Starting phenix.real_space_refine on Wed Feb 4 22:28:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgr_32485/02_2026/7wgr_32485.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgr_32485/02_2026/7wgr_32485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wgr_32485/02_2026/7wgr_32485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgr_32485/02_2026/7wgr_32485.map" model { file = "/net/cci-nas-00/data/ceres_data/7wgr_32485/02_2026/7wgr_32485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgr_32485/02_2026/7wgr_32485.cif" } resolution = 2.92 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= -0.002 sd= 0.077 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 Ca 2 9.91 5 P 4 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 8624 2.51 5 N 2374 2.21 5 O 2526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13614 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6779 Classifications: {'peptide': 850} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 802} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6779 Classifications: {'peptide': 850} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 802} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' CA': 1, ' MG': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' CA': 1, ' MG': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.96, per 1000 atoms: 0.22 Number of scatterers: 13614 At special positions: 0 Unit cell: (107.315, 117.455, 122.525, 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) Ca 2 19.99 S 82 16.00 P 4 15.00 Mg 2 11.99 O 2526 8.00 N 2374 7.00 C 8624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 516.3 milliseconds 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3196 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 47.6% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 129 through 145 removed outlier: 4.206A pdb=" N LEU A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N HIS A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 175 removed outlier: 3.761A pdb=" N LEU A 172 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.726A pdb=" N CYS A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 272 Processing helix chain 'A' and resid 285 through 301 Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.734A pdb=" N ASP A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 396 Processing helix chain 'A' and resid 418 through 429 removed outlier: 4.474A pdb=" N ASP A 428 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 removed outlier: 3.676A pdb=" N THR A 433 " --> pdb=" O PRO A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 433' Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.763A pdb=" N ALA A 465 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 466 " --> pdb=" O ASP A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 466' Processing helix chain 'A' and resid 479 through 498 removed outlier: 3.653A pdb=" N VAL A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.718A pdb=" N TYR A 527 " --> pdb=" O GLN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 Processing helix chain 'A' and resid 551 through 574 Processing helix chain 'A' and resid 610 through 622 removed outlier: 3.573A pdb=" N LEU A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 648 Processing helix chain 'A' and resid 652 through 667 removed outlier: 3.592A pdb=" N GLU A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.697A pdb=" N LEU A 706 " --> pdb=" O MET A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 733 Processing helix chain 'A' and resid 749 through 753 removed outlier: 3.970A pdb=" N ASN A 752 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 761 Processing helix chain 'A' and resid 794 through 800 removed outlier: 3.790A pdb=" N PHE A 798 " --> pdb=" O ARG A 794 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 removed outlier: 3.517A pdb=" N ASP A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS A 825 " --> pdb=" O GLN A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 848 removed outlier: 3.523A pdb=" N PHE A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 875 No H-bonds generated for 'chain 'A' and resid 873 through 875' Processing helix chain 'A' and resid 889 through 894 Processing helix chain 'A' and resid 895 through 898 Processing helix chain 'A' and resid 907 through 919 removed outlier: 3.533A pdb=" N ASP A 911 " --> pdb=" O LYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 948 removed outlier: 3.723A pdb=" N TYR A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 977 Proline residue: A 971 - end of helix Processing helix chain 'A' and resid 998 through 1015 removed outlier: 3.702A pdb=" N HIS A1002 " --> pdb=" O ASN A 998 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A1004 " --> pdb=" O LYS A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1023 removed outlier: 3.609A pdb=" N PHE A1022 " --> pdb=" O PHE A1019 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A1023 " --> pdb=" O LYS A1020 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1019 through 1023' Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.758A pdb=" N LEU B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 173 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 227 through 239 removed outlier: 3.693A pdb=" N CYS B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 272 Processing helix chain 'B' and resid 285 through 301 Processing helix chain 'B' and resid 313 through 321 Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.729A pdb=" N ASP B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 396 Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.685A pdb=" N ALA B 415 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 416 " --> pdb=" O ALA B 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 412 through 416' Processing helix chain 'B' and resid 418 through 426 Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.703A pdb=" N ALA B 465 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 468 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 469 " --> pdb=" O ARG B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 498 removed outlier: 3.622A pdb=" N VAL B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 531 removed outlier: 3.653A pdb=" N TYR B 527 " --> pdb=" O GLN B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 548 Processing helix chain 'B' and resid 551 through 574 Processing helix chain 'B' and resid 610 through 622 removed outlier: 3.580A pdb=" N LEU B 614 " --> pdb=" O THR B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 648 Processing helix chain 'B' and resid 652 through 667 removed outlier: 3.592A pdb=" N GLU B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 706 Processing helix chain 'B' and resid 723 through 735 removed outlier: 3.914A pdb=" N ALA B 735 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 753 removed outlier: 4.157A pdb=" N ASN B 752 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 753 " --> pdb=" O PHE B 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 749 through 753' Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 794 through 801 removed outlier: 3.887A pdb=" N PHE B 798 " --> pdb=" O ARG B 794 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 801 " --> pdb=" O ARG B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 824 Processing helix chain 'B' and resid 834 through 848 removed outlier: 3.800A pdb=" N LEU B 842 " --> pdb=" O PHE B 838 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 846 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 848 " --> pdb=" O ARG B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 875 No H-bonds generated for 'chain 'B' and resid 873 through 875' Processing helix chain 'B' and resid 889 through 894 removed outlier: 3.514A pdb=" N GLN B 893 " --> pdb=" O GLY B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 898 removed outlier: 3.530A pdb=" N VAL B 898 " --> pdb=" O PRO B 895 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 895 through 898' Processing helix chain 'B' and resid 907 through 919 removed outlier: 3.531A pdb=" N ASP B 911 " --> pdb=" O LYS B 907 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 915 " --> pdb=" O ASP B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 946 Processing helix chain 'B' and resid 965 through 977 Proline residue: B 971 - end of helix Processing helix chain 'B' and resid 998 through 1013 removed outlier: 3.702A pdb=" N HIS B1002 " --> pdb=" O ASN B 998 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B1003 " --> pdb=" O LYS B 999 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B1004 " --> pdb=" O LYS B1000 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1023 removed outlier: 3.673A pdb=" N PHE B1022 " --> pdb=" O PHE B1019 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 removed outlier: 3.708A pdb=" N LEU A 201 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 221 removed outlier: 6.275A pdb=" N PHE A 473 " --> pdb=" O ASP A 504 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 506 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 475 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL A 438 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER A 405 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL A 440 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 407 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL A 442 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS A 409 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR A 304 " --> pdb=" O MET A 404 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE A 406 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 306 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU A 408 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A 308 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N GLY A 410 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 650 through 651 Processing sheet with id=AA4, first strand: chain 'A' and resid 713 through 717 removed outlier: 3.621A pdb=" N GLY A 675 " --> pdb=" O CYS A 716 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL A 776 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 741 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU A 778 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP A 743 " --> pdb=" O LEU A 778 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 829 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 690 through 691 Processing sheet with id=AA6, first strand: chain 'A' and resid 925 through 929 removed outlier: 3.991A pdb=" N ALA A 926 " --> pdb=" O ARG A 900 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ALA A 954 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A 901 " --> pdb=" O ALA A 954 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS A 956 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE A 903 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N GLU A 958 " --> pdb=" O PHE A 903 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TRP A 955 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG A 988 " --> pdb=" O TRP A 955 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLN A 957 " --> pdb=" O ARG A 988 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AA8, first strand: chain 'B' and resid 218 through 221 removed outlier: 6.341A pdb=" N PHE B 473 " --> pdb=" O ASP B 504 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL B 506 " --> pdb=" O PHE B 473 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 475 " --> pdb=" O VAL B 506 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR B 304 " --> pdb=" O MET B 404 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE B 406 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 306 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU B 408 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY B 308 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N GLY B 410 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AB1, first strand: chain 'B' and resid 713 through 715 removed outlier: 7.540A pdb=" N VAL B 776 " --> pdb=" O ALA B 739 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 741 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU B 778 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP B 743 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 829 " --> pdb=" O LEU B 933 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 690 through 691 Processing sheet with id=AB3, first strand: chain 'B' and resid 925 through 929 removed outlier: 3.924A pdb=" N ALA B 926 " --> pdb=" O ARG B 900 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N ALA B 954 " --> pdb=" O LYS B 899 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU B 901 " --> pdb=" O ALA B 954 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N CYS B 956 " --> pdb=" O LEU B 901 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE B 903 " --> pdb=" O CYS B 956 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TRP B 955 " --> pdb=" O ALA B 986 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1575 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: 2.67 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2282 1.30 - 1.43: 3595 1.43 - 1.56: 7921 1.56 - 1.68: 8 1.68 - 1.81: 126 Bond restraints: 13932 Sorted by residual: bond pdb=" C PRO A 937 " pdb=" O PRO A 937 " ideal model delta sigma weight residual 1.235 1.174 0.062 1.30e-02 5.92e+03 2.24e+01 bond pdb=" O1A TPP A1103 " pdb=" PA TPP A1103 " ideal model delta sigma weight residual 1.479 1.522 -0.043 1.00e-02 1.00e+04 1.88e+01 bond pdb=" O1A TPP B1103 " pdb=" PA TPP B1103 " ideal model delta sigma weight residual 1.479 1.522 -0.043 1.00e-02 1.00e+04 1.86e+01 bond pdb=" N CYS B 763 " pdb=" CA CYS B 763 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.63e+01 bond pdb=" N CYS A 763 " pdb=" CA CYS A 763 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.61e+01 ... (remaining 13927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 17744 2.16 - 4.32: 1019 4.32 - 6.49: 111 6.49 - 8.65: 13 8.65 - 10.81: 1 Bond angle restraints: 18888 Sorted by residual: angle pdb=" N GLN A 766 " pdb=" CA GLN A 766 " pdb=" C GLN A 766 " ideal model delta sigma weight residual 114.12 106.29 7.83 1.39e+00 5.18e-01 3.17e+01 angle pdb=" C ASP A 818 " pdb=" CA ASP A 818 " pdb=" CB ASP A 818 " ideal model delta sigma weight residual 110.42 99.61 10.81 1.99e+00 2.53e-01 2.95e+01 angle pdb=" O3A TPP A1103 " pdb=" PB TPP A1103 " pdb=" O3B TPP A1103 " ideal model delta sigma weight residual 104.26 111.41 -7.15 1.33e+00 5.64e-01 2.88e+01 angle pdb=" O3A TPP B1103 " pdb=" PB TPP B1103 " pdb=" O3B TPP B1103 " ideal model delta sigma weight residual 104.26 111.32 -7.06 1.33e+00 5.64e-01 2.81e+01 angle pdb=" C PRO A 937 " pdb=" CA PRO A 937 " pdb=" CB PRO A 937 " ideal model delta sigma weight residual 111.56 103.07 8.49 1.65e+00 3.67e-01 2.64e+01 ... (remaining 18883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7485 17.75 - 35.50: 722 35.50 - 53.25: 134 53.25 - 71.00: 33 71.00 - 88.75: 16 Dihedral angle restraints: 8390 sinusoidal: 3450 harmonic: 4940 Sorted by residual: dihedral pdb=" CA SER A 934 " pdb=" C SER A 934 " pdb=" N PRO A 935 " pdb=" CA PRO A 935 " ideal model delta harmonic sigma weight residual 0.00 -41.59 41.59 0 5.00e+00 4.00e-02 6.92e+01 dihedral pdb=" C ASP A 818 " pdb=" N ASP A 818 " pdb=" CA ASP A 818 " pdb=" CB ASP A 818 " ideal model delta harmonic sigma weight residual -122.60 -107.67 -14.93 0 2.50e+00 1.60e-01 3.57e+01 dihedral pdb=" C PHE B 817 " pdb=" N PHE B 817 " pdb=" CA PHE B 817 " pdb=" CB PHE B 817 " ideal model delta harmonic sigma weight residual -122.60 -134.80 12.20 0 2.50e+00 1.60e-01 2.38e+01 ... (remaining 8387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1702 0.073 - 0.146: 285 0.146 - 0.219: 48 0.219 - 0.292: 19 0.292 - 0.365: 2 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CA PHE B 817 " pdb=" N PHE B 817 " pdb=" C PHE B 817 " pdb=" CB PHE B 817 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA ASP A 818 " pdb=" N ASP A 818 " pdb=" C ASP A 818 " pdb=" CB ASP A 818 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA GLN B 772 " pdb=" N GLN B 772 " pdb=" C GLN B 772 " pdb=" CB GLN B 772 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2053 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 706 " -0.026 2.00e-02 2.50e+03 5.13e-02 2.63e+01 pdb=" C LEU A 706 " 0.089 2.00e-02 2.50e+03 pdb=" O LEU A 706 " -0.033 2.00e-02 2.50e+03 pdb=" N TRP A 707 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 144 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C VAL B 144 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL B 144 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA B 145 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 427 " 0.019 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C SER A 427 " -0.064 2.00e-02 2.50e+03 pdb=" O SER A 427 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A 428 " 0.021 2.00e-02 2.50e+03 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 33 2.48 - 3.09: 8969 3.09 - 3.69: 19978 3.69 - 4.30: 30132 4.30 - 4.90: 51365 Nonbonded interactions: 110477 Sorted by model distance: nonbonded pdb=" OD1 ASN B 444 " pdb="MG MG B1102 " model vdw 1.877 2.170 nonbonded pdb=" OD1 ASN A 444 " pdb="MG MG A1102 " model vdw 1.952 2.170 nonbonded pdb="MG MG B1102 " pdb=" O2A TPP B1103 " model vdw 2.035 2.170 nonbonded pdb="MG MG B1102 " pdb=" O3B TPP B1103 " model vdw 2.035 2.170 nonbonded pdb="MG MG A1102 " pdb=" O2B TPP A1103 " model vdw 2.044 2.170 ... (remaining 110472 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.510 Find NCS groups from input model: 0.280 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:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 : 0.007 0.062 13932 Z= 0.479 Angle : 0.986 10.812 18888 Z= 0.662 Chirality : 0.061 0.365 2056 Planarity : 0.005 0.051 2468 Dihedral : 14.818 88.752 5194 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.56 % Favored : 95.08 % Rotamer: Outliers : 0.54 % Allowed : 2.49 % Favored : 96.97 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -0.28 (0.21), residues: 1688 helix: 1.03 (0.21), residues: 710 sheet: -0.08 (0.37), residues: 216 loop : -1.40 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 235 TYR 0.024 0.002 TYR B 985 PHE 0.045 0.002 PHE A 817 TRP 0.030 0.002 TRP B 827 HIS 0.009 0.001 HIS A 960 Details of bonding type rmsd covalent geometry : bond 0.00677 (13932) covalent geometry : angle 0.98592 (18888) hydrogen bonds : bond 0.17690 ( 556) hydrogen bonds : angle 5.91442 ( 1575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 249 time to evaluate : 0.448 Fit side-chains REVERT: B 628 ASN cc_start: 0.6740 (p0) cc_final: 0.5761 (t160) outliers start: 8 outliers final: 4 residues processed: 254 average time/residue: 0.6538 time to fit residues: 178.5492 Evaluate side-chains 170 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 166 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 818 ASP Chi-restraints excluded: chain B residue 826 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 HIS B 751 HIS B 760 GLN B 773 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN B 924 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS B1007 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.166392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.139980 restraints weight = 16337.023| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.94 r_work: 0.3613 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13932 Z= 0.115 Angle : 0.538 8.554 18888 Z= 0.278 Chirality : 0.043 0.140 2056 Planarity : 0.004 0.042 2468 Dihedral : 5.812 83.656 1871 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.56 % Allowed : 10.97 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.14 (0.21), residues: 1688 helix: 1.46 (0.21), residues: 694 sheet: -0.05 (0.37), residues: 222 loop : -1.16 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 135 TYR 0.013 0.001 TYR A 527 PHE 0.022 0.001 PHE A 193 TRP 0.017 0.001 TRP B 827 HIS 0.003 0.001 HIS B 705 Details of bonding type rmsd covalent geometry : bond 0.00262 (13932) covalent geometry : angle 0.53818 (18888) hydrogen bonds : bond 0.04021 ( 556) hydrogen bonds : angle 4.44972 ( 1575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.432 Fit side-chains REVERT: A 223 MET cc_start: 0.7919 (tpt) cc_final: 0.7568 (tpt) REVERT: A 270 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7314 (ptt-90) REVERT: A 309 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7467 (ppp) REVERT: A 453 ARG cc_start: 0.7544 (tpm-80) cc_final: 0.7331 (tpm-80) REVERT: A 454 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7235 (mtt) REVERT: A 722 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: A 1006 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8146 (tt) REVERT: B 246 PHE cc_start: 0.7083 (m-10) cc_final: 0.6865 (m-10) REVERT: B 722 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: B 766 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.7032 (mm-40) outliers start: 38 outliers final: 7 residues processed: 214 average time/residue: 0.5895 time to fit residues: 136.7705 Evaluate side-chains 178 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 818 ASP Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1012 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 417 GLN A 476 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN A1002 HIS B 616 HIS ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.160750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.134216 restraints weight = 16579.341| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.92 r_work: 0.3545 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13932 Z= 0.148 Angle : 0.553 8.803 18888 Z= 0.284 Chirality : 0.045 0.139 2056 Planarity : 0.004 0.041 2468 Dihedral : 5.744 79.856 1867 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.62 % Allowed : 14.00 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.18 (0.21), residues: 1688 helix: 1.46 (0.21), residues: 702 sheet: 0.15 (0.35), residues: 238 loop : -1.22 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 135 TYR 0.021 0.002 TYR A 562 PHE 0.017 0.001 PHE A 683 TRP 0.013 0.001 TRP B 827 HIS 0.005 0.001 HIS B 840 Details of bonding type rmsd covalent geometry : bond 0.00357 (13932) covalent geometry : angle 0.55308 (18888) hydrogen bonds : bond 0.04623 ( 556) hydrogen bonds : angle 4.26499 ( 1575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 223 MET cc_start: 0.7941 (tpt) cc_final: 0.7586 (tpt) REVERT: A 244 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6670 (mtt) REVERT: A 270 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7202 (ptt-90) REVERT: A 309 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7427 (ptm) REVERT: A 650 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8246 (m) REVERT: A 1006 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8097 (tt) REVERT: B 454 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7780 (mtt) outliers start: 39 outliers final: 11 residues processed: 206 average time/residue: 0.6285 time to fit residues: 140.3656 Evaluate side-chains 177 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 818 ASP Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1016 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 115 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 HIS A 476 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.162506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.136216 restraints weight = 16446.087| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.92 r_work: 0.3568 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13932 Z= 0.116 Angle : 0.515 9.216 18888 Z= 0.262 Chirality : 0.043 0.137 2056 Planarity : 0.004 0.039 2468 Dihedral : 5.112 75.336 1864 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.09 % Allowed : 16.02 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.21), residues: 1688 helix: 1.59 (0.21), residues: 700 sheet: 0.01 (0.36), residues: 218 loop : -1.09 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 135 TYR 0.016 0.001 TYR B 562 PHE 0.017 0.001 PHE A 193 TRP 0.012 0.001 TRP B 827 HIS 0.010 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00273 (13932) covalent geometry : angle 0.51547 (18888) hydrogen bonds : bond 0.03751 ( 556) hydrogen bonds : angle 4.15124 ( 1575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 223 MET cc_start: 0.7920 (tpt) cc_final: 0.7651 (tpt) REVERT: A 244 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6666 (mtt) REVERT: A 270 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7249 (ptt-90) REVERT: A 309 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7372 (ptm) REVERT: A 766 GLN cc_start: 0.7088 (tp40) cc_final: 0.6768 (mm110) REVERT: A 1006 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8115 (tt) REVERT: B 154 ASP cc_start: 0.5824 (OUTLIER) cc_final: 0.5340 (t0) REVERT: B 281 GLU cc_start: 0.7157 (mp0) cc_final: 0.6908 (mp0) REVERT: B 454 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7698 (mtt) REVERT: B 766 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6793 (tp40) outliers start: 31 outliers final: 10 residues processed: 185 average time/residue: 0.6356 time to fit residues: 127.2843 Evaluate side-chains 165 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1016 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 51 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 125 optimal weight: 0.0370 chunk 85 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 831 ASN B 950 ASN B1002 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.162883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136602 restraints weight = 16535.443| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.93 r_work: 0.3572 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 13932 Z= 0.109 Angle : 0.504 9.237 18888 Z= 0.257 Chirality : 0.043 0.134 2056 Planarity : 0.004 0.043 2468 Dihedral : 5.030 74.679 1862 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.22 % Allowed : 17.56 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1688 helix: 1.68 (0.21), residues: 702 sheet: 0.04 (0.34), residues: 240 loop : -1.09 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 135 TYR 0.017 0.001 TYR B 562 PHE 0.035 0.001 PHE B 817 TRP 0.010 0.001 TRP B 827 HIS 0.008 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00263 (13932) covalent geometry : angle 0.50378 (18888) hydrogen bonds : bond 0.03552 ( 556) hydrogen bonds : angle 4.06050 ( 1575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 223 MET cc_start: 0.7938 (tpt) cc_final: 0.7698 (tpt) REVERT: A 244 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6588 (mtt) REVERT: A 248 ASN cc_start: 0.7198 (m-40) cc_final: 0.6283 (t0) REVERT: A 270 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7199 (ptt-90) REVERT: A 309 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7354 (ptm) REVERT: A 766 GLN cc_start: 0.7224 (tp40) cc_final: 0.6935 (mm110) REVERT: A 1006 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8125 (tt) REVERT: B 154 ASP cc_start: 0.5802 (OUTLIER) cc_final: 0.5356 (t0) REVERT: B 248 ASN cc_start: 0.7282 (m-40) cc_final: 0.6330 (t0) REVERT: B 281 GLU cc_start: 0.7192 (mp0) cc_final: 0.6972 (mp0) REVERT: B 454 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7702 (mtt) REVERT: B 722 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: B 766 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6804 (tp40) outliers start: 33 outliers final: 14 residues processed: 177 average time/residue: 0.6472 time to fit residues: 123.3955 Evaluate side-chains 170 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain B residue 1012 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 165 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 62 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 425 HIS B 950 ASN B1002 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.159922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133526 restraints weight = 16629.106| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.92 r_work: 0.3534 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13932 Z= 0.155 Angle : 0.554 9.658 18888 Z= 0.283 Chirality : 0.045 0.142 2056 Planarity : 0.004 0.044 2468 Dihedral : 5.213 78.215 1862 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.21 % Favored : 95.73 % Rotamer: Outliers : 2.49 % Allowed : 18.17 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.24 (0.21), residues: 1688 helix: 1.55 (0.21), residues: 704 sheet: 0.01 (0.34), residues: 238 loop : -1.16 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 135 TYR 0.024 0.002 TYR B 562 PHE 0.032 0.001 PHE B 817 TRP 0.009 0.001 TRP A 233 HIS 0.009 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00379 (13932) covalent geometry : angle 0.55405 (18888) hydrogen bonds : bond 0.04406 ( 556) hydrogen bonds : angle 4.15412 ( 1575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6681 (tp30) cc_final: 0.6301 (tm-30) REVERT: A 223 MET cc_start: 0.7993 (tpt) cc_final: 0.7704 (tpt) REVERT: A 270 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7261 (ptt-90) REVERT: A 309 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7460 (ptm) REVERT: A 698 ARG cc_start: 0.8253 (ttp80) cc_final: 0.8039 (ttp80) REVERT: A 766 GLN cc_start: 0.7329 (tp40) cc_final: 0.7076 (mm110) REVERT: A 1006 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8127 (tt) REVERT: B 154 ASP cc_start: 0.5976 (OUTLIER) cc_final: 0.5401 (t0) REVERT: B 281 GLU cc_start: 0.7349 (mp0) cc_final: 0.7005 (mp0) REVERT: B 454 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7768 (mtt) REVERT: B 722 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: B 766 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6916 (tp40) outliers start: 37 outliers final: 21 residues processed: 176 average time/residue: 0.6162 time to fit residues: 117.5127 Evaluate side-chains 174 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1016 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 150 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 514 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN A1002 HIS B 474 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.154671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.128330 restraints weight = 16739.139| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.90 r_work: 0.3469 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 13932 Z= 0.275 Angle : 0.706 10.956 18888 Z= 0.363 Chirality : 0.050 0.147 2056 Planarity : 0.005 0.041 2468 Dihedral : 5.955 88.621 1862 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.33 % Favored : 94.55 % Rotamer: Outliers : 3.50 % Allowed : 17.90 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.41 (0.20), residues: 1688 helix: 0.92 (0.20), residues: 712 sheet: -0.17 (0.34), residues: 236 loop : -1.51 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 135 TYR 0.036 0.003 TYR B 562 PHE 0.027 0.002 PHE A 683 TRP 0.013 0.002 TRP A 233 HIS 0.009 0.002 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00683 (13932) covalent geometry : angle 0.70587 (18888) hydrogen bonds : bond 0.06378 ( 556) hydrogen bonds : angle 4.59489 ( 1575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6673 (tp30) cc_final: 0.6228 (tm-30) REVERT: A 270 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7264 (ptt-90) REVERT: A 309 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7622 (ptm) REVERT: A 694 ASN cc_start: 0.6945 (OUTLIER) cc_final: 0.6327 (p0) REVERT: A 698 ARG cc_start: 0.8270 (ttp80) cc_final: 0.8050 (ttp80) REVERT: A 722 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: A 766 GLN cc_start: 0.7641 (tp40) cc_final: 0.7414 (mm110) REVERT: A 817 PHE cc_start: 0.7096 (t80) cc_final: 0.6862 (t80) REVERT: A 1006 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8163 (tt) REVERT: B 154 ASP cc_start: 0.6195 (OUTLIER) cc_final: 0.5543 (t70) REVERT: B 281 GLU cc_start: 0.7317 (mp0) cc_final: 0.7023 (mp0) REVERT: B 454 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7965 (mtt) REVERT: B 722 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7831 (mp0) outliers start: 52 outliers final: 24 residues processed: 203 average time/residue: 0.5732 time to fit residues: 126.0427 Evaluate side-chains 192 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 819 ILE Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1012 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 67 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 248 ASN B 950 ASN B1002 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.160712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.134559 restraints weight = 16437.971| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.90 r_work: 0.3547 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13932 Z= 0.111 Angle : 0.548 10.051 18888 Z= 0.278 Chirality : 0.043 0.140 2056 Planarity : 0.004 0.040 2468 Dihedral : 5.239 75.538 1862 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.78 % Favored : 97.16 % Rotamer: Outliers : 2.09 % Allowed : 20.52 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.09 (0.21), residues: 1688 helix: 1.34 (0.20), residues: 710 sheet: -0.09 (0.34), residues: 238 loop : -1.16 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 135 TYR 0.023 0.001 TYR B 562 PHE 0.030 0.001 PHE B 817 TRP 0.015 0.001 TRP B 827 HIS 0.007 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00263 (13932) covalent geometry : angle 0.54844 (18888) hydrogen bonds : bond 0.03689 ( 556) hydrogen bonds : angle 4.13801 ( 1575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6660 (tp30) cc_final: 0.6198 (mt-10) REVERT: A 223 MET cc_start: 0.8058 (tpt) cc_final: 0.7766 (tpt) REVERT: A 244 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6725 (mtt) REVERT: A 309 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7472 (ptm) REVERT: A 694 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6179 (p0) REVERT: A 698 ARG cc_start: 0.8281 (ttp80) cc_final: 0.8080 (ttp80) REVERT: A 722 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: A 766 GLN cc_start: 0.7205 (tp40) cc_final: 0.6994 (mm110) REVERT: A 1006 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8106 (tt) REVERT: B 154 ASP cc_start: 0.6094 (OUTLIER) cc_final: 0.5514 (t0) REVERT: B 281 GLU cc_start: 0.7287 (mp0) cc_final: 0.6975 (mp0) REVERT: B 722 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7785 (mp0) outliers start: 31 outliers final: 13 residues processed: 184 average time/residue: 0.6091 time to fit residues: 121.4041 Evaluate side-chains 177 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1012 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 28 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 950 ASN B1002 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.159382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133124 restraints weight = 16588.403| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.91 r_work: 0.3533 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13932 Z= 0.133 Angle : 0.563 9.307 18888 Z= 0.285 Chirality : 0.044 0.136 2056 Planarity : 0.004 0.054 2468 Dihedral : 5.224 75.241 1862 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 2.02 % Allowed : 20.59 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.15 (0.21), residues: 1688 helix: 1.45 (0.20), residues: 708 sheet: -0.15 (0.33), residues: 238 loop : -1.16 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 135 TYR 0.027 0.002 TYR B 562 PHE 0.028 0.001 PHE B 817 TRP 0.010 0.001 TRP B 827 HIS 0.008 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00323 (13932) covalent geometry : angle 0.56285 (18888) hydrogen bonds : bond 0.04076 ( 556) hydrogen bonds : angle 4.12778 ( 1575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7770 (mmm160) cc_final: 0.7016 (mtm110) REVERT: A 211 GLU cc_start: 0.6682 (tp30) cc_final: 0.6309 (tm-30) REVERT: A 223 MET cc_start: 0.8038 (tpt) cc_final: 0.7771 (tpt) REVERT: A 244 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6670 (mtt) REVERT: A 309 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7462 (ptm) REVERT: A 694 ASN cc_start: 0.6808 (OUTLIER) cc_final: 0.6134 (p0) REVERT: A 722 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: A 766 GLN cc_start: 0.7321 (tp40) cc_final: 0.7099 (mm110) REVERT: A 1006 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8141 (tt) REVERT: B 154 ASP cc_start: 0.6066 (OUTLIER) cc_final: 0.5506 (t0) REVERT: B 281 GLU cc_start: 0.7331 (mp0) cc_final: 0.7019 (mp0) REVERT: B 722 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7739 (mp0) outliers start: 30 outliers final: 16 residues processed: 178 average time/residue: 0.6191 time to fit residues: 119.0405 Evaluate side-chains 176 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1012 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 6 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 152 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 950 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.161901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135763 restraints weight = 16514.656| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.91 r_work: 0.3563 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13932 Z= 0.108 Angle : 0.550 9.977 18888 Z= 0.276 Chirality : 0.043 0.139 2056 Planarity : 0.004 0.050 2468 Dihedral : 5.071 72.133 1862 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.92 % Rotamer: Outliers : 1.68 % Allowed : 20.93 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.28 (0.21), residues: 1688 helix: 1.56 (0.21), residues: 710 sheet: -0.25 (0.35), residues: 218 loop : -1.01 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 135 TYR 0.026 0.001 TYR B 562 PHE 0.029 0.001 PHE B 817 TRP 0.012 0.001 TRP B 827 HIS 0.007 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00258 (13932) covalent geometry : angle 0.54959 (18888) hydrogen bonds : bond 0.03420 ( 556) hydrogen bonds : angle 4.01066 ( 1575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7617 (mmm160) cc_final: 0.6947 (mtm110) REVERT: A 211 GLU cc_start: 0.6673 (tp30) cc_final: 0.6246 (mt-10) REVERT: A 223 MET cc_start: 0.8013 (tpt) cc_final: 0.7680 (tpt) REVERT: A 244 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6712 (mtt) REVERT: A 309 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7415 (ptm) REVERT: A 694 ASN cc_start: 0.6803 (OUTLIER) cc_final: 0.6163 (p0) REVERT: A 698 ARG cc_start: 0.8239 (ttp80) cc_final: 0.8037 (ttp-170) REVERT: A 1006 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8119 (tt) REVERT: B 154 ASP cc_start: 0.6003 (OUTLIER) cc_final: 0.5449 (t0) REVERT: B 211 GLU cc_start: 0.6511 (mm-30) cc_final: 0.6220 (mt-10) REVERT: B 281 GLU cc_start: 0.7317 (mp0) cc_final: 0.7033 (mp0) REVERT: B 722 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7739 (mp0) outliers start: 25 outliers final: 14 residues processed: 175 average time/residue: 0.5791 time to fit residues: 109.8699 Evaluate side-chains 171 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1012 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.0270 chunk 107 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 950 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.161491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135450 restraints weight = 16605.114| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.91 r_work: 0.3559 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13932 Z= 0.113 Angle : 0.553 9.039 18888 Z= 0.276 Chirality : 0.043 0.139 2056 Planarity : 0.004 0.055 2468 Dihedral : 5.067 72.969 1862 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 1.55 % Allowed : 21.27 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.33 (0.21), residues: 1688 helix: 1.61 (0.21), residues: 706 sheet: -0.25 (0.35), residues: 218 loop : -0.96 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 135 TYR 0.025 0.001 TYR B 562 PHE 0.030 0.001 PHE A 683 TRP 0.010 0.001 TRP B 769 HIS 0.007 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00272 (13932) covalent geometry : angle 0.55312 (18888) hydrogen bonds : bond 0.03515 ( 556) hydrogen bonds : angle 3.99414 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4209.52 seconds wall clock time: 72 minutes 28.18 seconds (4348.18 seconds total)