Starting phenix.real_space_refine on Thu Jun 12 05:44:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgr_32485/06_2025/7wgr_32485.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgr_32485/06_2025/7wgr_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_32485/06_2025/7wgr_32485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgr_32485/06_2025/7wgr_32485.map" model { file = "/net/cci-nas-00/data/ceres_data/7wgr_32485/06_2025/7wgr_32485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgr_32485/06_2025/7wgr_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.97, per 1000 atoms: 0.66 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: 3.62 Conformation dependent library (CDL) restraints added in 1.9 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: 1.75 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: 5.19 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 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: 0.07 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.720 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.650 ------------------------------------------------------------------------------- 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 : 5.78 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 Details of bonding type rmsd hydrogen bonds : bond 0.17690 ( 556) hydrogen bonds : angle 5.91442 ( 1575) covalent geometry : bond 0.00677 (13932) covalent geometry : angle 0.98592 (18888) *********************** 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 : 1.530 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: 1.3870 time to fit residues: 382.5814 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 : 1.504 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.162327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135713 restraints weight = 16371.552| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.93 r_work: 0.3564 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1521 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= 0.151 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 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 556) hydrogen bonds : angle 4.50015 ( 1575) covalent geometry : bond 0.00358 (13932) covalent geometry : angle 0.57685 (18888) *********************** 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 : 1.513 Fit side-chains REVERT: A 223 MET cc_start: 0.7925 (tpt) cc_final: 0.7530 (tpt) REVERT: A 270 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7255 (ptt-90) REVERT: A 309 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7406 (ptm) REVERT: A 453 ARG cc_start: 0.7584 (tpm-80) cc_final: 0.7369 (tpm-80) REVERT: A 454 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7271 (mtt) REVERT: A 722 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: A 1006 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8136 (tt) REVERT: B 223 MET cc_start: 0.7956 (mmt) cc_final: 0.7719 (tpt) REVERT: B 323 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7533 (mpt-90) REVERT: B 722 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: B 1011 ASP cc_start: 0.6693 (m-30) cc_final: 0.6480 (m-30) outliers start: 42 outliers final: 10 residues processed: 213 average time/residue: 1.3603 time to fit residues: 315.1311 Evaluate side-chains 183 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 1.801 ------------------------------------------------------------------------------- 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 323 ARG 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 56 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 476 ASN ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** 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 = 0.3965 r_free = 0.3965 target = 0.160483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133986 restraints weight = 16516.841| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.92 r_work: 0.3541 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13932 Z= 0.146 Angle : 0.550 8.772 18888 Z= 0.283 Chirality : 0.044 0.138 2056 Planarity : 0.004 0.042 2468 Dihedral : 5.378 79.734 1864 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.76 % Allowed : 14.74 % Favored : 82.50 % 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: 0.09 (0.21), residues: 1688 helix: 1.41 (0.21), residues: 704 sheet: 0.12 (0.34), residues: 238 loop : -1.30 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 827 HIS 0.005 0.001 HIS B 840 PHE 0.018 0.001 PHE B 683 TYR 0.021 0.002 TYR A 562 ARG 0.006 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 556) hydrogen bonds : angle 4.29246 ( 1575) covalent geometry : bond 0.00351 (13932) covalent geometry : angle 0.55017 (18888) *********************** 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 219 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 1.473 Fit side-chains REVERT: A 223 MET cc_start: 0.7932 (tpt) cc_final: 0.7668 (tpt) REVERT: A 270 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7222 (ptt-90) REVERT: A 309 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7382 (ptm) REVERT: A 1006 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8112 (tt) REVERT: B 453 ARG cc_start: 0.7663 (tpm-80) cc_final: 0.7434 (tpm-80) REVERT: B 454 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7777 (mtt) REVERT: B 1007 GLN cc_start: 0.8377 (tp40) cc_final: 0.7857 (tp40) REVERT: B 1011 ASP cc_start: 0.6803 (m-30) cc_final: 0.6548 (m-30) outliers start: 41 outliers final: 15 residues processed: 200 average time/residue: 1.4440 time to fit residues: 313.8878 Evaluate side-chains 181 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 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 766 GLN Chi-restraints excluded: chain B residue 818 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 59 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** ** A 831 ASN ** 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 = 0.3969 r_free = 0.3969 target = 0.160824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.134485 restraints weight = 16338.267| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.92 r_work: 0.3548 rms_B_bonded: 2.60 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: 0.7954 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13932 Z= 0.131 Angle : 0.533 9.018 18888 Z= 0.272 Chirality : 0.043 0.137 2056 Planarity : 0.004 0.040 2468 Dihedral : 5.226 76.712 1864 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.42 % Allowed : 16.62 % Favored : 80.96 % 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: 0.14 (0.21), residues: 1688 helix: 1.45 (0.21), residues: 704 sheet: -0.04 (0.36), residues: 218 loop : -1.18 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 827 HIS 0.003 0.001 HIS B 840 PHE 0.039 0.001 PHE B 817 TYR 0.017 0.001 TYR B 562 ARG 0.007 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 556) hydrogen bonds : angle 4.23077 ( 1575) covalent geometry : bond 0.00318 (13932) covalent geometry : angle 0.53292 (18888) *********************** 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 210 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: A 223 MET cc_start: 0.7954 (tpt) cc_final: 0.7700 (tpt) REVERT: A 270 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7238 (ptt-90) REVERT: A 309 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7345 (ptm) REVERT: A 1006 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8139 (tt) REVERT: B 223 MET cc_start: 0.7800 (tpt) cc_final: 0.7461 (tpt) REVERT: B 454 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7730 (mtt) REVERT: B 1007 GLN cc_start: 0.8403 (tp40) cc_final: 0.7831 (tp40) REVERT: B 1011 ASP cc_start: 0.6680 (m-30) cc_final: 0.6424 (m-30) outliers start: 36 outliers final: 18 residues processed: 193 average time/residue: 1.4015 time to fit residues: 294.0898 Evaluate side-chains 177 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 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 771 ARG 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 307 MET 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 720 LEU 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 1008 ARG 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 136 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 93 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.132389 restraints weight = 16559.878| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.92 r_work: 0.3522 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2199 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= 0.161 Angle : 0.568 9.530 18888 Z= 0.291 Chirality : 0.045 0.140 2056 Planarity : 0.004 0.038 2468 Dihedral : 5.353 79.296 1862 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 2.96 % Allowed : 17.63 % Favored : 79.41 % 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 (0.21), residues: 702 sheet: -0.01 (0.34), residues: 238 loop : -1.33 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 769 HIS 0.005 0.001 HIS B 376 PHE 0.015 0.001 PHE B 683 TYR 0.022 0.002 TYR B 562 ARG 0.008 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 556) hydrogen bonds : angle 4.28504 ( 1575) covalent geometry : bond 0.00394 (13932) covalent geometry : angle 0.56827 (18888) *********************** 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 212 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6735 (tp30) cc_final: 0.6251 (mt-10) REVERT: A 223 MET cc_start: 0.7964 (tpt) cc_final: 0.7631 (tpt) REVERT: A 244 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6637 (mtt) REVERT: A 270 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7159 (ptt-90) REVERT: A 309 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7467 (ptm) REVERT: A 694 ASN cc_start: 0.6696 (OUTLIER) cc_final: 0.6014 (p0) REVERT: A 959 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: A 1006 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8091 (tt) REVERT: B 154 ASP cc_start: 0.6004 (OUTLIER) cc_final: 0.5424 (t0) REVERT: B 223 MET cc_start: 0.7840 (tpt) cc_final: 0.7442 (tpt) REVERT: B 453 ARG cc_start: 0.7581 (tpm-80) cc_final: 0.7325 (tpm-80) REVERT: B 454 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7730 (mtt) REVERT: B 722 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7828 (mp0) outliers start: 44 outliers final: 21 residues processed: 196 average time/residue: 1.3718 time to fit residues: 293.2431 Evaluate side-chains 184 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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 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 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 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 766 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 13 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 128 optimal weight: 0.0040 chunk 41 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- 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** B1002 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.159979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.133676 restraints weight = 16652.910| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.93 r_work: 0.3534 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2235 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= 0.131 Angle : 0.541 9.452 18888 Z= 0.276 Chirality : 0.044 0.136 2056 Planarity : 0.004 0.040 2468 Dihedral : 5.224 75.151 1862 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.67 % Favored : 96.21 % Rotamer: Outliers : 2.96 % Allowed : 18.10 % Favored : 78.94 % 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: 0.09 (0.21), residues: 1688 helix: 1.45 (0.20), residues: 706 sheet: -0.18 (0.35), residues: 218 loop : -1.22 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 769 HIS 0.003 0.001 HIS B1002 PHE 0.013 0.001 PHE A 839 TYR 0.021 0.001 TYR B 562 ARG 0.008 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 556) hydrogen bonds : angle 4.17610 ( 1575) covalent geometry : bond 0.00316 (13932) covalent geometry : angle 0.54101 (18888) *********************** 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 209 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 1.521 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6703 (tp30) cc_final: 0.6233 (mt-10) REVERT: A 223 MET cc_start: 0.7914 (tpt) cc_final: 0.7631 (tpt) REVERT: A 244 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6615 (mtt) REVERT: A 270 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7202 (ptt-90) REVERT: A 309 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7456 (ptm) REVERT: A 694 ASN cc_start: 0.6731 (OUTLIER) cc_final: 0.6034 (p0) REVERT: A 722 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: A 1006 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8135 (tt) REVERT: B 154 ASP cc_start: 0.5950 (OUTLIER) cc_final: 0.5350 (t0) REVERT: B 223 MET cc_start: 0.7824 (tpt) cc_final: 0.7497 (tpt) REVERT: B 281 GLU cc_start: 0.7352 (mp0) cc_final: 0.7104 (mp0) REVERT: B 454 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7721 (mtt) outliers start: 44 outliers final: 22 residues processed: 188 average time/residue: 1.4196 time to fit residues: 290.1142 Evaluate side-chains 184 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 299 GLU 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 607 THR Chi-restraints excluded: chain A residue 645 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 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 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 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 1008 ARG 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 56 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.160069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133767 restraints weight = 16568.639| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.91 r_work: 0.3538 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13932 Z= 0.132 Angle : 0.543 9.241 18888 Z= 0.277 Chirality : 0.044 0.136 2056 Planarity : 0.004 0.036 2468 Dihedral : 5.217 75.121 1862 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 3.10 % Allowed : 18.64 % Favored : 78.26 % 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: 0.10 (0.21), residues: 1688 helix: 1.48 (0.21), residues: 704 sheet: -0.16 (0.33), residues: 240 loop : -1.26 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 769 HIS 0.003 0.001 HIS B1002 PHE 0.013 0.001 PHE A 839 TYR 0.026 0.001 TYR B 562 ARG 0.011 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 556) hydrogen bonds : angle 4.12688 ( 1575) covalent geometry : bond 0.00321 (13932) covalent geometry : angle 0.54284 (18888) *********************** 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 209 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6729 (tp30) cc_final: 0.6306 (tm-30) REVERT: A 223 MET cc_start: 0.7933 (tpt) cc_final: 0.7621 (tpt) REVERT: A 244 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6628 (mtt) REVERT: A 263 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7993 (mmp-170) REVERT: A 270 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7187 (ptt-90) REVERT: A 309 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7413 (ptm) REVERT: A 694 ASN cc_start: 0.6762 (OUTLIER) cc_final: 0.6075 (p0) REVERT: A 722 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: A 959 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: A 1006 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8124 (tt) REVERT: B 154 ASP cc_start: 0.5995 (OUTLIER) cc_final: 0.5395 (t0) REVERT: B 211 GLU cc_start: 0.6613 (tp30) cc_final: 0.6244 (mt-10) REVERT: B 223 MET cc_start: 0.7835 (tpt) cc_final: 0.7531 (tpt) REVERT: B 281 GLU cc_start: 0.7311 (mp0) cc_final: 0.7073 (mp0) REVERT: B 453 ARG cc_start: 0.7549 (tpm-80) cc_final: 0.7338 (tpm-80) REVERT: B 454 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7761 (mtt) REVERT: B 722 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: B 766 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7038 (tp40) outliers start: 46 outliers final: 21 residues processed: 189 average time/residue: 1.3935 time to fit residues: 286.1855 Evaluate side-chains 189 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 263 ARG 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 607 THR Chi-restraints excluded: chain A residue 645 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 52 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 81 optimal weight: 0.3980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN B1002 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.160938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134830 restraints weight = 16474.133| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.90 r_work: 0.3551 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13932 Z= 0.120 Angle : 0.543 8.741 18888 Z= 0.274 Chirality : 0.043 0.135 2056 Planarity : 0.004 0.046 2468 Dihedral : 5.148 74.079 1862 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.45 % Rotamer: Outliers : 2.56 % Allowed : 19.78 % Favored : 77.66 % 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: 1.55 (0.21), residues: 702 sheet: -0.21 (0.35), residues: 218 loop : -1.13 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 769 HIS 0.003 0.001 HIS B1002 PHE 0.026 0.001 PHE A 683 TYR 0.025 0.001 TYR B 562 ARG 0.011 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 556) hydrogen bonds : angle 4.07485 ( 1575) covalent geometry : bond 0.00293 (13932) covalent geometry : angle 0.54279 (18888) *********************** 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 199 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 1.683 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6710 (tp30) cc_final: 0.6271 (tm-30) REVERT: A 223 MET cc_start: 0.7921 (tpt) cc_final: 0.7624 (tpt) REVERT: A 244 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6634 (mtt) REVERT: A 263 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8044 (mmp-170) REVERT: A 270 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7220 (ptt-90) REVERT: A 309 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7465 (ptm) REVERT: A 722 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: A 959 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: A 1006 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8144 (tt) REVERT: B 154 ASP cc_start: 0.5940 (OUTLIER) cc_final: 0.5365 (t0) REVERT: B 211 GLU cc_start: 0.6594 (tp30) cc_final: 0.6289 (mt-10) REVERT: B 223 MET cc_start: 0.7827 (tpt) cc_final: 0.7483 (tpt) REVERT: B 281 GLU cc_start: 0.7289 (mp0) cc_final: 0.7053 (mp0) REVERT: B 454 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7708 (mtt) REVERT: B 722 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7821 (mp0) outliers start: 38 outliers final: 19 residues processed: 182 average time/residue: 1.4600 time to fit residues: 288.4599 Evaluate side-chains 183 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 263 ARG 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 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 142 optimal weight: 0.4980 chunk 168 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 831 ASN B1002 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.162837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136794 restraints weight = 16354.960| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.90 r_work: 0.3577 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 13932 Z= 0.103 Angle : 0.523 8.273 18888 Z= 0.265 Chirality : 0.042 0.132 2056 Planarity : 0.004 0.046 2468 Dihedral : 5.014 70.890 1862 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 1.88 % Allowed : 20.46 % Favored : 77.66 % 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: 0.36 (0.21), residues: 1688 helix: 1.74 (0.21), residues: 692 sheet: -0.17 (0.35), residues: 220 loop : -1.03 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 827 HIS 0.004 0.001 HIS B1002 PHE 0.011 0.001 PHE A 839 TYR 0.024 0.001 TYR B 562 ARG 0.011 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 556) hydrogen bonds : angle 3.99515 ( 1575) covalent geometry : bond 0.00244 (13932) covalent geometry : angle 0.52270 (18888) *********************** 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: 28 poor density : 163 time to evaluate : 1.938 Fit side-chains revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7552 (mmm160) cc_final: 0.6894 (mtm110) REVERT: A 211 GLU cc_start: 0.6701 (tp30) cc_final: 0.6271 (tm-30) REVERT: A 244 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6598 (mtt) REVERT: A 263 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7988 (mmp-170) REVERT: A 309 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7336 (ptm) REVERT: A 694 ASN cc_start: 0.6751 (OUTLIER) cc_final: 0.6069 (p0) REVERT: A 716 CYS cc_start: 0.7938 (m) cc_final: 0.7720 (t) REVERT: A 722 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: A 959 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: A 1006 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8151 (tt) REVERT: B 154 ASP cc_start: 0.5894 (OUTLIER) cc_final: 0.5374 (t0) REVERT: B 211 GLU cc_start: 0.6523 (tp30) cc_final: 0.6257 (mt-10) REVERT: B 223 MET cc_start: 0.7810 (tpt) cc_final: 0.7424 (tpt) REVERT: B 263 ARG cc_start: 0.8188 (mpt180) cc_final: 0.7951 (mmp-170) REVERT: B 281 GLU cc_start: 0.7264 (mp0) cc_final: 0.7019 (mp0) REVERT: B 454 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7683 (mtt) outliers start: 28 outliers final: 10 residues processed: 178 average time/residue: 1.4872 time to fit residues: 288.6129 Evaluate side-chains 171 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 366 ILE 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 454 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 1008 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 52 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 946 GLN A1002 HIS B 425 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** B1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.133650 restraints weight = 16487.607| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.90 r_work: 0.3540 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13932 Z= 0.143 Angle : 0.568 8.792 18888 Z= 0.286 Chirality : 0.044 0.137 2056 Planarity : 0.004 0.055 2468 Dihedral : 5.188 75.592 1862 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 1.55 % Allowed : 21.06 % 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 (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: 0.22 (0.21), residues: 1688 helix: 1.54 (0.20), residues: 706 sheet: -0.14 (0.33), residues: 240 loop : -1.14 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 769 HIS 0.004 0.001 HIS B1002 PHE 0.021 0.001 PHE B 683 TYR 0.027 0.002 TYR B 562 ARG 0.011 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 556) hydrogen bonds : angle 4.09612 ( 1575) covalent geometry : bond 0.00351 (13932) covalent geometry : angle 0.56778 (18888) ********************** 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 178 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.731 Fit side-chains revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7623 (mmm160) cc_final: 0.6954 (mtm110) REVERT: A 211 GLU cc_start: 0.6705 (tp30) cc_final: 0.6291 (tm-30) REVERT: A 244 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6622 (mtt) REVERT: A 263 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.8020 (mmp-170) REVERT: A 309 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7479 (ptm) REVERT: A 694 ASN cc_start: 0.6838 (OUTLIER) cc_final: 0.6193 (p0) REVERT: A 722 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: A 959 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: A 1006 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8130 (tt) REVERT: B 154 ASP cc_start: 0.5917 (OUTLIER) cc_final: 0.5387 (t0) REVERT: B 211 GLU cc_start: 0.6569 (tp30) cc_final: 0.6296 (mt-10) REVERT: B 223 MET cc_start: 0.7848 (tpt) cc_final: 0.7505 (tpt) REVERT: B 263 ARG cc_start: 0.8164 (mpt180) cc_final: 0.7940 (mmp-170) REVERT: B 281 GLU cc_start: 0.7294 (mp0) cc_final: 0.7050 (mp0) REVERT: B 453 ARG cc_start: 0.7489 (tpm-80) cc_final: 0.7278 (tpm-80) REVERT: B 454 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7761 (mtt) outliers start: 23 outliers final: 13 residues processed: 171 average time/residue: 1.4880 time to fit residues: 276.2661 Evaluate side-chains 175 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 263 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 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 454 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 950 ASN Chi-restraints excluded: chain B residue 1003 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 60 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 946 GLN A1002 HIS B 425 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133524 restraints weight = 16545.800| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.91 r_work: 0.3534 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 13932 Z= 0.203 Angle : 0.818 59.194 18888 Z= 0.462 Chirality : 0.048 0.720 2056 Planarity : 0.005 0.053 2468 Dihedral : 5.257 75.561 1862 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 1.95 % Allowed : 20.66 % Favored : 77.39 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.53 (0.20), residues: 706 sheet: -0.14 (0.33), residues: 240 loop : -1.15 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 769 HIS 0.004 0.001 HIS B 474 PHE 0.014 0.001 PHE B 683 TYR 0.022 0.002 TYR B 562 ARG 0.012 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 556) hydrogen bonds : angle 4.09604 ( 1575) covalent geometry : bond 0.00473 (13932) covalent geometry : angle 0.81804 (18888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9782.09 seconds wall clock time: 167 minutes 24.83 seconds (10044.83 seconds total)