Starting phenix.real_space_refine on Sat Sep 12 05:12:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6npl_0473/09_2026/6npl_0473.cif Found real_map, /net/cci-nas-00/data/ceres_data/6npl_0473/09_2026/6npl_0473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6npl_0473/09_2026/6npl_0473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6npl_0473/09_2026/6npl_0473.map" model { file = "/net/cci-nas-00/data/ceres_data/6npl_0473/09_2026/6npl_0473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6npl_0473/09_2026/6npl_0473.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6npl_0473/09_2026/6npl_0473.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6npl_0473/09_2026/6npl_0473.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 7 5.49 5 S 76 5.16 5 Cl 4 4.86 5 C 9002 2.51 5 N 2235 2.21 5 O 2448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13774 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6702 Classifications: {'peptide': 861} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 834} Chain breaks: 1 Chain: "B" Number of atoms: 6702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6702 Classifications: {'peptide': 861} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 834} Chain breaks: 1 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 159 Unusual residues: {' K': 1, ' CL': 2, 'POV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 211 Unusual residues: {' K': 1, ' CL': 2, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 2.57, per 1000 atoms: 0.19 Number of scatterers: 13774 At special positions: 0 Unit cell: (118.16, 88.62, 161.415, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 76 16.00 P 7 15.00 O 2448 8.00 N 2235 7.00 C 9002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 507 " distance=2.04 Simple disulfide: pdb=" SG CYS B 496 " - pdb=" SG CYS B 507 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 618.4 milliseconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 2 sheets defined 56.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.639A pdb=" N ILE A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 265 Processing helix chain 'A' and resid 273 through 282 removed outlier: 4.180A pdb=" N LEU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 319 removed outlier: 4.038A pdb=" N SER A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 349 removed outlier: 3.868A pdb=" N ARG A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 375 removed outlier: 4.096A pdb=" N GLU A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA A 354 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 398 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.697A pdb=" N ALA A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY A 425 " --> pdb=" O ILE A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 421 through 425' Processing helix chain 'A' and resid 434 through 463 Proline residue: A 440 - end of helix removed outlier: 3.599A pdb=" N LEU A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.728A pdb=" N VAL A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 545 removed outlier: 3.842A pdb=" N LEU A 537 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 removed outlier: 3.524A pdb=" N VAL A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 removed outlier: 4.144A pdb=" N ALA A 564 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE A 565 " --> pdb=" O GLY A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 592 removed outlier: 3.646A pdb=" N LEU A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 625 removed outlier: 3.511A pdb=" N ILE A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Proline residue: A 601 - end of helix removed outlier: 3.540A pdb=" N ASN A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 656 removed outlier: 3.577A pdb=" N ASN A 656 " --> pdb=" O MET A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 676 removed outlier: 3.583A pdb=" N VAL A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 removed outlier: 3.653A pdb=" N TYR A 692 " --> pdb=" O GLN A 688 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 736 removed outlier: 3.850A pdb=" N LEU A 730 " --> pdb=" O ARG A 726 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 774 Processing helix chain 'A' and resid 787 through 797 removed outlier: 3.979A pdb=" N TYR A 794 " --> pdb=" O GLN A 790 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET A 795 " --> pdb=" O GLY A 791 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A 797 " --> pdb=" O GLN A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 836 removed outlier: 3.758A pdb=" N ASN A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 832 " --> pdb=" O TYR A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 936 Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.954A pdb=" N LEU A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) Proline residue: A 964 - end of helix Processing helix chain 'A' and resid 991 through 1003 removed outlier: 3.841A pdb=" N LEU A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1030 removed outlier: 3.750A pdb=" N GLU A1027 " --> pdb=" O GLU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1049 removed outlier: 3.865A pdb=" N LYS A1049 " --> pdb=" O GLU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1084 removed outlier: 3.682A pdb=" N GLY A1070 " --> pdb=" O TYR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1115 removed outlier: 3.569A pdb=" N SER A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 5.144A pdb=" N VAL B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ARG B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 238 through 265 Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.722A pdb=" N ILE B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 319 removed outlier: 3.850A pdb=" N SER B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 349 removed outlier: 4.030A pdb=" N ARG B 332 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 375 removed outlier: 3.575A pdb=" N GLN B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 398 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 421 through 425 removed outlier: 3.673A pdb=" N ALA B 424 " --> pdb=" O GLY B 421 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY B 425 " --> pdb=" O ILE B 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 421 through 425' Processing helix chain 'B' and resid 434 through 463 Proline residue: B 440 - end of helix removed outlier: 3.974A pdb=" N LEU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 522 removed outlier: 3.711A pdb=" N VAL B 520 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 545 removed outlier: 3.682A pdb=" N LEU B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 removed outlier: 3.513A pdb=" N VAL B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 removed outlier: 4.084A pdb=" N ALA B 564 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE B 565 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 592 removed outlier: 3.586A pdb=" N PHE B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 Proline residue: B 601 - end of helix Processing helix chain 'B' and resid 637 through 656 removed outlier: 3.537A pdb=" N ASN B 656 " --> pdb=" O MET B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 676 removed outlier: 3.536A pdb=" N VAL B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 704 Processing helix chain 'B' and resid 726 through 736 removed outlier: 3.677A pdb=" N LEU B 730 " --> pdb=" O ARG B 726 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 774 removed outlier: 3.607A pdb=" N ARG B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 774 " --> pdb=" O TRP B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.658A pdb=" N MET B 795 " --> pdb=" O GLY B 791 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN B 797 " --> pdb=" O GLN B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 824 through 836 removed outlier: 3.767A pdb=" N LEU B 831 " --> pdb=" O THR B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 839 No H-bonds generated for 'chain 'B' and resid 837 through 839' Processing helix chain 'B' and resid 927 through 937 removed outlier: 3.633A pdb=" N ASP B 935 " --> pdb=" O GLN B 931 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 937 " --> pdb=" O LEU B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 969 removed outlier: 3.514A pdb=" N LEU B 962 " --> pdb=" O GLY B 958 " (cutoff:3.500A) Proline residue: B 964 - end of helix removed outlier: 3.533A pdb=" N ASN B 969 " --> pdb=" O TYR B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1003 removed outlier: 3.721A pdb=" N LEU B 999 " --> pdb=" O ALA B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1032 removed outlier: 3.644A pdb=" N PHE B1028 " --> pdb=" O GLY B1024 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B1032 " --> pdb=" O PHE B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1036 removed outlier: 3.789A pdb=" N LYS B1036 " --> pdb=" O GLU B1033 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1033 through 1036' Processing helix chain 'B' and resid 1041 through 1052 removed outlier: 3.585A pdb=" N GLU B1045 " --> pdb=" O ASP B1041 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B1050 " --> pdb=" O ALA B1046 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B1052 " --> pdb=" O GLU B1048 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1084 removed outlier: 3.522A pdb=" N GLY B1070 " --> pdb=" O TYR B1066 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B1078 " --> pdb=" O ILE B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1114 removed outlier: 3.614A pdb=" N THR B1113 " --> pdb=" O ALA B1109 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B1114 " --> pdb=" O TRP B1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 778 through 784 removed outlier: 6.216A pdb=" N LEU A 717 " --> pdb=" O VAL A 810 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLY A 812 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N MET A 719 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A1093 " --> pdb=" O TRP A 951 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 950 " --> pdb=" O PHE A 981 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N GLY A 983 " --> pdb=" O VAL A 950 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TRP A 952 " --> pdb=" O GLY A 983 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 778 through 784 removed outlier: 6.932A pdb=" N MET B 743 " --> pdb=" O PHE B 779 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N THR B 781 " --> pdb=" O MET B 743 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS B 745 " --> pdb=" O THR B 781 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 783 " --> pdb=" O CYS B 745 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N HIS B 747 " --> pdb=" O VAL B 783 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN B 715 " --> pdb=" O THR B 808 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL B 810 " --> pdb=" O GLN B 715 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU B 717 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLY B 812 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N MET B 719 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 809 " --> pdb=" O VAL B 843 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU B 845 " --> pdb=" O LEU B 809 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 811 " --> pdb=" O LEU B 845 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 846 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B1121 " --> pdb=" O ARG B 846 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE B1090 " --> pdb=" O LEU B1122 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL B1124 " --> pdb=" O ILE B1090 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N MET B1092 " --> pdb=" O VAL B1124 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N LEU B1089 " --> pdb=" O LYS B 945 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR B 947 " --> pdb=" O LEU B1089 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL B1091 " --> pdb=" O THR B 947 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP B 949 " --> pdb=" O VAL B1091 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N SER B1093 " --> pdb=" O ASP B 949 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N TRP B 951 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 983 " --> pdb=" O TRP B 952 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N THR B1011 " --> pdb=" O ILE B 978 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL B 980 " --> pdb=" O THR B1011 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU B1013 " --> pdb=" O VAL B 980 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 982 " --> pdb=" O LEU B1013 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.41 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: 7812 27.83 - 55.67: 426 55.67 - 83.50: 53 83.50 - 111.34: 8 111.34 - 139.17: 6 Dihedral angle restraints: 8305 sinusoidal: 3357 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 8302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1716 0.064 - 0.128: 379 0.128 - 0.192: 38 0.192 - 0.256: 4 0.256 - 0.320: 2 Chirality restraints: 2139 Sorted by residual: chirality pdb=" CB VAL B 339 " pdb=" CA VAL B 339 " pdb=" CG1 VAL B 339 " pdb=" CG2 VAL B 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB VAL A 339 " pdb=" CA VAL A 339 " pdb=" CG1 VAL A 339 " pdb=" CG2 VAL A 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE B1058 " pdb=" CA ILE B1058 " pdb=" CG1 ILE B1058 " pdb=" CG2 ILE B1058 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2136 not shown) Planarity restraints: 2349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B1119 " 0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO B1120 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO B1120 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B1120 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1119 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO A1120 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A1120 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A1120 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 416 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO A 417 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 417 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 417 " 0.042 5.00e-02 4.00e+02 ... (remaining 2346 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 4482 2.84 - 3.41: 13940 3.41 - 3.99: 25027 3.99 - 4.56: 35425 4.56 - 5.14: 52233 Nonbonded interactions: 131107 Sorted by model distance: nonbonded pdb=" O LEU A 771 " pdb=" OG SER A 776 " model vdw 2.264 3.040 nonbonded pdb=" O CYS A 496 " pdb=" OG SER A 505 " model vdw 2.294 3.040 nonbonded pdb=" OE1 GLN B 406 " pdb=" OG SER B 410 " model vdw 2.300 3.040 nonbonded pdb=" O GLU B 824 " pdb=" OG1 THR B 827 " model vdw 2.308 3.040 nonbonded pdb=" OD2 ASP A 391 " pdb=" OH TYR A 489 " model vdw 2.314 3.040 ... (remaining 131102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 206 through 1206) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.330 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 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 : 16.966 139.172 5127 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.46 % Favored : 91.48 % Rotamer: Outliers : 7.67 % Allowed : 12.55 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.62 (0.15), residues: 1714 helix: -2.57 (0.12), residues: 927 sheet: -2.45 (0.41), residues: 130 loop : -3.80 (0.18), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 404 TYR 0.025 0.002 TYR A 676 PHE 0.033 0.003 PHE B 606 TRP 0.039 0.002 TRP B 639 HIS 0.007 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00869 / 0.41 (14061) covalent geometry : angle 1.18040 / 0.54 (18999) SS BOND : bond 0.00477 / 0.24 ( 2) SS BOND : angle 4.84549 / 2.58 ( 4) hydrogen bonds : bond 0.15948 / 10.72 ( 633) hydrogen bonds : angle 6.88900 / 4.83 ( 1893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 358 time to evaluate : 0.462 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: 0.3980 time to fit residues: 196.4972 Evaluate side-chains 236 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1057 ARG Chi-restraints excluded: chain B residue 1124 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 ASN A 436 GLN A 573 ASN A 664 ASN A 739 ASN A 768 GLN A 815 ASN A1061 ASN B 298 ASN B 327 GLN B 427 ASN B 436 GLN B 664 ASN B 701 GLN B 724 ASN B 938 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.119547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.084145 restraints weight = 24377.298| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.97 r_work: 0.3133 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14063 Z= 0.138 Angle : 0.833 32.274 19003 Z= 0.376 Chirality : 0.044 0.234 2139 Planarity : 0.005 0.072 2349 Dihedral : 14.246 120.916 2146 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.29 % Favored : 92.65 % Rotamer: Outliers : 5.65 % Allowed : 20.36 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.19), residues: 1714 helix: -0.54 (0.16), residues: 928 sheet: -1.62 (0.42), residues: 140 loop : -3.34 (0.20), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 713 TYR 0.019 0.001 TYR A 965 PHE 0.026 0.002 PHE B 369 TRP 0.020 0.001 TRP A 770 HIS 0.004 0.001 HIS B 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (14061) covalent geometry : angle 0.83308 / 0.38 (18999) SS BOND : bond 0.00679 / 0.35 ( 2) SS BOND : angle 0.47980 / 0.24 ( 4) hydrogen bonds : bond 0.04067 / 2.71 ( 633) hydrogen bonds : angle 4.35595 / 3.02 ( 1893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 266 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7978 (ttmm) REVERT: A 577 LEU cc_start: 0.7756 (mm) cc_final: 0.7535 (mp) REVERT: A 796 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8348 (tm) REVERT: A 829 ILE cc_start: 0.7352 (mm) cc_final: 0.7009 (mm) REVERT: A 836 PHE cc_start: 0.7783 (m-10) cc_final: 0.7410 (m-10) REVERT: A 844 ILE cc_start: 0.7737 (mm) cc_final: 0.7488 (mm) REVERT: A 956 ASP cc_start: 0.6765 (m-30) cc_final: 0.6520 (m-30) REVERT: A 975 ASP cc_start: 0.5670 (OUTLIER) cc_final: 0.4456 (t70) REVERT: A 1112 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8333 (t0) REVERT: A 1118 LEU cc_start: 0.8506 (tt) cc_final: 0.8027 (tm) REVERT: B 304 MET cc_start: 0.8480 (ttp) cc_final: 0.8164 (ttp) REVERT: B 345 ILE cc_start: 0.8766 (mt) cc_final: 0.8565 (mp) REVERT: B 483 THR cc_start: 0.8276 (p) cc_final: 0.8017 (m) REVERT: B 719 MET cc_start: 0.7290 (mmm) cc_final: 0.5383 (tmt) REVERT: B 932 ARG cc_start: 0.5221 (OUTLIER) cc_final: 0.5006 (ppt170) REVERT: B 934 LEU cc_start: 0.8792 (mt) cc_final: 0.8558 (mt) REVERT: B 977 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8000 (ptpp) REVERT: B 1036 LYS cc_start: 0.8387 (mttt) cc_final: 0.8086 (mmtp) REVERT: B 1038 ARG cc_start: 0.5517 (tpt90) cc_final: 0.5307 (tpm170) outliers start: 81 outliers final: 12 residues processed: 321 average time/residue: 0.3878 time to fit residues: 140.9174 Evaluate side-chains 220 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 693 HIS Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 932 ARG Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 998 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 20 optimal weight: 0.2980 chunk 161 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 109 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 GLN A 734 HIS A1073 GLN B 329 ASN B 734 HIS B 833 HIS B1017 ASN B1073 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.119145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.083193 restraints weight = 24800.628| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.98 r_work: 0.3108 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.5412 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= 0.170 Angle : 0.852 31.892 19003 Z= 0.387 Chirality : 0.047 0.223 2139 Planarity : 0.005 0.078 2349 Dihedral : 13.251 107.068 2109 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 5.58 % Allowed : 21.90 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.20), residues: 1714 helix: 0.20 (0.17), residues: 925 sheet: -1.49 (0.41), residues: 145 loop : -3.12 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1098 TYR 0.017 0.002 TYR B 276 PHE 0.023 0.002 PHE A1007 TRP 0.026 0.002 TRP A 770 HIS 0.021 0.001 HIS B 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (14061) covalent geometry : angle 0.85190 / 0.39 (18999) SS BOND : bond 0.00346 / 0.18 ( 2) SS BOND : angle 1.46006 / 0.83 ( 4) hydrogen bonds : bond 0.04428 / 2.87 ( 633) hydrogen bonds : angle 4.23954 / 2.92 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 239 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: A 391 ASP cc_start: 0.8137 (t0) cc_final: 0.7886 (m-30) REVERT: A 478 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5919 (mt) REVERT: A 678 LYS cc_start: 0.8126 (pttt) cc_final: 0.7918 (mppt) REVERT: A 719 MET cc_start: 0.7932 (mmm) cc_final: 0.5615 (tmt) REVERT: A 760 LEU cc_start: 0.8414 (mp) cc_final: 0.8167 (mm) REVERT: A 796 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8440 (tm) REVERT: A 951 TRP cc_start: 0.8813 (m100) cc_final: 0.8586 (m100) REVERT: A 1009 ASP cc_start: 0.7762 (m-30) cc_final: 0.7523 (t0) REVERT: A 1025 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7254 (mp) REVERT: A 1086 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8029 (p) REVERT: A 1106 LEU cc_start: 0.8602 (pp) cc_final: 0.8375 (tt) REVERT: A 1110 TRP cc_start: 0.7085 (m-10) cc_final: 0.6866 (m-10) REVERT: B 229 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8300 (tpt170) REVERT: B 304 MET cc_start: 0.9023 (ttp) cc_final: 0.8777 (ttt) REVERT: B 325 ILE cc_start: 0.6116 (OUTLIER) cc_final: 0.5771 (mt) REVERT: B 483 THR cc_start: 0.8280 (p) cc_final: 0.8005 (m) REVERT: B 719 MET cc_start: 0.7735 (mmm) cc_final: 0.5559 (tmt) REVERT: B 724 ASN cc_start: 0.8322 (t160) cc_final: 0.7986 (m110) REVERT: B 932 ARG cc_start: 0.5303 (OUTLIER) cc_final: 0.5059 (ppt170) REVERT: B 954 PHE cc_start: 0.7855 (t80) cc_final: 0.7576 (t80) REVERT: B 977 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7950 (mtmm) REVERT: B 1076 LEU cc_start: 0.8915 (mp) cc_final: 0.8712 (mp) REVERT: B 1079 LEU cc_start: 0.9263 (mt) cc_final: 0.8828 (tm) REVERT: B 1094 MET cc_start: 0.8203 (ttp) cc_final: 0.7837 (mtm) REVERT: B 1121 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8451 (pp) outliers start: 80 outliers final: 24 residues processed: 293 average time/residue: 0.4030 time to fit residues: 133.5623 Evaluate side-chains 233 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 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 720 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 932 ARG 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 1025 LEU Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1131 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 49 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 GLN A 693 HIS A 768 GLN A 938 GLN B 698 HIS B 734 HIS B 775 ASN B 793 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.118363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.082263 restraints weight = 24548.287| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.02 r_work: 0.3078 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14063 Z= 0.159 Angle : 0.822 32.176 19003 Z= 0.365 Chirality : 0.045 0.257 2139 Planarity : 0.005 0.072 2349 Dihedral : 13.020 109.880 2109 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.53 % Allowed : 23.71 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.20), residues: 1714 helix: 0.62 (0.17), residues: 923 sheet: -1.30 (0.43), residues: 143 loop : -3.13 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 713 TYR 0.016 0.002 TYR B 676 PHE 0.021 0.002 PHE B 813 TRP 0.025 0.002 TRP A 770 HIS 0.022 0.002 HIS B 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (14061) covalent geometry : angle 0.82185 / 0.37 (18999) SS BOND : bond 0.00330 / 0.17 ( 2) SS BOND : angle 0.96039 / 0.54 ( 4) hydrogen bonds : bond 0.04031 / 2.63 ( 633) hydrogen bonds : angle 4.02144 / 2.79 ( 1893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 ASP cc_start: 0.8299 (t0) cc_final: 0.8069 (m-30) REVERT: A 593 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7806 (pt) REVERT: A 700 LEU cc_start: 0.8751 (tm) cc_final: 0.8494 (tp) REVERT: A 719 MET cc_start: 0.8183 (mmm) cc_final: 0.5914 (tmt) REVERT: A 760 LEU cc_start: 0.8521 (mp) cc_final: 0.8260 (mm) REVERT: A 836 PHE cc_start: 0.8621 (m-10) cc_final: 0.8418 (m-10) REVERT: A 951 TRP cc_start: 0.8885 (m100) cc_final: 0.8575 (m100) REVERT: A 1009 ASP cc_start: 0.7811 (m-30) cc_final: 0.7588 (t0) REVERT: A 1025 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7323 (mp) REVERT: B 229 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8310 (tpt170) REVERT: B 248 MET cc_start: 0.8558 (ttm) cc_final: 0.8213 (mtp) REVERT: B 304 MET cc_start: 0.8989 (ttp) cc_final: 0.8774 (ttt) REVERT: B 315 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7383 (mt-10) REVERT: B 353 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: B 395 LEU cc_start: 0.8769 (tm) cc_final: 0.8525 (tp) REVERT: B 427 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8494 (m-40) REVERT: B 483 THR cc_start: 0.8385 (p) cc_final: 0.8078 (m) REVERT: B 952 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7621 (t60) REVERT: B 1000 LEU cc_start: 0.8917 (tm) cc_final: 0.8424 (mm) REVERT: B 1038 ARG cc_start: 0.5411 (tpm-80) cc_final: 0.4871 (tpt170) REVERT: B 1065 LEU cc_start: 0.8626 (mp) cc_final: 0.8389 (mm) REVERT: B 1094 MET cc_start: 0.8260 (ttp) cc_final: 0.7904 (mtm) REVERT: B 1121 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8616 (pp) outliers start: 65 outliers final: 24 residues processed: 272 average time/residue: 0.3802 time to fit residues: 118.3256 Evaluate side-chains 227 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 391 ASP 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 534 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 952 TRP 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 97 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 731 HIS A1017 ASN B 775 ASN B1061 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.113392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.076576 restraints weight = 24712.227| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.04 r_work: 0.2974 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.7482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 14063 Z= 0.337 Angle : 0.944 31.676 19003 Z= 0.436 Chirality : 0.052 0.211 2139 Planarity : 0.006 0.073 2349 Dihedral : 13.939 119.034 2109 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 6.28 % Allowed : 23.71 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.20), residues: 1714 helix: 0.25 (0.17), residues: 951 sheet: -1.35 (0.44), residues: 141 loop : -3.05 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1098 TYR 0.023 0.003 TYR B 676 PHE 0.034 0.003 PHE A 606 TRP 0.028 0.003 TRP A 770 HIS 0.009 0.002 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.34 (14061) covalent geometry : angle 0.94391 / 0.44 (18999) SS BOND : bond 0.00239 / 0.12 ( 2) SS BOND : angle 1.43164 / 0.78 ( 4) hydrogen bonds : bond 0.05192 / 3.40 ( 633) hydrogen bonds : angle 4.32114 / 3.00 ( 1893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 207 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: A 357 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7981 (mt0) REVERT: A 391 ASP cc_start: 0.8392 (t0) cc_final: 0.8140 (m-30) REVERT: A 476 PHE cc_start: 0.8010 (m-80) cc_final: 0.7801 (m-80) REVERT: A 700 LEU cc_start: 0.8799 (tm) cc_final: 0.8579 (tp) REVERT: A 719 MET cc_start: 0.8637 (mmm) cc_final: 0.6833 (tmt) REVERT: A 732 LEU cc_start: 0.8551 (tm) cc_final: 0.8262 (tt) REVERT: A 1009 ASP cc_start: 0.8186 (m-30) cc_final: 0.7924 (t0) REVERT: A 1025 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7484 (mp) REVERT: A 1031 MET cc_start: 0.8359 (ppp) cc_final: 0.8036 (ppp) REVERT: A 1079 LEU cc_start: 0.8724 (tp) cc_final: 0.8335 (tt) REVERT: A 1128 HIS cc_start: 0.8429 (p-80) cc_final: 0.8201 (p90) REVERT: B 214 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8514 (tp) REVERT: B 229 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8693 (mmt-90) REVERT: B 315 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7817 (mt-10) REVERT: B 325 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6332 (mt) REVERT: B 395 LEU cc_start: 0.9050 (tm) cc_final: 0.8812 (tp) REVERT: B 427 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8667 (m-40) REVERT: B 688 GLN cc_start: 0.7540 (mm-40) cc_final: 0.6871 (tp-100) REVERT: B 796 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8868 (mm) REVERT: B 1038 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.5117 (tpt-90) REVERT: B 1065 LEU cc_start: 0.8733 (mp) cc_final: 0.8503 (mm) REVERT: B 1094 MET cc_start: 0.8506 (ttp) cc_final: 0.8107 (ttm) REVERT: B 1108 MET cc_start: 0.9219 (mmm) cc_final: 0.7770 (tmm) outliers start: 90 outliers final: 36 residues processed: 271 average time/residue: 0.3857 time to fit residues: 118.8528 Evaluate side-chains 227 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 357 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 SER 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 593 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 956 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 1064 GLU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 427 ASN Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 610 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 840 TYR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1038 ARG Chi-restraints excluded: chain B residue 1040 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 43 optimal weight: 1.9990 chunk 147 optimal weight: 0.0870 chunk 163 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 GLN B 688 GLN B 775 ASN B 830 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.116350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.080614 restraints weight = 24695.803| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.07 r_work: 0.3039 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.7655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14063 Z= 0.130 Angle : 0.826 33.003 19003 Z= 0.364 Chirality : 0.045 0.199 2139 Planarity : 0.005 0.071 2349 Dihedral : 13.044 115.979 2109 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.39 % Allowed : 25.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.21), residues: 1714 helix: 0.75 (0.17), residues: 945 sheet: -1.14 (0.44), residues: 141 loop : -2.95 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 932 TYR 0.012 0.001 TYR B 676 PHE 0.014 0.001 PHE A 387 TRP 0.030 0.002 TRP A 770 HIS 0.004 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (14061) covalent geometry : angle 0.82562 / 0.36 (18999) SS BOND : bond 0.00224 / 0.12 ( 2) SS BOND : angle 0.64607 / 0.35 ( 4) hydrogen bonds : bond 0.03869 / 2.55 ( 633) hydrogen bonds : angle 3.96207 / 2.74 ( 1893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 200 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: A 357 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: A 391 ASP cc_start: 0.8298 (t0) cc_final: 0.8073 (m-30) REVERT: A 700 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8541 (tp) REVERT: A 719 MET cc_start: 0.8533 (mmm) cc_final: 0.6635 (tmt) REVERT: A 732 LEU cc_start: 0.8528 (tm) cc_final: 0.8205 (tt) REVERT: A 932 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7785 (tmm-80) REVERT: A 1009 ASP cc_start: 0.8112 (m-30) cc_final: 0.7846 (t0) REVERT: A 1025 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7377 (mp) REVERT: A 1040 ASP cc_start: 0.7695 (t0) cc_final: 0.7451 (t0) REVERT: A 1061 ASN cc_start: 0.7293 (p0) cc_final: 0.7038 (p0) REVERT: B 229 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8577 (mmt-90) REVERT: B 248 MET cc_start: 0.8845 (ttm) cc_final: 0.8596 (mtp) REVERT: B 315 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7762 (mt-10) REVERT: B 319 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: B 325 ILE cc_start: 0.6538 (OUTLIER) cc_final: 0.6188 (mt) REVERT: B 395 LEU cc_start: 0.9055 (tm) cc_final: 0.8790 (tp) REVERT: B 719 MET cc_start: 0.8086 (mmp) cc_final: 0.5765 (tmt) REVERT: B 733 VAL cc_start: 0.8516 (t) cc_final: 0.8274 (p) REVERT: B 844 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8362 (mt) REVERT: B 954 PHE cc_start: 0.8148 (t80) cc_final: 0.7727 (t80) REVERT: B 1033 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8358 (tp30) REVERT: B 1038 ARG cc_start: 0.6151 (tpm-80) cc_final: 0.5292 (tmt-80) REVERT: B 1042 MET cc_start: 0.8445 (tpp) cc_final: 0.8037 (tpt) REVERT: B 1065 LEU cc_start: 0.8711 (mp) cc_final: 0.8470 (OUTLIER) REVERT: B 1094 MET cc_start: 0.8410 (ttp) cc_final: 0.8043 (ttm) REVERT: B 1108 MET cc_start: 0.9135 (mmm) cc_final: 0.7916 (tmm) REVERT: B 1121 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8770 (pp) outliers start: 63 outliers final: 26 residues processed: 247 average time/residue: 0.4026 time to fit residues: 112.3196 Evaluate side-chains 219 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 357 GLN Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 718 VAL 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 947 THR Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain B residue 1040 ASP 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 84 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 161 optimal weight: 0.0770 chunk 115 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 GLN A 698 HIS A 927 ASN B 830 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.118359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.082900 restraints weight = 24578.145| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.07 r_work: 0.3072 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.7751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14063 Z= 0.116 Angle : 0.823 34.815 19003 Z= 0.359 Chirality : 0.044 0.160 2139 Planarity : 0.005 0.071 2349 Dihedral : 12.438 114.044 2108 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.63 % Allowed : 26.43 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.21), residues: 1714 helix: 1.07 (0.18), residues: 933 sheet: -1.10 (0.43), residues: 143 loop : -2.80 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 766 TYR 0.010 0.001 TYR A 965 PHE 0.026 0.001 PHE A 954 TRP 0.031 0.002 TRP A 770 HIS 0.003 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (14061) covalent geometry : angle 0.82279 / 0.36 (18999) SS BOND : bond 0.00593 / 0.29 ( 2) SS BOND : angle 1.76435 / 0.82 ( 4) hydrogen bonds : bond 0.03616 / 2.37 ( 633) hydrogen bonds : angle 3.83780 / 2.65 ( 1893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: A 357 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: A 593 ILE cc_start: 0.8336 (tt) cc_final: 0.8045 (pt) REVERT: A 652 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8888 (ttm) REVERT: A 693 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.7182 (t70) REVERT: A 700 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8549 (tp) REVERT: A 719 MET cc_start: 0.8185 (mmm) cc_final: 0.6566 (tmt) REVERT: A 732 LEU cc_start: 0.8558 (tm) cc_final: 0.8231 (tt) REVERT: A 1009 ASP cc_start: 0.8059 (m-30) cc_final: 0.7801 (t0) REVERT: A 1025 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7464 (mp) REVERT: A 1061 ASN cc_start: 0.7324 (p0) cc_final: 0.7068 (p0) REVERT: A 1092 MET cc_start: 0.7983 (tpt) cc_final: 0.7758 (tpt) REVERT: B 229 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8621 (mmt-90) REVERT: B 315 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7837 (mt-10) REVERT: B 325 ILE cc_start: 0.6590 (OUTLIER) cc_final: 0.6269 (mt) REVERT: B 353 GLU cc_start: 0.8092 (mp0) cc_final: 0.7843 (mp0) REVERT: B 395 LEU cc_start: 0.9014 (tm) cc_final: 0.8776 (tp) REVERT: B 719 MET cc_start: 0.8063 (mmp) cc_final: 0.5859 (tmt) REVERT: B 733 VAL cc_start: 0.8554 (t) cc_final: 0.8309 (p) REVERT: B 807 ASN cc_start: 0.8516 (p0) cc_final: 0.8032 (p0) REVERT: B 830 ASN cc_start: 0.8332 (m-40) cc_final: 0.8084 (m110) REVERT: B 844 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8332 (mt) REVERT: B 949 ASP cc_start: 0.8095 (p0) cc_final: 0.7808 (t0) REVERT: B 951 TRP cc_start: 0.8998 (m100) cc_final: 0.8604 (m100) REVERT: B 954 PHE cc_start: 0.8171 (t80) cc_final: 0.7668 (t80) REVERT: B 996 MET cc_start: 0.8898 (tpt) cc_final: 0.8647 (tmm) REVERT: B 1033 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8353 (tp30) REVERT: B 1038 ARG cc_start: 0.6115 (tpm-80) cc_final: 0.5306 (tmt-80) REVERT: B 1042 MET cc_start: 0.8445 (tpp) cc_final: 0.8072 (tpt) REVERT: B 1065 LEU cc_start: 0.8692 (mp) cc_final: 0.8459 (OUTLIER) REVERT: B 1076 LEU cc_start: 0.8936 (mp) cc_final: 0.8723 (mm) REVERT: B 1094 MET cc_start: 0.8353 (ttp) cc_final: 0.8062 (ttm) REVERT: B 1108 MET cc_start: 0.9079 (mmm) cc_final: 0.7713 (tmm) REVERT: B 1121 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8715 (pp) outliers start: 52 outliers final: 27 residues processed: 227 average time/residue: 0.3714 time to fit residues: 95.7336 Evaluate side-chains 214 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 357 GLN 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 652 MET Chi-restraints excluded: chain A residue 693 HIS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 718 VAL 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 950 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain B residue 1040 ASP Chi-restraints excluded: chain B residue 1121 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 0.0670 chunk 62 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 68 optimal weight: 0.0040 chunk 34 optimal weight: 0.8980 overall best weight: 0.9934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.117941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082572 restraints weight = 24459.881| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.00 r_work: 0.3050 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.7842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14063 Z= 0.128 Angle : 0.669 15.440 19003 Z= 0.321 Chirality : 0.045 0.207 2139 Planarity : 0.005 0.069 2349 Dihedral : 12.179 112.361 2108 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.84 % Allowed : 26.92 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.21), residues: 1714 helix: 1.15 (0.18), residues: 932 sheet: -1.02 (0.43), residues: 143 loop : -2.76 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 932 TYR 0.010 0.001 TYR B 828 PHE 0.026 0.001 PHE B 712 TRP 0.033 0.002 TRP A 770 HIS 0.003 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14061) covalent geometry : angle 0.66784 / 0.32 (18999) SS BOND : bond 0.00993 / 0.48 ( 2) SS BOND : angle 2.26740 / 1.08 ( 4) hydrogen bonds : bond 0.03632 / 2.40 ( 633) hydrogen bonds : angle 3.83971 / 2.66 ( 1893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: A 593 ILE cc_start: 0.8329 (tt) cc_final: 0.8054 (pt) REVERT: A 693 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.7152 (t70) REVERT: A 700 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8564 (tp) REVERT: A 719 MET cc_start: 0.8092 (mmm) cc_final: 0.6522 (tmt) REVERT: A 732 LEU cc_start: 0.8496 (tm) cc_final: 0.8137 (tt) REVERT: A 823 LYS cc_start: 0.9117 (tmmm) cc_final: 0.8905 (tmtt) REVERT: A 1009 ASP cc_start: 0.8087 (m-30) cc_final: 0.7809 (t0) REVERT: A 1025 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7494 (mp) REVERT: A 1061 ASN cc_start: 0.7335 (p0) cc_final: 0.7094 (p0) REVERT: B 229 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8631 (mmt-90) REVERT: B 315 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7831 (mt-10) REVERT: B 325 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.6253 (mt) REVERT: B 353 GLU cc_start: 0.8071 (mp0) cc_final: 0.7817 (mp0) REVERT: B 395 LEU cc_start: 0.9020 (tm) cc_final: 0.8787 (tp) REVERT: B 427 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8437 (m110) REVERT: B 719 MET cc_start: 0.8085 (mmp) cc_final: 0.5909 (tmt) REVERT: B 807 ASN cc_start: 0.8527 (p0) cc_final: 0.8099 (p0) REVERT: B 844 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8325 (mt) REVERT: B 933 LEU cc_start: 0.8864 (tm) cc_final: 0.8663 (tt) REVERT: B 949 ASP cc_start: 0.8043 (p0) cc_final: 0.7608 (t0) REVERT: B 954 PHE cc_start: 0.8142 (t80) cc_final: 0.7614 (t80) REVERT: B 981 PHE cc_start: 0.7953 (m-10) cc_final: 0.7427 (m-10) REVERT: B 996 MET cc_start: 0.8933 (tpt) cc_final: 0.8613 (tmm) REVERT: B 1033 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8342 (tp30) REVERT: B 1038 ARG cc_start: 0.6099 (tpm-80) cc_final: 0.5323 (tmt-80) REVERT: B 1042 MET cc_start: 0.8487 (tpp) cc_final: 0.8115 (tpt) REVERT: B 1065 LEU cc_start: 0.8698 (mp) cc_final: 0.8459 (OUTLIER) REVERT: B 1094 MET cc_start: 0.8349 (ttp) cc_final: 0.8091 (ttm) REVERT: B 1108 MET cc_start: 0.9055 (mmm) cc_final: 0.7756 (tmm) outliers start: 55 outliers final: 31 residues processed: 225 average time/residue: 0.3696 time to fit residues: 95.0914 Evaluate side-chains 218 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 693 HIS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 718 VAL 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 796 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 427 ASN Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain B residue 1040 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 6 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 GLN A 927 ASN A1077 ASN B 724 ASN B 830 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.117927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.081718 restraints weight = 24712.380| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.96 r_work: 0.3070 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.7955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14063 Z= 0.118 Angle : 0.664 15.993 19003 Z= 0.318 Chirality : 0.045 0.371 2139 Planarity : 0.005 0.079 2349 Dihedral : 11.759 108.939 2108 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.28 % Allowed : 27.62 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.21), residues: 1714 helix: 1.35 (0.18), residues: 922 sheet: -1.03 (0.43), residues: 143 loop : -2.76 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 932 TYR 0.010 0.001 TYR A 965 PHE 0.018 0.001 PHE A 712 TRP 0.037 0.002 TRP A 770 HIS 0.003 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (14061) covalent geometry : angle 0.66386 / 0.32 (18999) SS BOND : bond 0.00356 / 0.18 ( 2) SS BOND : angle 1.74631 / 0.82 ( 4) hydrogen bonds : bond 0.03538 / 2.32 ( 633) hydrogen bonds : angle 3.80400 / 2.62 ( 1893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: A 593 ILE cc_start: 0.8266 (tt) cc_final: 0.7993 (pt) REVERT: A 693 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.7015 (t70) REVERT: A 700 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8549 (tp) REVERT: A 719 MET cc_start: 0.8058 (mmm) cc_final: 0.6516 (tmt) REVERT: A 830 ASN cc_start: 0.8237 (m-40) cc_final: 0.7924 (m-40) REVERT: A 996 MET cc_start: 0.8524 (mmm) cc_final: 0.8261 (tpt) REVERT: A 1009 ASP cc_start: 0.8072 (m-30) cc_final: 0.7859 (t0) REVERT: A 1025 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7599 (mp) REVERT: A 1040 ASP cc_start: 0.7226 (t0) cc_final: 0.6947 (t0) REVERT: A 1042 MET cc_start: 0.7866 (pmm) cc_final: 0.7593 (ppp) REVERT: B 229 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8625 (mmt-90) REVERT: B 315 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7799 (mt-10) REVERT: B 325 ILE cc_start: 0.6584 (OUTLIER) cc_final: 0.6247 (mt) REVERT: B 353 GLU cc_start: 0.8061 (mp0) cc_final: 0.7825 (mp0) REVERT: B 395 LEU cc_start: 0.9001 (tm) cc_final: 0.8768 (tp) REVERT: B 427 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8375 (m110) REVERT: B 497 ARG cc_start: 0.7726 (mtm110) cc_final: 0.7492 (ptt-90) REVERT: B 844 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8177 (mt) REVERT: B 933 LEU cc_start: 0.8862 (tm) cc_final: 0.8647 (tt) REVERT: B 949 ASP cc_start: 0.7993 (p0) cc_final: 0.7642 (t0) REVERT: B 954 PHE cc_start: 0.8079 (t80) cc_final: 0.7517 (t80) REVERT: B 981 PHE cc_start: 0.7812 (m-10) cc_final: 0.7462 (m-10) REVERT: B 996 MET cc_start: 0.8932 (tpt) cc_final: 0.8623 (tmm) REVERT: B 1033 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8284 (tp30) REVERT: B 1038 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.5341 (tmt-80) REVERT: B 1042 MET cc_start: 0.8456 (tpp) cc_final: 0.8085 (tpt) REVERT: B 1094 MET cc_start: 0.8231 (ttp) cc_final: 0.7971 (ttm) REVERT: B 1108 MET cc_start: 0.9030 (mmm) cc_final: 0.8618 (tmm) outliers start: 47 outliers final: 22 residues processed: 211 average time/residue: 0.3752 time to fit residues: 90.8606 Evaluate side-chains 208 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 693 HIS 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 950 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 427 ASN Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain B residue 1038 ARG Chi-restraints excluded: chain B residue 1040 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 724 ASN B 830 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.116190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.079894 restraints weight = 24413.997| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.02 r_work: 0.3021 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.8142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14063 Z= 0.195 Angle : 0.720 15.054 19003 Z= 0.349 Chirality : 0.048 0.355 2139 Planarity : 0.005 0.073 2349 Dihedral : 12.195 112.724 2108 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.79 % Allowed : 28.59 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.21), residues: 1714 helix: 1.08 (0.18), residues: 933 sheet: -1.05 (0.42), residues: 143 loop : -2.74 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 988 TYR 0.012 0.002 TYR B 676 PHE 0.025 0.002 PHE B 712 TRP 0.041 0.002 TRP A 770 HIS 0.005 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (14061) covalent geometry : angle 0.71946 / 0.35 (18999) SS BOND : bond 0.00182 / 0.09 ( 2) SS BOND : angle 1.96052 / 0.95 ( 4) hydrogen bonds : bond 0.04191 / 2.74 ( 633) hydrogen bonds : angle 3.96123 / 2.74 ( 1893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: A 593 ILE cc_start: 0.8351 (tt) cc_final: 0.7825 (pt) REVERT: A 700 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8570 (tp) REVERT: A 719 MET cc_start: 0.8470 (mmm) cc_final: 0.6780 (tmt) REVERT: A 823 LYS cc_start: 0.9035 (tmmm) cc_final: 0.8724 (mppt) REVERT: A 830 ASN cc_start: 0.8311 (m-40) cc_final: 0.7953 (m-40) REVERT: A 996 MET cc_start: 0.8605 (mmm) cc_final: 0.8280 (tpt) REVERT: A 1042 MET cc_start: 0.7805 (pmm) cc_final: 0.7590 (ppp) REVERT: A 1118 LEU cc_start: 0.9012 (tp) cc_final: 0.8804 (tp) REVERT: B 229 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8627 (mmt-90) REVERT: B 315 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7863 (mt-10) REVERT: B 325 ILE cc_start: 0.6547 (OUTLIER) cc_final: 0.6291 (mt) REVERT: B 353 GLU cc_start: 0.8089 (mp0) cc_final: 0.7816 (mp0) REVERT: B 395 LEU cc_start: 0.9009 (tm) cc_final: 0.8803 (tp) REVERT: B 427 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8530 (m110) REVERT: B 497 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7568 (ptt-90) REVERT: B 710 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7239 (mppt) REVERT: B 803 ARG cc_start: 0.8448 (ttm-80) cc_final: 0.8246 (ttm-80) REVERT: B 807 ASN cc_start: 0.8511 (p0) cc_final: 0.8198 (p0) REVERT: B 844 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8256 (mt) REVERT: B 949 ASP cc_start: 0.8019 (p0) cc_final: 0.7641 (t0) REVERT: B 954 PHE cc_start: 0.8165 (t80) cc_final: 0.7550 (t80) REVERT: B 981 PHE cc_start: 0.7889 (m-10) cc_final: 0.7365 (m-10) REVERT: B 996 MET cc_start: 0.8989 (tpt) cc_final: 0.8621 (tmm) REVERT: B 1033 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8393 (tp30) REVERT: B 1036 LYS cc_start: 0.8903 (mttt) cc_final: 0.8626 (mmtm) REVERT: B 1038 ARG cc_start: 0.6038 (OUTLIER) cc_final: 0.5524 (tpt170) REVERT: B 1042 MET cc_start: 0.8546 (tpp) cc_final: 0.8169 (tpt) REVERT: B 1108 MET cc_start: 0.9040 (mmm) cc_final: 0.8664 (tmm) outliers start: 40 outliers final: 22 residues processed: 218 average time/residue: 0.3898 time to fit residues: 96.5729 Evaluate side-chains 214 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 504 VAL 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 956 ASP Chi-restraints excluded: chain A residue 1000 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 427 ASN Chi-restraints excluded: chain B residue 484 ASP 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 760 LEU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain B residue 1038 ARG Chi-restraints excluded: chain B residue 1040 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 170 optimal weight: 0.0000 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 0.0050 chunk 137 optimal weight: 0.4980 chunk 112 optimal weight: 0.0470 chunk 158 optimal weight: 3.9990 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 797 GLN A 927 ASN B 724 ASN B 830 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.119600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.083936 restraints weight = 24640.960| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.96 r_work: 0.3095 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.8231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14063 Z= 0.114 Angle : 0.695 16.301 19003 Z= 0.330 Chirality : 0.045 0.370 2139 Planarity : 0.004 0.072 2349 Dihedral : 11.461 106.830 2108 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.09 % Allowed : 29.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.21), residues: 1714 helix: 1.48 (0.18), residues: 913 sheet: -0.99 (0.42), residues: 143 loop : -2.68 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 988 TYR 0.026 0.001 TYR B 965 PHE 0.019 0.001 PHE A 712 TRP 0.039 0.002 TRP A 770 HIS 0.003 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (14061) covalent geometry : angle 0.69505 / 0.33 (18999) SS BOND : bond 0.00287 / 0.15 ( 2) SS BOND : angle 1.15557 / 0.54 ( 4) hydrogen bonds : bond 0.03388 / 2.25 ( 633) hydrogen bonds : angle 3.83377 / 2.62 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4841.17 seconds wall clock time: 83 minutes 8.79 seconds (4988.79 seconds total)