Starting phenix.real_space_refine on Mon Dec 30 17:19:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgr_32485/12_2024/7wgr_32485.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgr_32485/12_2024/7wgr_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_32485/12_2024/7wgr_32485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgr_32485/12_2024/7wgr_32485.map" model { file = "/net/cci-nas-00/data/ceres_data/7wgr_32485/12_2024/7wgr_32485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgr_32485/12_2024/7wgr_32485.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.54, per 1000 atoms: 0.63 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: 3.32 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.63 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: 4.93 Time building geometry restraints manager: 3.86 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: 0.00 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.990 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.240 ------------------------------------------------------------------------------- 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= 0.440 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 : 5.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (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 TRP 0.030 0.002 TRP B 827 HIS 0.009 0.001 HIS A 960 PHE 0.045 0.002 PHE A 817 TYR 0.024 0.002 TYR B 985 ARG 0.008 0.000 ARG A 235 *********************** 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 : 1.555 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: 1.5126 time to fit residues: 416.1384 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 : 1.803 ------------------------------------------------------------------------------- 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 143 optimal weight: 0.8980 chunk 128 optimal weight: 0.0770 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN B 924 GLN B 957 GLN B1002 HIS B1007 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13932 Z= 0.235 Angle : 0.577 8.894 18888 Z= 0.298 Chirality : 0.045 0.143 2056 Planarity : 0.004 0.045 2468 Dihedral : 5.984 85.449 1871 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.83 % Allowed : 11.57 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1688 helix: 1.24 (0.20), residues: 710 sheet: 0.02 (0.35), residues: 242 loop : -1.38 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 827 HIS 0.006 0.001 HIS B 840 PHE 0.024 0.002 PHE A 193 TYR 0.017 0.002 TYR A 527 ARG 0.006 0.000 ARG B 979 *********************** 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 235 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 1.450 Fit side-chains REVERT: A 223 MET cc_start: 0.7389 (tpt) cc_final: 0.6882 (tpt) REVERT: A 270 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7230 (ptt-90) REVERT: A 309 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7237 (ptm) REVERT: A 454 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6682 (mtt) REVERT: A 722 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: A 1006 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8373 (tt) REVERT: B 223 MET cc_start: 0.7412 (mmt) cc_final: 0.7209 (tpt) REVERT: B 722 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6910 (mp0) outliers start: 42 outliers final: 10 residues processed: 213 average time/residue: 1.4675 time to fit residues: 340.1518 Evaluate side-chains 182 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 607 THR 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 293 ILE Chi-restraints excluded: chain B residue 299 GLU 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 722 GLU Chi-restraints excluded: chain B residue 818 ASP 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 85 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 425 HIS ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13932 Z= 0.343 Angle : 0.626 9.455 18888 Z= 0.324 Chirality : 0.047 0.144 2056 Planarity : 0.005 0.042 2468 Dihedral : 5.742 84.986 1864 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.23 % Allowed : 14.94 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1688 helix: 1.14 (0.20), residues: 706 sheet: 0.04 (0.34), residues: 238 loop : -1.47 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 769 HIS 0.008 0.002 HIS B 376 PHE 0.022 0.002 PHE A 683 TYR 0.025 0.002 TYR A 562 ARG 0.005 0.001 ARG A 135 *********************** 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 225 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 1.544 Fit side-chains REVERT: A 223 MET cc_start: 0.7446 (tpt) cc_final: 0.6986 (tpt) REVERT: A 270 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7159 (ptt-90) REVERT: A 309 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7367 (ptm) REVERT: A 1006 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8381 (tt) REVERT: B 454 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6817 (mtt) REVERT: B 697 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7046 (mtmt) outliers start: 48 outliers final: 19 residues processed: 204 average time/residue: 1.5069 time to fit residues: 333.5031 Evaluate side-chains 180 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 565 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 720 LEU 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 697 LYS Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 818 ASP Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 977 ILE 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 152 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 155 optimal weight: 0.0050 chunk 164 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 376 HIS ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 248 ASN B 425 HIS ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13932 Z= 0.186 Angle : 0.526 9.314 18888 Z= 0.269 Chirality : 0.043 0.136 2056 Planarity : 0.004 0.041 2468 Dihedral : 5.245 75.554 1864 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.02 % Allowed : 17.36 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1688 helix: 1.36 (0.20), residues: 708 sheet: -0.00 (0.36), residues: 216 loop : -1.20 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 827 HIS 0.004 0.001 HIS B1002 PHE 0.019 0.001 PHE A 193 TYR 0.016 0.001 TYR A 562 ARG 0.006 0.000 ARG A 135 *********************** 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 198 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.642 Fit side-chains revert: symmetry clash REVERT: A 270 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7290 (ptt-90) REVERT: A 309 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7211 (ptm) REVERT: A 722 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: A 1006 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8361 (tt) REVERT: B 154 ASP cc_start: 0.6210 (OUTLIER) cc_final: 0.5730 (t0) REVERT: B 454 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6751 (mtt) outliers start: 30 outliers final: 11 residues processed: 186 average time/residue: 1.5136 time to fit residues: 305.8207 Evaluate side-chains 174 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ARG 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 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 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 1003 LEU Chi-restraints excluded: chain B residue 1012 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 2 optimal weight: 0.0170 chunk 122 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- 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** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 425 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13932 Z= 0.279 Angle : 0.582 9.780 18888 Z= 0.298 Chirality : 0.045 0.139 2056 Planarity : 0.005 0.038 2468 Dihedral : 5.415 79.684 1862 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 3.03 % Allowed : 18.24 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1688 helix: 1.27 (0.20), residues: 708 sheet: -0.06 (0.34), residues: 238 loop : -1.37 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 769 HIS 0.005 0.001 HIS B 376 PHE 0.037 0.002 PHE B 817 TYR 0.019 0.002 TYR B 562 ARG 0.009 0.000 ARG B 135 *********************** 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 211 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6390 (mtt) REVERT: A 270 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7096 (ptt-90) REVERT: A 309 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7303 (ptm) REVERT: A 694 ASN cc_start: 0.6468 (OUTLIER) cc_final: 0.5814 (p0) REVERT: A 722 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: A 959 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7199 (mt-10) REVERT: A 1006 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8361 (tt) REVERT: B 454 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6746 (mtt) REVERT: B 722 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7071 (mp0) outliers start: 45 outliers final: 19 residues processed: 195 average time/residue: 1.4195 time to fit residues: 300.9545 Evaluate side-chains 182 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.702 ------------------------------------------------------------------------------- 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 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 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 959 GLU Chi-restraints excluded: chain A residue 1006 LEU 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 720 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 736 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** A 831 ASN A1002 HIS B 425 HIS ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 13932 Z= 0.173 Angle : 0.517 9.448 18888 Z= 0.264 Chirality : 0.043 0.135 2056 Planarity : 0.004 0.038 2468 Dihedral : 5.095 72.310 1862 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 2.22 % Allowed : 19.65 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1688 helix: 1.59 (0.21), residues: 696 sheet: -0.26 (0.34), residues: 228 loop : -1.13 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 827 HIS 0.004 0.001 HIS B1002 PHE 0.033 0.001 PHE B 817 TYR 0.014 0.001 TYR B 562 ARG 0.010 0.000 ARG B 135 *********************** 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 200 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 270 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7217 (ptt-90) REVERT: A 309 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7289 (ptm) REVERT: A 694 ASN cc_start: 0.6373 (OUTLIER) cc_final: 0.5701 (p0) REVERT: A 722 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: A 1006 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8352 (tt) REVERT: B 154 ASP cc_start: 0.6221 (OUTLIER) cc_final: 0.5727 (t0) outliers start: 33 outliers final: 11 residues processed: 186 average time/residue: 1.4743 time to fit residues: 297.3295 Evaluate side-chains 166 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ARG 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 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 720 LEU Chi-restraints excluded: chain B residue 736 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13932 Z= 0.254 Angle : 0.566 9.405 18888 Z= 0.289 Chirality : 0.045 0.137 2056 Planarity : 0.004 0.045 2468 Dihedral : 5.293 77.454 1862 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 3.03 % Allowed : 19.18 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1688 helix: 1.41 (0.21), residues: 706 sheet: -0.09 (0.34), residues: 234 loop : -1.32 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 769 HIS 0.004 0.001 HIS B 376 PHE 0.028 0.001 PHE B 817 TYR 0.018 0.002 TYR A 527 ARG 0.012 0.000 ARG B 135 *********************** 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 204 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 1.526 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.6412 (mtt) REVERT: A 270 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7096 (ptt-90) REVERT: A 309 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7307 (ptm) REVERT: A 694 ASN cc_start: 0.6460 (OUTLIER) cc_final: 0.5814 (p0) REVERT: A 698 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7779 (ttp-170) REVERT: A 722 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: A 959 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: A 1006 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8355 (tt) REVERT: B 154 ASP cc_start: 0.6317 (OUTLIER) cc_final: 0.5825 (t0) REVERT: B 244 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.6404 (mtt) REVERT: B 454 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6735 (mtt) outliers start: 45 outliers final: 25 residues processed: 189 average time/residue: 1.5225 time to fit residues: 312.3911 Evaluate side-chains 189 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU 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 366 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 530 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 950 ASN Chi-restraints excluded: chain A residue 959 GLU 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 486 VAL 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 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 Chi-restraints excluded: chain B residue 1018 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 128 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 831 ASN B 950 ASN B1002 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 13932 Z= 0.161 Angle : 0.519 8.886 18888 Z= 0.263 Chirality : 0.042 0.132 2056 Planarity : 0.004 0.043 2468 Dihedral : 4.999 69.096 1862 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1688 helix: 1.67 (0.21), residues: 698 sheet: -0.20 (0.35), residues: 220 loop : -1.06 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 827 HIS 0.004 0.001 HIS B1002 PHE 0.030 0.001 PHE B 817 TYR 0.012 0.001 TYR A 527 ARG 0.012 0.000 ARG B 135 *********************** 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 188 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: A 309 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7204 (ptm) REVERT: A 694 ASN cc_start: 0.6415 (OUTLIER) cc_final: 0.5763 (p0) REVERT: A 698 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7740 (ttp-170) REVERT: A 722 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: A 959 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: A 1006 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8357 (tt) REVERT: B 135 ARG cc_start: 0.7174 (mmm160) cc_final: 0.6848 (mtm110) REVERT: B 154 ASP cc_start: 0.6235 (OUTLIER) cc_final: 0.5835 (t0) outliers start: 23 outliers final: 10 residues processed: 179 average time/residue: 1.5880 time to fit residues: 307.6648 Evaluate side-chains 166 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET 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 959 GLU 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 307 MET Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 736 SER 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 156 optimal weight: 0.2980 chunk 143 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13932 Z= 0.290 Angle : 0.594 9.037 18888 Z= 0.302 Chirality : 0.045 0.139 2056 Planarity : 0.005 0.052 2468 Dihedral : 5.417 80.511 1862 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.68 % Favored : 95.20 % Rotamer: Outliers : 2.15 % Allowed : 20.79 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1688 helix: 1.39 (0.20), residues: 708 sheet: -0.17 (0.33), residues: 234 loop : -1.29 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 769 HIS 0.004 0.001 HIS B 474 PHE 0.024 0.002 PHE B 817 TYR 0.027 0.002 TYR A 562 ARG 0.011 0.000 ARG A 135 *********************** 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 188 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7538 (mmm160) cc_final: 0.7024 (mtm110) REVERT: A 309 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7315 (ptm) REVERT: A 694 ASN cc_start: 0.6539 (OUTLIER) cc_final: 0.5949 (p0) REVERT: A 722 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: A 1006 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8354 (tt) REVERT: B 154 ASP cc_start: 0.6411 (OUTLIER) cc_final: 0.5926 (t0) outliers start: 32 outliers final: 19 residues processed: 176 average time/residue: 1.5288 time to fit residues: 291.8896 Evaluate side-chains 176 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 307 MET 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 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 307 MET Chi-restraints excluded: chain B residue 486 VAL 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 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 Chi-restraints excluded: chain B residue 1018 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 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 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 425 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 13932 Z= 0.279 Angle : 0.807 59.046 18888 Z= 0.449 Chirality : 0.045 0.296 2056 Planarity : 0.005 0.064 2468 Dihedral : 5.443 80.690 1862 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 1.88 % Allowed : 21.06 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1688 helix: 1.40 (0.20), residues: 708 sheet: -0.23 (0.33), residues: 238 loop : -1.28 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 769 HIS 0.004 0.001 HIS B 474 PHE 0.023 0.001 PHE B 817 TYR 0.024 0.002 TYR A 562 ARG 0.014 0.000 ARG B 135 ********************** 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 182 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 309 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7310 (ptm) REVERT: A 694 ASN cc_start: 0.6534 (OUTLIER) cc_final: 0.5942 (p0) REVERT: A 722 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: A 1006 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8351 (tt) REVERT: B 154 ASP cc_start: 0.6407 (OUTLIER) cc_final: 0.5927 (t0) REVERT: B 244 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6451 (mtt) REVERT: B 602 MET cc_start: 0.5909 (OUTLIER) cc_final: 0.5228 (ptm) outliers start: 28 outliers final: 20 residues processed: 172 average time/residue: 1.4657 time to fit residues: 275.5521 Evaluate side-chains 181 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 307 MET 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 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 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 486 VAL Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 720 LEU 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 1003 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1018 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 138 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 118 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.161151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.135011 restraints weight = 16313.224| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.90 r_work: 0.3554 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13932 Z= 0.176 Angle : 0.539 8.825 18888 Z= 0.274 Chirality : 0.043 0.157 2056 Planarity : 0.004 0.054 2468 Dihedral : 5.116 72.230 1862 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Rotamer: Outliers : 1.55 % Allowed : 21.47 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1688 helix: 1.59 (0.21), residues: 708 sheet: -0.21 (0.33), residues: 238 loop : -1.09 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 769 HIS 0.004 0.001 HIS B1002 PHE 0.027 0.001 PHE B 817 TYR 0.019 0.001 TYR B 562 ARG 0.012 0.000 ARG B 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5225.64 seconds wall clock time: 94 minutes 27.56 seconds (5667.56 seconds total)