 (mtp) REVERT: B 395 LEU cc_start: 0.9003 (tm) cc_final: 0.8770 (tp) REVERT: B 688 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7119 (mm110) REVERT: B 701 GLN cc_start: 0.8991 (tt0) cc_final: 0.8492 (tp-100) REVERT: B 719 MET cc_start: 0.8059 (mmp) cc_final: 0.5868 (tmt) REVERT: B 733 VAL cc_start: 0.8297 (t) cc_final: 0.8054 (p) REVERT: B 748 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8348 (t) REVERT: B 954 PHE cc_start: 0.8099 (t80) cc_final: 0.7638 (t80) REVERT: B 1000 LEU cc_start: 0.8759 (tm) cc_final: 0.8555 (mm) REVERT: B 1076 LEU cc_start: 0.8891 (mt) cc_final: 0.8685 (mp) REVERT: B 1108 MET cc_start: 0.9164 (mmm) cc_final: 0.8048 (tmm) REVERT: B 1121 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8684 (pp) outliers start: 81 outliers final: 31 residues processed: 261 average time/residue: 1.0425 time to fit residues: 307.9670 Evaluate side-chains 221 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 441 LYS Chi-restraints excluded: chain A residue 470 THR 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 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1037 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 363 ILE 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 573 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 810 VAL 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 1121 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 833 HIS A 927 ASN A 937 GLN B 220 ASN B 724 ASN ** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.116384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.080064 restraints weight = 24863.453| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.02 r_work: 0.3021 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.7495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14063 Z= 0.170 Angle : 0.692 14.956 19003 Z= 0.336 Chirality : 0.046 0.205 2139 Planarity : 0.005 0.072 2349 Dihedral : 13.097 115.180 2152 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.09 % Allowed : 25.03 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1714 helix: 0.94 (0.18), residues: 931 sheet: -1.08 (0.43), residues: 143 loop : -2.88 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 770 HIS 0.010 0.001 HIS B 734 PHE 0.022 0.002 PHE B 387 TYR 0.009 0.001 TYR A 965 ARG 0.006 0.001 ARG B 766 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 633) hydrogen bonds : angle 3.93430 ( 1893) SS BOND : bond 0.00238 ( 2) SS BOND : angle 0.82873 ( 4) covalent geometry : bond 0.00409 (14061) covalent geometry : angle 0.69229 (18999) *********************** 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 273 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 200 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: A 330 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: A 441 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8727 (ttpp) REVERT: A 473 GLU cc_start: 0.8404 (tt0) cc_final: 0.8178 (tt0) REVERT: A 593 ILE cc_start: 0.8331 (tt) cc_final: 0.8048 (pt) REVERT: A 700 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8566 (tp) REVERT: A 719 MET cc_start: 0.8151 (mmm) cc_final: 0.6553 (tmt) REVERT: A 732 LEU cc_start: 0.8569 (tm) cc_final: 0.8209 (tt) REVERT: A 745 CYS cc_start: 0.7940 (m) cc_final: 0.7158 (p) REVERT: A 795 MET cc_start: 0.9265 (mtp) cc_final: 0.9009 (mtm) REVERT: A 1025 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7682 (mp) REVERT: A 1031 MET cc_start: 0.8307 (ppp) cc_final: 0.7838 (ppp) REVERT: A 1061 ASN cc_start: 0.7394 (p0) cc_final: 0.7142 (p0) REVERT: B 229 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8638 (mmt-90) REVERT: B 248 MET cc_start: 0.8787 (ttm) cc_final: 0.8527 (mtp) REVERT: B 353 GLU cc_start: 0.8139 (mp0) cc_final: 0.7913 (mp0) REVERT: B 395 LEU cc_start: 0.9050 (tm) cc_final: 0.8813 (tp) REVERT: B 688 GLN cc_start: 0.7447 (mm-40) cc_final: 0.7121 (mm110) REVERT: B 701 GLN cc_start: 0.9038 (tt0) cc_final: 0.8532 (tp-100) REVERT: B 733 VAL cc_start: 0.8396 (t) cc_final: 0.8183 (p) REVERT: B 748 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8235 (t) REVERT: B 830 ASN cc_start: 0.8427 (m-40) cc_final: 0.8179 (m110) REVERT: B 954 PHE cc_start: 0.8137 (t80) cc_final: 0.7598 (t80) REVERT: B 1045 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8630 (tm-30) REVERT: B 1076 LEU cc_start: 0.8943 (mt) cc_final: 0.8671 (mp) REVERT: B 1108 MET cc_start: 0.9158 (mmm) cc_final: 0.8112 (tmm) REVERT: B 1121 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8709 (pp) outliers start: 73 outliers final: 28 residues processed: 250 average time/residue: 1.6754 time to fit residues: 479.1980 Evaluate side-chains 218 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 330 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 441 LYS 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 730 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 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 525 SER 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 748 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 810 VAL 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 1118 LEU Chi-restraints excluded: chain B residue 1121 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 110 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 GLN B 724 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.116538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081362 restraints weight = 24645.262| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.98 r_work: 0.3033 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.7649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14063 Z= 0.152 Angle : 0.672 15.413 19003 Z= 0.326 Chirality : 0.045 0.182 2139 Planarity : 0.005 0.078 2349 Dihedral : 12.875 114.755 2151 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.60 % Allowed : 25.59 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1714 helix: 1.05 (0.18), residues: 931 sheet: -0.95 (0.43), residues: 143 loop : -2.81 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 770 HIS 0.009 0.001 HIS B 734 PHE 0.022 0.002 PHE B 712 TYR 0.010 0.001 TYR B1135 ARG 0.007 0.001 ARG A 932 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 633) hydrogen bonds : angle 3.92049 ( 1893) SS BOND : bond 0.01124 ( 2) SS BOND : angle 1.44148 ( 4) covalent geometry : bond 0.00363 (14061) covalent geometry : angle 0.67140 (18999) *********************** 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 255 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 189 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: A 473 GLU cc_start: 0.8425 (tt0) cc_final: 0.8200 (tt0) REVERT: A 478 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6920 (tt) REVERT: A 593 ILE cc_start: 0.8328 (tt) cc_final: 0.8055 (pt) REVERT: A 700 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8547 (tp) REVERT: A 719 MET cc_start: 0.8383 (mmm) cc_final: 0.6616 (tmt) REVERT: A 795 MET cc_start: 0.9239 (mtp) cc_final: 0.9031 (mtm) REVERT: A 823 LYS cc_start: 0.9200 (tmmm) cc_final: 0.8953 (tmtt) REVERT: A 830 ASN cc_start: 0.8289 (m-40) cc_final: 0.7901 (m-40) REVERT: A 1025 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7729 (mp) REVERT: A 1040 ASP cc_start: 0.7576 (t0) cc_final: 0.7194 (t0) REVERT: A 1042 MET cc_start: 0.7802 (pmm) cc_final: 0.7587 (ppp) REVERT: A 1061 ASN cc_start: 0.7418 (p0) cc_final: 0.7183 (p0) REVERT: A 1106 LEU cc_start: 0.8839 (tt) cc_final: 0.8457 (tm) REVERT: B 229 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8647 (mmt-90) REVERT: B 248 MET cc_start: 0.8790 (ttm) cc_final: 0.8555 (mtp) REVERT: B 353 GLU cc_start: 0.8093 (mp0) cc_final: 0.7828 (mp0) REVERT: B 395 LEU cc_start: 0.9051 (tm) cc_final: 0.8817 (tp) REVERT: B 497 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7650 (ptt-90) REVERT: B 688 GLN cc_start: 0.7453 (mm-40) cc_final: 0.7135 (mm110) REVERT: B 701 GLN cc_start: 0.9043 (tt0) cc_final: 0.8515 (tp-100) REVERT: B 733 VAL cc_start: 0.8393 (t) cc_final: 0.8171 (p) REVERT: B 748 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8245 (t) REVERT: B 807 ASN cc_start: 0.8526 (p0) cc_final: 0.8085 (p0) REVERT: B 830 ASN cc_start: 0.8465 (m-40) cc_final: 0.8227 (m110) REVERT: B 954 PHE cc_start: 0.8120 (t80) cc_final: 0.7569 (t80) REVERT: B 1076 LEU cc_start: 0.8993 (mt) cc_final: 0.8740 (mp) REVERT: B 1108 MET cc_start: 0.9103 (mmm) cc_final: 0.8073 (tmm) REVERT: B 1121 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8683 (pp) outliers start: 66 outliers final: 29 residues processed: 244 average time/residue: 0.8984 time to fit residues: 247.8893 Evaluate side-chains 222 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 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 730 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 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 810 VAL 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 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 109 optimal weight: 0.7980 chunk 152 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 ASN A 937 GLN A1073 GLN B 724 ASN B1073 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.117252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.081221 restraints weight = 24565.224| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.97 r_work: 0.3063 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.7795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14063 Z= 0.122 Angle : 0.663 15.284 19003 Z= 0.319 Chirality : 0.044 0.173 2139 Planarity : 0.005 0.072 2349 Dihedral : 12.513 111.958 2151 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.28 % Allowed : 26.99 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1714 helix: 1.28 (0.18), residues: 923 sheet: -0.90 (0.43), residues: 143 loop : -2.77 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 770 HIS 0.008 0.001 HIS B 734 PHE 0.017 0.001 PHE A 712 TYR 0.010 0.001 TYR A 965 ARG 0.013 0.001 ARG A 932 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 633) hydrogen bonds : angle 3.82615 ( 1893) SS BOND : bond 0.00676 ( 2) SS BOND : angle 1.46932 ( 4) covalent geometry : bond 0.00281 (14061) covalent geometry : angle 0.66308 (18999) *********************** 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 248 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: A 473 GLU cc_start: 0.8448 (tt0) cc_final: 0.8223 (tt0) REVERT: A 478 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6635 (tt) REVERT: A 593 ILE cc_start: 0.8285 (tt) cc_final: 0.8055 (pt) REVERT: A 700 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8543 (tp) REVERT: A 719 MET cc_start: 0.8355 (mmm) cc_final: 0.6584 (tmt) REVERT: A 795 MET cc_start: 0.9207 (mtp) cc_final: 0.8941 (mtm) REVERT: A 823 LYS cc_start: 0.9172 (tmmm) cc_final: 0.8912 (tmtt) REVERT: A 830 ASN cc_start: 0.8200 (m-40) cc_final: 0.7992 (m-40) REVERT: A 932 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7809 (tmm-80) REVERT: A 1025 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 1106 LEU cc_start: 0.8953 (tt) cc_final: 0.8666 (tm) REVERT: A 1121 ILE cc_start: 0.8263 (tp) cc_final: 0.7600 (pp) REVERT: B 229 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8555 (mmt-90) REVERT: B 353 GLU cc_start: 0.8060 (mp0) cc_final: 0.7812 (mp0) REVERT: B 395 LEU cc_start: 0.8991 (tm) cc_final: 0.8778 (tp) REVERT: B 497 ARG cc_start: 0.7818 (mtm110) cc_final: 0.7604 (ptt-90) REVERT: B 688 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7166 (mm110) REVERT: B 701 GLN cc_start: 0.9050 (tt0) cc_final: 0.8502 (tp-100) REVERT: B 733 VAL cc_start: 0.8473 (t) cc_final: 0.8217 (p) REVERT: B 807 ASN cc_start: 0.8486 (p0) cc_final: 0.8101 (p0) REVERT: B 830 ASN cc_start: 0.8472 (m-40) cc_final: 0.8188 (m110) REVERT: B 954 PHE cc_start: 0.8020 (t80) cc_final: 0.7401 (t80) REVERT: B 996 MET cc_start: 0.8873 (tpt) cc_final: 0.8614 (tmm) REVERT: B 1038 ARG cc_start: 0.5972 (tpm170) cc_final: 0.4895 (tmt-80) REVERT: B 1076 LEU cc_start: 0.9038 (mt) cc_final: 0.8756 (mp) REVERT: B 1108 MET cc_start: 0.9058 (mmm) cc_final: 0.7743 (tmm) outliers start: 47 outliers final: 23 residues processed: 235 average time/residue: 0.9068 time to fit residues: 241.2016 Evaluate side-chains 209 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 470 THR Chi-restraints excluded: chain A residue 478 LEU 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 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 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG 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 810 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 78 optimal weight: 0.4980 chunk 165 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 151 optimal weight: 0.0050 chunk 168 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1073 GLN B 724 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.117005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.080663 restraints weight = 24337.266| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.03 r_work: 0.3067 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.7913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14063 Z= 0.139 Angle : 0.693 15.380 19003 Z= 0.331 Chirality : 0.045 0.234 2139 Planarity : 0.005 0.071 2349 Dihedral : 12.439 108.871 2151 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.00 % Allowed : 28.10 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1714 helix: 1.25 (0.18), residues: 930 sheet: -0.85 (0.43), residues: 143 loop : -2.72 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 952 HIS 0.009 0.001 HIS B 734 PHE 0.024 0.001 PHE B 712 TYR 0.023 0.001 TYR B 965 ARG 0.011 0.001 ARG A 932 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 633) hydrogen bonds : angle 3.83519 ( 1893) SS BOND : bond 0.00347 ( 2) SS BOND : angle 2.01755 ( 4) covalent geometry : bond 0.00327 (14061) covalent geometry : angle 0.69214 (18999) *********************** 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 233 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: A 473 GLU cc_start: 0.8417 (tt0) cc_final: 0.8175 (tt0) REVERT: A 478 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6730 (tt) REVERT: A 593 ILE cc_start: 0.8297 (tt) cc_final: 0.8066 (pt) REVERT: A 700 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8538 (tp) REVERT: A 719 MET cc_start: 0.8364 (mmm) cc_final: 0.6591 (tmt) REVERT: A 795 MET cc_start: 0.9217 (mtp) cc_final: 0.8997 (mtm) REVERT: A 823 LYS cc_start: 0.9172 (tmmm) cc_final: 0.8896 (tmtt) REVERT: A 830 ASN cc_start: 0.8198 (m-40) cc_final: 0.7989 (m-40) REVERT: A 932 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7660 (tmm-80) REVERT: A 1025 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 229 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8571 (mmt-90) REVERT: B 353 GLU cc_start: 0.8045 (mp0) cc_final: 0.7810 (mp0) REVERT: B 497 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7428 (ptt-90) REVERT: B 688 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7179 (mm110) REVERT: B 701 GLN cc_start: 0.9071 (tt0) cc_final: 0.8501 (tp-100) REVERT: B 710 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6823 (mppt) REVERT: B 732 LEU cc_start: 0.7983 (tm) cc_final: 0.7712 (tt) REVERT: B 733 VAL cc_start: 0.8451 (t) cc_final: 0.8203 (p) REVERT: B 748 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8197 (t) REVERT: B 807 ASN cc_start: 0.8434 (p0) cc_final: 0.8086 (p0) REVERT: B 830 ASN cc_start: 0.8462 (m-40) cc_final: 0.8184 (m110) REVERT: B 954 PHE cc_start: 0.8113 (t80) cc_final: 0.7500 (t80) REVERT: B 996 MET cc_start: 0.8964 (tpt) cc_final: 0.8620 (tmm) REVERT: B 1076 LEU cc_start: 0.9015 (mt) cc_final: 0.8734 (mp) REVERT: B 1108 MET cc_start: 0.9060 (mmm) cc_final: 0.7829 (tmm) outliers start: 43 outliers final: 24 residues processed: 218 average time/residue: 0.9273 time to fit residues: 229.3786 Evaluate side-chains 218 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 470 THR Chi-restraints excluded: chain A residue 478 LEU 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 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 1037 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 710 LYS Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 810 VAL 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 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 163 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 0.0980 chunk 78 optimal weight: 0.0020 chunk 92 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.119332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.083277 restraints weight = 24428.957| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.04 r_work: 0.3108 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.8051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14063 Z= 0.112 Angle : 0.686 16.117 19003 Z= 0.324 Chirality : 0.044 0.272 2139 Planarity : 0.004 0.071 2349 Dihedral : 11.899 103.757 2151 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.16 % Allowed : 29.01 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1714 helix: 1.52 (0.18), residues: 920 sheet: -0.82 (0.43), residues: 143 loop : -2.66 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 770 HIS 0.008 0.001 HIS B 734 PHE 0.021 0.001 PHE A 712 TYR 0.014 0.001 TYR B 828 ARG 0.010 0.000 ARG A 932 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 633) hydrogen bonds : angle 3.74351 ( 1893) SS BOND : bond 0.00921 ( 2) SS BOND : angle 1.57357 ( 4) covalent geometry : bond 0.00244 (14061) covalent geometry : angle 0.68595 (18999) ********************** 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 220 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ILE cc_start: 0.8777 (pt) cc_final: 0.8527 (mt) REVERT: A 473 GLU cc_start: 0.8385 (tt0) cc_final: 0.8146 (tt0) REVERT: A 678 LYS cc_start: 0.7773 (mppt) cc_final: 0.7562 (mppt) REVERT: A 700 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8553 (tp) REVERT: A 719 MET cc_start: 0.8005 (mmm) cc_final: 0.6499 (tmt) REVERT: A 795 MET cc_start: 0.9172 (mtp) cc_final: 0.8902 (mtm) REVERT: A 823 LYS cc_start: 0.9143 (tmmm) cc_final: 0.8871 (tmtt) REVERT: A 932 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7935 (tmm-80) REVERT: A 1025 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7746 (mp) REVERT: A 1086 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8419 (p) REVERT: B 229 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8603 (mmt-90) REVERT: B 353 GLU cc_start: 0.7995 (mp0) cc_final: 0.7772 (mp0) REVERT: B 497 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7413 (ptt-90) REVERT: B 688 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7160 (mm110) REVERT: B 701 GLN cc_start: 0.8996 (tt0) cc_final: 0.8408 (tp-100) REVERT: B 733 VAL cc_start: 0.8412 (t) cc_final: 0.8129 (p) REVERT: B 807 ASN cc_start: 0.8377 (p0) cc_final: 0.8060 (p0) REVERT: B 830 ASN cc_start: 0.8463 (m-40) cc_final: 0.8198 (m110) REVERT: B 954 PHE cc_start: 0.7978 (t80) cc_final: 0.7351 (t80) REVERT: B 996 MET cc_start: 0.8982 (tpt) cc_final: 0.8550 (tmm) REVERT: B 1042 MET cc_start: 0.8480 (tpp) cc_final: 0.8141 (tpt) REVERT: B 1076 LEU cc_start: 0.8993 (mt) cc_final: 0.8702 (mp) REVERT: B 1108 MET cc_start: 0.9017 (mmm) cc_final: 0.7749 (tmm) outliers start: 31 outliers final: 18 residues processed: 213 average time/residue: 0.9293 time to fit residues: 223.5963 Evaluate side-chains 201 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 470 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 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 1037 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG 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 810 VAL Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL 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 90 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1073 GLN 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 = 0.118766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.082834 restraints weight = 24584.648| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.01 r_work: 0.3116 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.8083 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= 0.118 Angle : 0.700 15.050 19003 Z= 0.328 Chirality : 0.044 0.267 2139 Planarity : 0.005 0.072 2349 Dihedral : 11.717 103.688 2151 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.02 % Allowed : 29.29 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1714 helix: 1.56 (0.18), residues: 920 sheet: -0.74 (0.43), residues: 143 loop : -2.62 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 770 HIS 0.008 0.001 HIS B 734 PHE 0.025 0.001 PHE B 712 TYR 0.023 0.001 TYR B 965 ARG 0.011 0.001 ARG A 805 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 633) hydrogen bonds : angle 3.71098 ( 1893) SS BOND : bond 0.00307 ( 2) SS BOND : angle 1.49631 ( 4) covalent geometry : bond 0.00268 (14061) covalent geometry : angle 0.69929 (18999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11919.52 seconds wall clock time: 211 minutes 8.29 seconds (12668.29 seconds total)