Starting phenix.real_space_refine on Sun Sep 13 03:47:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7egh_31117/09_2026/7egh_31117.cif Found real_map, /net/cci-nas-00/data/ceres_data/7egh_31117/09_2026/7egh_31117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7egh_31117/09_2026/7egh_31117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7egh_31117/09_2026/7egh_31117.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7egh_31117/09_2026/7egh_31117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7egh_31117/09_2026/7egh_31117.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 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: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 114 5.16 5 C 12790 2.51 5 N 3606 2.21 5 O 3943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20543 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5199 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 41, 'TRANS': 588} Chain breaks: 9 Chain: "B" Number of atoms: 7796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7796 Classifications: {'peptide': 963} Link IDs: {'PTRANS': 45, 'TRANS': 917} Chain breaks: 1 Chain: "F" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2006 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 14, 'TRANS': 252} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "G" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1171 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 2 Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 580 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 6, 'TRANS': 65} Chain: "X" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 918 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "Y" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 927 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "f" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1946 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 13, 'TRANS': 246} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 57 Time building chain proxies: 3.39, per 1000 atoms: 0.17 Number of scatterers: 20543 At special positions: 0 Unit cell: (141.37, 215.22, 142.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 90 15.00 O 3943 8.00 N 3606 7.00 C 12790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 945 " - pdb=" SG CYS B 986 " distance=2.23 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 633.4 milliseconds 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 15 sheets defined 51.3% alpha, 14.6% beta 45 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 569 through 574 removed outlier: 3.637A pdb=" N TYR A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 640 through 657 Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.032A pdb=" N THR A 672 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 817 Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.980A pdb=" N ILE A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 848 removed outlier: 3.625A pdb=" N ILE A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 removed outlier: 3.857A pdb=" N VAL A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 901 Processing helix chain 'A' and resid 925 through 929 Processing helix chain 'A' and resid 930 through 944 Processing helix chain 'A' and resid 993 through 998 Processing helix chain 'A' and resid 998 through 1011 removed outlier: 3.862A pdb=" N ASN A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1019 removed outlier: 3.528A pdb=" N ILE A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1035 Processing helix chain 'A' and resid 1055 through 1079 Processing helix chain 'A' and resid 1187 through 1204 removed outlier: 3.599A pdb=" N ILE A1197 " --> pdb=" O ALA A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1242 Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.736A pdb=" N PHE B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 185 through 189 removed outlier: 3.547A pdb=" N PHE B 188 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 273 through 281 Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.717A pdb=" N VAL B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 295 " --> pdb=" O TYR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 366 through 409 removed outlier: 4.079A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N ASN B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.559A pdb=" N LEU B 441 " --> pdb=" O PRO B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 464 Processing helix chain 'B' and resid 465 through 484 Processing helix chain 'B' and resid 492 through 495 removed outlier: 3.541A pdb=" N GLN B 495 " --> pdb=" O MET B 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 595 through 600 removed outlier: 3.821A pdb=" N ASN B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 600 " --> pdb=" O SER B 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 595 through 600' Processing helix chain 'B' and resid 645 through 656 removed outlier: 3.799A pdb=" N GLU B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 669 Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 674 through 686 Processing helix chain 'B' and resid 691 through 709 removed outlier: 3.542A pdb=" N ARG B 695 " --> pdb=" O PHE B 691 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 728 removed outlier: 3.722A pdb=" N CYS B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 758 Proline residue: B 754 - end of helix Processing helix chain 'B' and resid 768 through 781 removed outlier: 3.533A pdb=" N THR B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 805 removed outlier: 3.508A pdb=" N SER B 805 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 843 removed outlier: 4.204A pdb=" N LEU B 828 " --> pdb=" O PRO B 824 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 829 " --> pdb=" O ASP B 825 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 842 " --> pdb=" O ASN B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 864 Processing helix chain 'B' and resid 871 through 878 Processing helix chain 'B' and resid 883 through 901 Processing helix chain 'B' and resid 903 through 916 removed outlier: 3.521A pdb=" N LEU B 907 " --> pdb=" O SER B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 933 Processing helix chain 'B' and resid 946 through 959 removed outlier: 3.561A pdb=" N VAL B 950 " --> pdb=" O ASN B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 980 Processing helix chain 'F' and resid 217 through 231 Processing helix chain 'F' and resid 235 through 249 Processing helix chain 'F' and resid 250 through 253 removed outlier: 4.354A pdb=" N TYR F 253 " --> pdb=" O PRO F 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 250 through 253' Processing helix chain 'F' and resid 255 through 270 Processing helix chain 'F' and resid 275 through 291 Processing helix chain 'F' and resid 300 through 314 Proline residue: F 306 - end of helix Processing helix chain 'F' and resid 323 through 344 Processing helix chain 'F' and resid 351 through 364 Processing helix chain 'F' and resid 369 through 382 Processing helix chain 'F' and resid 384 through 391 removed outlier: 4.249A pdb=" N ILE F 388 " --> pdb=" O GLY F 384 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS F 389 " --> pdb=" O HIS F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 395 through 409 Processing helix chain 'F' and resid 415 through 438 Proline residue: F 433 - end of helix removed outlier: 3.540A pdb=" N LEU F 438 " --> pdb=" O VAL F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 452 removed outlier: 3.597A pdb=" N PHE F 452 " --> pdb=" O ARG F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 473 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 37 through 42 removed outlier: 3.678A pdb=" N ASP G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 176 Processing helix chain 'H' and resid 171 through 197 Processing helix chain 'H' and resid 221 through 228 removed outlier: 4.264A pdb=" N THR H 225 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'f' and resid 217 through 231 removed outlier: 3.543A pdb=" N CYS f 231 " --> pdb=" O ILE f 227 " (cutoff:3.500A) Processing helix chain 'f' and resid 235 through 248 removed outlier: 3.630A pdb=" N ARG f 239 " --> pdb=" O CYS f 235 " (cutoff:3.500A) Processing helix chain 'f' and resid 255 through 269 Processing helix chain 'f' and resid 275 through 291 removed outlier: 3.526A pdb=" N LEU f 279 " --> pdb=" O ASN f 275 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP f 291 " --> pdb=" O LYS f 287 " (cutoff:3.500A) Processing helix chain 'f' and resid 300 through 314 removed outlier: 3.633A pdb=" N LEU f 304 " --> pdb=" O TYR f 300 " (cutoff:3.500A) Proline residue: f 306 - end of helix Processing helix chain 'f' and resid 325 through 341 removed outlier: 4.120A pdb=" N LEU f 329 " --> pdb=" O ASN f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 350 through 364 Processing helix chain 'f' and resid 369 through 384 removed outlier: 4.055A pdb=" N GLY f 384 " --> pdb=" O LEU f 380 " (cutoff:3.500A) Processing helix chain 'f' and resid 384 through 391 removed outlier: 3.544A pdb=" N ILE f 388 " --> pdb=" O GLY f 384 " (cutoff:3.500A) Processing helix chain 'f' and resid 392 through 396 removed outlier: 3.689A pdb=" N LEU f 396 " --> pdb=" O LEU f 393 " (cutoff:3.500A) Processing helix chain 'f' and resid 397 through 404 removed outlier: 3.693A pdb=" N GLU f 401 " --> pdb=" O GLN f 397 " (cutoff:3.500A) Processing helix chain 'f' and resid 415 through 438 removed outlier: 3.825A pdb=" N GLY f 419 " --> pdb=" O ILE f 415 " (cutoff:3.500A) Proline residue: f 433 - end of helix Processing helix chain 'f' and resid 445 through 450 Processing helix chain 'f' and resid 454 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 786 through 787 removed outlier: 6.509A pdb=" N LEU A 680 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 782 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU A 682 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL G 73 " --> pdb=" O TYR A 683 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU G 43 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR A 771 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLN G 15 " --> pdb=" O GLN G 93 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LEU G 95 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE G 17 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER G 97 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG G 19 " --> pdb=" O SER G 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 786 through 787 removed outlier: 6.509A pdb=" N LEU A 680 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 782 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU A 682 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL G 73 " --> pdb=" O TYR A 683 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LYS G 66 " --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N THR G 98 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL G 68 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL G 96 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU G 70 " --> pdb=" O MET G 94 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N MET G 94 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N CYS G 72 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N CYS G 92 " --> pdb=" O CYS G 72 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET G 74 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP G 90 " --> pdb=" O MET G 74 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER G 76 " --> pdb=" O THR G 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 786 through 787 removed outlier: 4.290A pdb=" N GLN A 741 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU A 754 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 12.853A pdb=" N LEU A 739 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 825 removed outlier: 3.732A pdb=" N TRP A 861 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 947 through 948 Processing sheet with id=AA6, first strand: chain 'A' and resid 1180 through 1185 removed outlier: 3.613A pdb=" N LYS A1166 " --> pdb=" O GLU G 182 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G 182 " --> pdb=" O LYS A1166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 80 through 81 removed outlier: 5.552A pdb=" N ILE B 72 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER B 151 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 74 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL B 46 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN B 37 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N PHE B 48 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE B 35 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLU B 50 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL B 33 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR B 52 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN B 31 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N PHE B 54 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR B 29 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N THR B 201 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 29 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LYS B 203 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN B 31 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU B 205 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 33 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N THR B 207 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE B 35 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ASP B 209 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N ASN B 37 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS B 200 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 240 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 222 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET B 237 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU B 220 " --> pdb=" O MET B 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 65 removed outlier: 4.055A pdb=" N ALA B 83 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 162 removed outlier: 5.758A pdb=" N LEU B 249 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 255 through 258 removed outlier: 6.354A pdb=" N LYS B 305 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE B 325 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL B 307 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET B 322 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 360 through 361 removed outlier: 6.559A pdb=" N SER B 360 " --> pdb=" O VAL B 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 587 through 591 removed outlier: 4.570A pdb=" N PHE B 535 " --> pdb=" O GLU B 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 573 through 580 removed outlier: 7.404A pdb=" N LYS B 565 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE B 630 " --> pdb=" O LYS B 565 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR B 567 " --> pdb=" O ILE B 628 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE B 628 " --> pdb=" O THR B 567 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN B 569 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 604 through 605 Processing sheet with id=AB6, first strand: chain 'H' and resid 200 through 201 954 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 117 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3176 1.31 - 1.43: 6045 1.43 - 1.56: 11603 1.56 - 1.69: 180 1.69 - 1.81: 178 Bond restraints: 21182 Sorted by residual: bond pdb=" C ASN B 61 " pdb=" O ASN B 61 " ideal model delta sigma weight residual 1.239 1.181 0.058 9.60e-03 1.09e+04 3.63e+01 bond pdb=" C ARG F 395 " pdb=" O ARG F 395 " ideal model delta sigma weight residual 1.237 1.315 -0.078 1.39e-02 5.18e+03 3.15e+01 bond pdb=" CA SER B 903 " pdb=" CB SER B 903 " ideal model delta sigma weight residual 1.528 1.456 0.073 1.49e-02 4.50e+03 2.39e+01 bond pdb=" CA SER f 217 " pdb=" CB SER f 217 " ideal model delta sigma weight residual 1.528 1.453 0.075 1.54e-02 4.22e+03 2.38e+01 bond pdb=" N ARG F 395 " pdb=" CA ARG F 395 " ideal model delta sigma weight residual 1.458 1.516 -0.058 1.22e-02 6.72e+03 2.28e+01 ... (remaining 21177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 26874 2.28 - 4.55: 1939 4.55 - 6.83: 192 6.83 - 9.11: 43 9.11 - 11.38: 13 Bond angle restraints: 29061 Sorted by residual: angle pdb=" N HIS B 491 " pdb=" CA HIS B 491 " pdb=" C HIS B 491 " ideal model delta sigma weight residual 111.28 100.96 10.32 1.09e+00 8.42e-01 8.97e+01 angle pdb=" N VAL F 271 " pdb=" CA VAL F 271 " pdb=" C VAL F 271 " ideal model delta sigma weight residual 112.90 106.03 6.87 9.60e-01 1.09e+00 5.13e+01 angle pdb=" N PRO A 715 " pdb=" CA PRO A 715 " pdb=" C PRO A 715 " ideal model delta sigma weight residual 111.03 100.08 10.95 1.54e+00 4.22e-01 5.06e+01 angle pdb=" N GLN B 495 " pdb=" CA GLN B 495 " pdb=" C GLN B 495 " ideal model delta sigma weight residual 113.28 104.69 8.59 1.22e+00 6.72e-01 4.96e+01 angle pdb=" N LEU A 396 " pdb=" CA LEU A 396 " pdb=" C LEU A 396 " ideal model delta sigma weight residual 113.16 104.83 8.33 1.24e+00 6.50e-01 4.51e+01 ... (remaining 29056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.02: 11625 30.02 - 60.03: 948 60.03 - 90.05: 27 90.05 - 120.07: 1 120.07 - 150.09: 1 Dihedral angle restraints: 12602 sinusoidal: 5714 harmonic: 6888 Sorted by residual: dihedral pdb=" C THR F 310 " pdb=" N THR F 310 " pdb=" CA THR F 310 " pdb=" CB THR F 310 " ideal model delta harmonic sigma weight residual -122.00 -140.15 18.15 0 2.50e+00 1.60e-01 5.27e+01 dihedral pdb=" C GLN A1067 " pdb=" N GLN A1067 " pdb=" CA GLN A1067 " pdb=" CB GLN A1067 " ideal model delta harmonic sigma weight residual -122.60 -140.12 17.52 0 2.50e+00 1.60e-01 4.91e+01 dihedral pdb=" N GLN A1067 " pdb=" C GLN A1067 " pdb=" CA GLN A1067 " pdb=" CB GLN A1067 " ideal model delta harmonic sigma weight residual 122.80 138.94 -16.14 0 2.50e+00 1.60e-01 4.17e+01 ... (remaining 12599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2885 0.132 - 0.263: 316 0.263 - 0.395: 33 0.395 - 0.527: 4 0.527 - 0.659: 3 Chirality restraints: 3241 Sorted by residual: chirality pdb=" CA GLN A1067 " pdb=" N GLN A1067 " pdb=" C GLN A1067 " pdb=" CB GLN A1067 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA THR F 310 " pdb=" N THR F 310 " pdb=" C THR F 310 " pdb=" CB THR F 310 " both_signs ideal model delta sigma weight residual False 2.53 1.90 0.62 2.00e-01 2.50e+01 9.74e+00 chirality pdb=" CA ARG F 268 " pdb=" N ARG F 268 " pdb=" C ARG F 268 " pdb=" CB ARG F 268 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.31e+00 ... (remaining 3238 not shown) Planarity restraints: 3397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 969 " -0.028 2.00e-02 2.50e+03 5.75e-02 3.30e+01 pdb=" C PRO A 969 " 0.099 2.00e-02 2.50e+03 pdb=" O PRO A 969 " -0.039 2.00e-02 2.50e+03 pdb=" N ASN A 970 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 263 " -0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C ILE F 263 " 0.085 2.00e-02 2.50e+03 pdb=" O ILE F 263 " -0.032 2.00e-02 2.50e+03 pdb=" N SER F 264 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 260 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C PRO B 260 " -0.076 2.00e-02 2.50e+03 pdb=" O PRO B 260 " 0.028 2.00e-02 2.50e+03 pdb=" N TYR B 261 " 0.026 2.00e-02 2.50e+03 ... (remaining 3394 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2242 2.74 - 3.28: 18838 3.28 - 3.82: 35103 3.82 - 4.36: 42782 4.36 - 4.90: 69789 Nonbonded interactions: 168754 Sorted by model distance: nonbonded pdb=" N ASN A 970 " pdb=" OD1 ASN A 970 " model vdw 2.206 3.120 nonbonded pdb=" O CYS A 725 " pdb=" SG CYS A 725 " model vdw 2.219 3.400 nonbonded pdb=" O LYS G 129 " pdb=" NZ LYS G 129 " model vdw 2.228 3.120 nonbonded pdb=" O GLN f 352 " pdb=" OG1 THR f 356 " model vdw 2.247 3.040 nonbonded pdb=" O PRO A 931 " pdb=" OG1 THR A 935 " model vdw 2.255 3.040 ... (remaining 168749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and resid 214 through 473) selection = chain 'f' } 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: 11.020 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.330 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.197 21183 Z= 0.595 Angle : 1.260 38.137 29063 Z= 0.856 Chirality : 0.086 0.659 3241 Planarity : 0.008 0.075 3397 Dihedral : 18.684 150.086 8111 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 5.07 % Allowed : 9.54 % Favored : 85.39 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.16), residues: 2300 helix: -1.12 (0.14), residues: 1110 sheet: -1.14 (0.30), residues: 271 loop : -1.78 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG F 335 TYR 0.019 0.002 TYR H 223 PHE 0.035 0.003 PHE B 190 TRP 0.029 0.003 TRP A 416 HIS 0.014 0.002 HIS F 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00928 / 0.59 (21182) covalent geometry : angle 1.22743 / 0.85 (29061) SS BOND : bond 0.19687 / 10.36 ( 1) SS BOND : angle 34.11467 / 19.30 ( 2) hydrogen bonds : bond 0.14179 / 9.31 ( 1048) hydrogen bonds : angle 6.42313 / 4.46 ( 2961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 373 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: A 653 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6925 (mt-10) REVERT: A 691 MET cc_start: 0.8230 (tpp) cc_final: 0.7785 (tpp) REVERT: A 744 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6918 (tp30) REVERT: A 786 CYS cc_start: 0.7758 (m) cc_final: 0.7359 (m) REVERT: A 821 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.5584 (tpp-160) REVERT: A 943 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8316 (mtmm) REVERT: A 1058 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6524 (t-170) REVERT: A 1071 ASP cc_start: 0.7620 (t0) cc_final: 0.7193 (m-30) REVERT: B 41 GLN cc_start: 0.7660 (mp10) cc_final: 0.7429 (mp10) REVERT: B 71 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6798 (ttt-90) REVERT: B 80 LEU cc_start: 0.7970 (mt) cc_final: 0.7713 (mt) REVERT: B 120 ASP cc_start: 0.7287 (m-30) cc_final: 0.6676 (m-30) REVERT: B 137 HIS cc_start: 0.7448 (t70) cc_final: 0.7083 (t70) REVERT: B 145 LYS cc_start: 0.8296 (mttt) cc_final: 0.7684 (mtpp) REVERT: B 156 LYS cc_start: 0.8370 (mttm) cc_final: 0.8141 (mttm) REVERT: B 205 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7643 (mp0) REVERT: B 212 MET cc_start: 0.8399 (mtt) cc_final: 0.8140 (mtt) REVERT: B 262 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8012 (mtm) REVERT: B 264 GLU cc_start: 0.7282 (pm20) cc_final: 0.6950 (pm20) REVERT: B 337 ASP cc_start: 0.7706 (t0) cc_final: 0.7496 (t0) REVERT: B 437 HIS cc_start: 0.7543 (t-90) cc_final: 0.6740 (m90) REVERT: B 448 MET cc_start: 0.8851 (mmt) cc_final: 0.8500 (mmt) REVERT: B 520 LYS cc_start: 0.8396 (tttt) cc_final: 0.8092 (ttmm) REVERT: B 582 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7242 (mt-10) REVERT: B 615 ASP cc_start: 0.7793 (t0) cc_final: 0.7502 (t0) REVERT: B 639 LYS cc_start: 0.8333 (tttm) cc_final: 0.7976 (tttt) REVERT: B 640 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8809 (t) REVERT: B 641 GLU cc_start: 0.7600 (mp0) cc_final: 0.7315 (mp0) REVERT: B 648 MET cc_start: 0.8580 (mtt) cc_final: 0.8368 (mtp) REVERT: B 683 ASP cc_start: 0.7976 (m-30) cc_final: 0.7387 (m-30) REVERT: B 765 ASN cc_start: 0.7867 (m110) cc_final: 0.7363 (m-40) REVERT: B 785 ARG cc_start: 0.8571 (mtm180) cc_final: 0.8303 (mtm-85) REVERT: B 798 MET cc_start: 0.7476 (mmm) cc_final: 0.7215 (mtp) REVERT: B 892 GLU cc_start: 0.8178 (tt0) cc_final: 0.7917 (tt0) REVERT: F 236 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6512 (tm-30) REVERT: F 254 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7580 (tm-30) REVERT: F 295 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7776 (pp) REVERT: F 296 TYR cc_start: 0.7358 (t80) cc_final: 0.7150 (t80) REVERT: F 298 GLU cc_start: 0.7418 (pm20) cc_final: 0.7165 (pt0) REVERT: F 352 GLN cc_start: 0.8290 (tt0) cc_final: 0.8074 (mp10) REVERT: F 391 LEU cc_start: 0.8083 (tp) cc_final: 0.7850 (tt) REVERT: F 398 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8332 (tp-100) REVERT: G 14 SER cc_start: 0.7748 (t) cc_final: 0.7260 (p) REVERT: G 46 GLU cc_start: 0.6887 (tt0) cc_final: 0.6266 (tt0) REVERT: G 66 LYS cc_start: 0.5673 (mtmt) cc_final: 0.5473 (mttm) REVERT: G 69 ASP cc_start: 0.6914 (m-30) cc_final: 0.6671 (m-30) REVERT: G 75 GLU cc_start: 0.8284 (pt0) cc_final: 0.7818 (pt0) REVERT: G 98 THR cc_start: 0.7775 (m) cc_final: 0.7542 (p) REVERT: G 153 LYS cc_start: 0.3636 (OUTLIER) cc_final: 0.3035 (tptt) REVERT: H 177 GLU cc_start: 0.7660 (tp30) cc_final: 0.7387 (tp30) REVERT: H 178 LYS cc_start: 0.7285 (mmtp) cc_final: 0.7031 (mmmm) REVERT: f 215 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: f 238 LYS cc_start: 0.8293 (mtpt) cc_final: 0.7731 (mttt) REVERT: f 389 LYS cc_start: 0.8218 (mtpt) cc_final: 0.7930 (mtpp) outliers start: 103 outliers final: 21 residues processed: 451 average time/residue: 0.1668 time to fit residues: 110.0958 Evaluate side-chains 292 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 416 TRP Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1073 GLN Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 182 GLU Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 326 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.0270 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN A 505 ASN A 508 ASN A 590 GLN A 860 ASN A 896 GLN A1238 GLN B 30 HIS B 69 GLN B 137 HIS B 176 HIS B 183 GLN B 235 HIS B 348 GLN B 432 HIS B 439 HIS B 450 GLN B 509 ASN B 521 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN B 813 ASN B 882 HIS B 908 GLN B 916 ASN B 952 GLN F 221 GLN F 270 ASN F 422 HIS G 48 HIS f 343 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.165030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112377 restraints weight = 28503.554| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.32 r_work: 0.3049 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21183 Z= 0.174 Angle : 0.666 7.582 29063 Z= 0.360 Chirality : 0.044 0.253 3241 Planarity : 0.005 0.054 3397 Dihedral : 18.774 152.066 3582 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.25 % Allowed : 12.25 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.17), residues: 2300 helix: 0.10 (0.15), residues: 1120 sheet: -0.85 (0.30), residues: 265 loop : -1.46 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1233 TYR 0.013 0.001 TYR A1194 PHE 0.025 0.002 PHE B 190 TRP 0.024 0.002 TRP A 341 HIS 0.009 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (21182) covalent geometry : angle 0.66556 / 0.36 (29061) SS BOND : bond 0.00395 / 0.21 ( 1) SS BOND : angle 2.85807 / 1.53 ( 2) hydrogen bonds : bond 0.04913 / 3.20 ( 1048) hydrogen bonds : angle 4.65492 / 3.22 ( 2961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 282 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.4917 (tmm160) REVERT: A 400 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6877 (tp30) REVERT: A 481 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: A 511 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7152 (mt) REVERT: A 625 PHE cc_start: 0.8097 (p90) cc_final: 0.7839 (p90) REVERT: A 691 MET cc_start: 0.8866 (tpp) cc_final: 0.8514 (tpp) REVERT: A 692 MET cc_start: 0.8964 (mtp) cc_final: 0.8732 (mtm) REVERT: A 744 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7857 (tp30) REVERT: A 786 CYS cc_start: 0.8572 (m) cc_final: 0.8308 (m) REVERT: A 945 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7160 (mtpp) REVERT: A 1058 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.6998 (t-170) REVERT: A 1061 ARG cc_start: 0.8055 (ttp-110) cc_final: 0.7702 (mtm110) REVERT: A 1071 ASP cc_start: 0.7921 (t0) cc_final: 0.7665 (m-30) REVERT: A 1073 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: A 1233 ARG cc_start: 0.9085 (ttp-110) cc_final: 0.8662 (ptt-90) REVERT: B 71 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7702 (ttt90) REVERT: B 80 LEU cc_start: 0.8598 (mt) cc_final: 0.8397 (mt) REVERT: B 120 ASP cc_start: 0.7967 (m-30) cc_final: 0.7348 (m-30) REVERT: B 145 LYS cc_start: 0.8817 (mttt) cc_final: 0.8345 (mtpp) REVERT: B 212 MET cc_start: 0.8861 (mtt) cc_final: 0.8620 (mtt) REVERT: B 262 MET cc_start: 0.8471 (ttm) cc_final: 0.8223 (mtm) REVERT: B 295 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8164 (mt) REVERT: B 437 HIS cc_start: 0.8038 (t-90) cc_final: 0.7807 (m90) REVERT: B 448 MET cc_start: 0.9376 (mmt) cc_final: 0.9058 (mmt) REVERT: B 492 MET cc_start: 0.8287 (mmm) cc_final: 0.8038 (mmt) REVERT: B 520 LYS cc_start: 0.8914 (tttt) cc_final: 0.8672 (ttmm) REVERT: B 582 GLU cc_start: 0.8214 (mt-10) cc_final: 0.8011 (mt-10) REVERT: B 615 ASP cc_start: 0.8392 (t0) cc_final: 0.8140 (t0) REVERT: B 639 LYS cc_start: 0.9032 (tttm) cc_final: 0.8647 (tttt) REVERT: B 640 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.9135 (t) REVERT: B 641 GLU cc_start: 0.8326 (mp0) cc_final: 0.8118 (mp0) REVERT: B 683 ASP cc_start: 0.8592 (m-30) cc_final: 0.8159 (m-30) REVERT: B 798 MET cc_start: 0.8826 (mmm) cc_final: 0.8451 (mtp) REVERT: B 892 GLU cc_start: 0.9039 (tt0) cc_final: 0.8826 (mt-10) REVERT: B 916 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8722 (p0) REVERT: F 259 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7707 (t80) REVERT: F 295 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7630 (pp) REVERT: F 327 TRP cc_start: 0.4889 (OUTLIER) cc_final: 0.4439 (t-100) REVERT: F 335 ARG cc_start: 0.7427 (ptt-90) cc_final: 0.7154 (ptt-90) REVERT: F 352 GLN cc_start: 0.8780 (tt0) cc_final: 0.8284 (mp10) REVERT: F 382 GLU cc_start: 0.7565 (tp30) cc_final: 0.6786 (tp30) REVERT: F 391 LEU cc_start: 0.8412 (tp) cc_final: 0.8066 (tt) REVERT: F 398 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8230 (tp-100) REVERT: H 177 GLU cc_start: 0.8442 (tp30) cc_final: 0.8095 (tp30) REVERT: H 178 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8185 (mmmm) REVERT: f 238 LYS cc_start: 0.8862 (mtpt) cc_final: 0.8612 (mtmt) REVERT: f 270 ASN cc_start: 0.5180 (OUTLIER) cc_final: 0.4088 (t0) REVERT: f 365 ASP cc_start: 0.8394 (t0) cc_final: 0.8105 (t0) REVERT: f 389 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7854 (mtpp) outliers start: 66 outliers final: 30 residues processed: 334 average time/residue: 0.1609 time to fit residues: 79.8966 Evaluate side-chains 298 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 945 LYS Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1073 GLN Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 259 PHE Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain G residue 24 TYR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Chi-restraints excluded: chain f residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 147 optimal weight: 0.1980 chunk 88 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 chunk 186 optimal weight: 0.0570 chunk 19 optimal weight: 0.6980 chunk 139 optimal weight: 0.0770 chunk 217 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 221 optimal weight: 0.6980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN A1058 HIS B 59 ASN B 415 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 GLN B 916 ASN F 343 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.165526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113699 restraints weight = 28560.747| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.28 r_work: 0.3068 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21183 Z= 0.141 Angle : 0.589 7.536 29063 Z= 0.319 Chirality : 0.042 0.267 3241 Planarity : 0.004 0.042 3397 Dihedral : 18.542 152.189 3552 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.49 % Allowed : 13.48 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2300 helix: 0.67 (0.15), residues: 1122 sheet: -0.65 (0.30), residues: 270 loop : -1.30 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 207 TYR 0.034 0.001 TYR F 281 PHE 0.021 0.001 PHE B 190 TRP 0.015 0.001 TRP A 341 HIS 0.008 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (21182) covalent geometry : angle 0.58873 / 0.32 (29061) SS BOND : bond 0.00666 / 0.35 ( 1) SS BOND : angle 2.32754 / 1.23 ( 2) hydrogen bonds : bond 0.04035 / 2.62 ( 1048) hydrogen bonds : angle 4.36498 / 3.01 ( 2961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 281 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6904 (tp30) REVERT: A 404 MET cc_start: 0.8572 (mmm) cc_final: 0.7930 (mmm) REVERT: A 481 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: A 511 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7141 (mt) REVERT: A 625 PHE cc_start: 0.8100 (p90) cc_final: 0.7811 (p90) REVERT: A 639 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7397 (pp) REVERT: A 691 MET cc_start: 0.8803 (tpp) cc_final: 0.8410 (tpp) REVERT: A 692 MET cc_start: 0.8937 (mtp) cc_final: 0.8554 (mtm) REVERT: A 744 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7804 (tp30) REVERT: A 786 CYS cc_start: 0.8522 (m) cc_final: 0.8253 (m) REVERT: A 945 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7202 (mtpp) REVERT: A 1058 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.6732 (t70) REVERT: B 41 GLN cc_start: 0.8209 (mp10) cc_final: 0.7961 (mp10) REVERT: B 80 LEU cc_start: 0.8559 (mt) cc_final: 0.8359 (mt) REVERT: B 120 ASP cc_start: 0.7965 (m-30) cc_final: 0.7322 (m-30) REVERT: B 145 LYS cc_start: 0.8798 (mttt) cc_final: 0.8285 (mtpp) REVERT: B 212 MET cc_start: 0.8859 (mtt) cc_final: 0.8615 (mtt) REVERT: B 262 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8242 (mtm) REVERT: B 295 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8094 (mt) REVERT: B 298 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.7969 (mmt-90) REVERT: B 437 HIS cc_start: 0.8032 (t-90) cc_final: 0.7765 (m90) REVERT: B 448 MET cc_start: 0.9393 (mmt) cc_final: 0.9074 (mmt) REVERT: B 492 MET cc_start: 0.8266 (mmm) cc_final: 0.8006 (mmt) REVERT: B 520 LYS cc_start: 0.8943 (tttt) cc_final: 0.8656 (ttmm) REVERT: B 615 ASP cc_start: 0.8398 (t0) cc_final: 0.8175 (t0) REVERT: B 625 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8650 (pp) REVERT: B 798 MET cc_start: 0.8761 (mmm) cc_final: 0.8378 (mtp) REVERT: B 892 GLU cc_start: 0.9002 (tt0) cc_final: 0.8738 (mt-10) REVERT: F 252 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7708 (tt) REVERT: F 259 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7679 (t80) REVERT: F 281 TYR cc_start: 0.7336 (m-80) cc_final: 0.7009 (m-80) REVERT: F 287 LYS cc_start: 0.8772 (tptp) cc_final: 0.8148 (ttmt) REVERT: F 295 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7582 (pp) REVERT: F 327 TRP cc_start: 0.4826 (OUTLIER) cc_final: 0.4407 (t-100) REVERT: F 335 ARG cc_start: 0.7300 (ptt-90) cc_final: 0.7025 (ptt-90) REVERT: F 342 LYS cc_start: 0.8994 (pttt) cc_final: 0.8747 (tttt) REVERT: F 352 GLN cc_start: 0.8739 (tt0) cc_final: 0.8383 (mp10) REVERT: F 382 GLU cc_start: 0.7542 (tp30) cc_final: 0.6676 (tp30) REVERT: F 389 LYS cc_start: 0.8492 (tptm) cc_final: 0.8042 (tppt) REVERT: F 391 LEU cc_start: 0.8405 (tp) cc_final: 0.8039 (tt) REVERT: F 398 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8251 (tp-100) REVERT: G 46 GLU cc_start: 0.7422 (tt0) cc_final: 0.6760 (tt0) REVERT: G 153 LYS cc_start: 0.5376 (OUTLIER) cc_final: 0.3342 (tptt) REVERT: H 177 GLU cc_start: 0.8465 (tp30) cc_final: 0.8134 (tp30) REVERT: H 178 LYS cc_start: 0.8538 (mmtp) cc_final: 0.8107 (mmmm) REVERT: f 238 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8561 (mtmt) REVERT: f 249 ASP cc_start: 0.8115 (m-30) cc_final: 0.7904 (m-30) REVERT: f 270 ASN cc_start: 0.5028 (OUTLIER) cc_final: 0.3862 (t0) REVERT: f 365 ASP cc_start: 0.8430 (t0) cc_final: 0.8086 (t0) REVERT: f 389 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7757 (mtpp) outliers start: 71 outliers final: 37 residues processed: 334 average time/residue: 0.1729 time to fit residues: 85.8061 Evaluate side-chains 314 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 945 LYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 764 HIS Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 259 PHE Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 chunk 157 optimal weight: 0.0980 chunk 235 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 137 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 GLN B 916 ASN F 343 HIS H 201 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.163425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110644 restraints weight = 28454.918| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.30 r_work: 0.3037 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21183 Z= 0.200 Angle : 0.605 8.035 29063 Z= 0.326 Chirality : 0.043 0.263 3241 Planarity : 0.004 0.043 3397 Dihedral : 18.472 152.975 3542 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.13 % Allowed : 14.51 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2300 helix: 0.91 (0.15), residues: 1121 sheet: -0.49 (0.30), residues: 274 loop : -1.20 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 320 TYR 0.027 0.001 TYR F 281 PHE 0.033 0.002 PHE F 344 TRP 0.017 0.002 TRP A 341 HIS 0.015 0.001 HIS F 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (21182) covalent geometry : angle 0.60489 / 0.33 (29061) SS BOND : bond 0.00774 / 0.41 ( 1) SS BOND : angle 2.21935 / 1.19 ( 2) hydrogen bonds : bond 0.04124 / 2.68 ( 1048) hydrogen bonds : angle 4.27832 / 2.96 ( 2961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 267 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7042 (tp30) REVERT: A 404 MET cc_start: 0.8602 (mmm) cc_final: 0.7948 (mmm) REVERT: A 481 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: A 511 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7195 (mt) REVERT: A 639 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7462 (pp) REVERT: A 692 MET cc_start: 0.8944 (mtp) cc_final: 0.8472 (mtm) REVERT: A 744 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7783 (tp30) REVERT: A 945 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7212 (mtpp) REVERT: A 1058 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.6488 (t70) REVERT: B 71 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7712 (ttt90) REVERT: B 120 ASP cc_start: 0.8022 (m-30) cc_final: 0.7431 (m-30) REVERT: B 145 LYS cc_start: 0.8794 (mttt) cc_final: 0.8348 (mtpp) REVERT: B 212 MET cc_start: 0.8893 (mtt) cc_final: 0.8654 (mtt) REVERT: B 263 HIS cc_start: 0.8562 (m90) cc_final: 0.8345 (m-70) REVERT: B 295 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8246 (mt) REVERT: B 298 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.8077 (mmt-90) REVERT: B 437 HIS cc_start: 0.8183 (t-90) cc_final: 0.7837 (m90) REVERT: B 469 MET cc_start: 0.9090 (tpt) cc_final: 0.8822 (tpp) REVERT: B 492 MET cc_start: 0.8337 (mmm) cc_final: 0.8076 (mmt) REVERT: B 520 LYS cc_start: 0.8909 (tttt) cc_final: 0.8641 (ttmm) REVERT: B 581 ILE cc_start: 0.8473 (mt) cc_final: 0.8080 (mm) REVERT: B 582 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7968 (mm-30) REVERT: B 615 ASP cc_start: 0.8393 (t0) cc_final: 0.8143 (t0) REVERT: B 797 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8595 (mm-30) REVERT: B 798 MET cc_start: 0.8728 (mmm) cc_final: 0.8364 (mtp) REVERT: B 892 GLU cc_start: 0.9024 (tt0) cc_final: 0.8759 (mt-10) REVERT: F 219 GLU cc_start: 0.5823 (OUTLIER) cc_final: 0.4865 (pp20) REVERT: F 252 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7676 (tt) REVERT: F 259 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.7732 (t80) REVERT: F 281 TYR cc_start: 0.7395 (m-80) cc_final: 0.6980 (m-80) REVERT: F 287 LYS cc_start: 0.8786 (tptp) cc_final: 0.8076 (ttmt) REVERT: F 295 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7534 (pp) REVERT: F 327 TRP cc_start: 0.4825 (OUTLIER) cc_final: 0.4378 (t-100) REVERT: F 335 ARG cc_start: 0.7324 (ptt-90) cc_final: 0.7004 (ptt-90) REVERT: F 342 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8480 (tttt) REVERT: F 352 GLN cc_start: 0.8778 (tt0) cc_final: 0.8355 (mp10) REVERT: F 361 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7709 (mttt) REVERT: F 389 LYS cc_start: 0.8490 (tptm) cc_final: 0.8073 (tppt) REVERT: F 391 LEU cc_start: 0.8401 (tp) cc_final: 0.8029 (tt) REVERT: F 398 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8288 (tp-100) REVERT: G 153 LYS cc_start: 0.5425 (OUTLIER) cc_final: 0.3349 (tptt) REVERT: H 177 GLU cc_start: 0.8521 (tp30) cc_final: 0.8229 (tp30) REVERT: H 178 LYS cc_start: 0.8563 (mmtp) cc_final: 0.8097 (mtpt) REVERT: f 238 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8552 (mtmt) REVERT: f 249 ASP cc_start: 0.8192 (m-30) cc_final: 0.7978 (m-30) REVERT: f 365 ASP cc_start: 0.8444 (t0) cc_final: 0.8097 (t0) REVERT: f 389 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7815 (mtpp) outliers start: 84 outliers final: 47 residues processed: 330 average time/residue: 0.1622 time to fit residues: 80.4537 Evaluate side-chains 321 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 945 LYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 764 HIS Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 259 PHE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 175 optimal weight: 0.8980 chunk 154 optimal weight: 0.2980 chunk 151 optimal weight: 0.5980 chunk 209 optimal weight: 9.9990 chunk 97 optimal weight: 0.2980 chunk 126 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 218 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 137 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN F 343 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.164520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112363 restraints weight = 28257.944| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.20 r_work: 0.3062 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21183 Z= 0.143 Angle : 0.567 7.282 29063 Z= 0.306 Chirality : 0.041 0.268 3241 Planarity : 0.004 0.044 3397 Dihedral : 18.436 153.084 3542 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.39 % Allowed : 15.89 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2300 helix: 1.14 (0.16), residues: 1121 sheet: -0.34 (0.30), residues: 274 loop : -1.05 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 354 TYR 0.021 0.001 TYR F 281 PHE 0.021 0.001 PHE B 190 TRP 0.014 0.001 TRP A 341 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (21182) covalent geometry : angle 0.56637 / 0.31 (29061) SS BOND : bond 0.00625 / 0.33 ( 1) SS BOND : angle 1.92811 / 1.04 ( 2) hydrogen bonds : bond 0.03778 / 2.47 ( 1048) hydrogen bonds : angle 4.15151 / 2.87 ( 2961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 268 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: A 481 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: A 511 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7048 (mt) REVERT: A 639 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7534 (pp) REVERT: A 692 MET cc_start: 0.8907 (mtp) cc_final: 0.8422 (mtm) REVERT: A 744 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7762 (tp30) REVERT: A 945 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7246 (mtpp) REVERT: A 1058 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.6441 (t70) REVERT: B 41 GLN cc_start: 0.8191 (mp10) cc_final: 0.7934 (mp10) REVERT: B 71 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7714 (ttt90) REVERT: B 120 ASP cc_start: 0.7964 (m-30) cc_final: 0.7349 (m-30) REVERT: B 145 LYS cc_start: 0.8785 (mttt) cc_final: 0.8338 (mtpp) REVERT: B 212 MET cc_start: 0.8876 (mtt) cc_final: 0.8638 (mtt) REVERT: B 295 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8227 (mt) REVERT: B 298 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.8061 (mmt-90) REVERT: B 437 HIS cc_start: 0.8159 (t-90) cc_final: 0.7817 (m90) REVERT: B 448 MET cc_start: 0.9395 (mmt) cc_final: 0.9062 (mmt) REVERT: B 492 MET cc_start: 0.8256 (mmm) cc_final: 0.7981 (mmt) REVERT: B 520 LYS cc_start: 0.8937 (tttt) cc_final: 0.8671 (ttmm) REVERT: B 581 ILE cc_start: 0.8449 (mt) cc_final: 0.8227 (mm) REVERT: B 615 ASP cc_start: 0.8368 (t0) cc_final: 0.8065 (t0) REVERT: B 798 MET cc_start: 0.8710 (mmm) cc_final: 0.8372 (mtp) REVERT: B 892 GLU cc_start: 0.9021 (tt0) cc_final: 0.8751 (mt-10) REVERT: F 215 GLU cc_start: 0.7557 (pm20) cc_final: 0.7232 (tt0) REVERT: F 252 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7646 (tt) REVERT: F 259 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7710 (t80) REVERT: F 281 TYR cc_start: 0.7332 (m-80) cc_final: 0.6920 (m-80) REVERT: F 287 LYS cc_start: 0.8819 (tptp) cc_final: 0.8176 (ttmt) REVERT: F 295 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7602 (pp) REVERT: F 327 TRP cc_start: 0.4681 (OUTLIER) cc_final: 0.4311 (t-100) REVERT: F 361 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7696 (mttm) REVERT: F 389 LYS cc_start: 0.8408 (tptm) cc_final: 0.8057 (tppt) REVERT: F 391 LEU cc_start: 0.8449 (tp) cc_final: 0.8072 (tt) REVERT: F 398 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8429 (tp40) REVERT: F 421 ASP cc_start: 0.8189 (p0) cc_final: 0.7943 (p0) REVERT: G 55 ILE cc_start: 0.8741 (mt) cc_final: 0.8396 (tp) REVERT: G 153 LYS cc_start: 0.5485 (OUTLIER) cc_final: 0.3377 (tptt) REVERT: H 177 GLU cc_start: 0.8486 (tp30) cc_final: 0.8227 (tp30) REVERT: H 178 LYS cc_start: 0.8523 (mmtp) cc_final: 0.8083 (mtpt) REVERT: f 238 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8528 (mtmt) REVERT: f 249 ASP cc_start: 0.8213 (m-30) cc_final: 0.7976 (m-30) REVERT: f 270 ASN cc_start: 0.5100 (OUTLIER) cc_final: 0.3963 (t0) REVERT: f 365 ASP cc_start: 0.8456 (t0) cc_final: 0.8116 (t0) REVERT: f 389 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7614 (ttmt) REVERT: f 424 GLN cc_start: 0.7918 (tt0) cc_final: 0.7716 (tt0) outliers start: 69 outliers final: 45 residues processed: 317 average time/residue: 0.1651 time to fit residues: 78.9703 Evaluate side-chains 323 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 264 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 945 LYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 259 PHE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 272 VAL Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 192 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 151 optimal weight: 0.5980 chunk 198 optimal weight: 9.9990 chunk 195 optimal weight: 0.3980 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 137 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN F 339 GLN ** G 134 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 = 0.4086 r_free = 0.4086 target = 0.164679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111911 restraints weight = 28402.868| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.44 r_work: 0.3042 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21183 Z= 0.155 Angle : 0.567 7.497 29063 Z= 0.306 Chirality : 0.042 0.269 3241 Planarity : 0.004 0.066 3397 Dihedral : 18.369 153.386 3540 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.54 % Allowed : 15.99 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2300 helix: 1.25 (0.16), residues: 1124 sheet: -0.23 (0.31), residues: 274 loop : -1.01 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 539 TYR 0.017 0.001 TYR F 281 PHE 0.025 0.001 PHE G 130 TRP 0.013 0.001 TRP A 932 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (21182) covalent geometry : angle 0.56696 / 0.31 (29061) SS BOND : bond 0.00636 / 0.33 ( 1) SS BOND : angle 1.82030 / 0.98 ( 2) hydrogen bonds : bond 0.03761 / 2.46 ( 1048) hydrogen bonds : angle 4.09611 / 2.83 ( 2961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7200 (tp30) REVERT: A 481 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: A 501 THR cc_start: 0.8560 (p) cc_final: 0.8351 (p) REVERT: A 511 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7116 (mt) REVERT: A 639 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7580 (pp) REVERT: A 692 MET cc_start: 0.8922 (mtp) cc_final: 0.8447 (mtm) REVERT: A 744 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7796 (tp30) REVERT: A 945 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7286 (mtpp) REVERT: B 71 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7764 (ttt90) REVERT: B 120 ASP cc_start: 0.7993 (m-30) cc_final: 0.7391 (m-30) REVERT: B 145 LYS cc_start: 0.8801 (mttt) cc_final: 0.8364 (mtpp) REVERT: B 212 MET cc_start: 0.8889 (mtt) cc_final: 0.8650 (mtt) REVERT: B 295 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8214 (mt) REVERT: B 437 HIS cc_start: 0.8194 (t-90) cc_final: 0.7863 (m90) REVERT: B 492 MET cc_start: 0.8279 (mmm) cc_final: 0.8014 (mmt) REVERT: B 520 LYS cc_start: 0.8958 (tttt) cc_final: 0.8698 (ttmm) REVERT: B 581 ILE cc_start: 0.8498 (mt) cc_final: 0.8258 (mm) REVERT: B 582 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7989 (mm-30) REVERT: B 615 ASP cc_start: 0.8365 (t0) cc_final: 0.8053 (t0) REVERT: B 798 MET cc_start: 0.8732 (mmm) cc_final: 0.8398 (mtp) REVERT: B 892 GLU cc_start: 0.9041 (tt0) cc_final: 0.8699 (mt-10) REVERT: F 215 GLU cc_start: 0.7502 (pm20) cc_final: 0.7257 (tt0) REVERT: F 252 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7657 (tt) REVERT: F 281 TYR cc_start: 0.7370 (m-80) cc_final: 0.6983 (m-80) REVERT: F 287 LYS cc_start: 0.8780 (tptp) cc_final: 0.8173 (ttmt) REVERT: F 295 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7559 (pp) REVERT: F 327 TRP cc_start: 0.4709 (OUTLIER) cc_final: 0.4320 (t-100) REVERT: F 335 ARG cc_start: 0.8085 (ppt170) cc_final: 0.7466 (ttp-170) REVERT: F 342 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8497 (tttt) REVERT: F 352 GLN cc_start: 0.8759 (tt0) cc_final: 0.8508 (mp10) REVERT: F 389 LYS cc_start: 0.8454 (tptm) cc_final: 0.8087 (tppt) REVERT: F 391 LEU cc_start: 0.8399 (tp) cc_final: 0.7922 (tt) REVERT: F 398 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8443 (tp40) REVERT: G 55 ILE cc_start: 0.8770 (mt) cc_final: 0.8441 (tp) REVERT: G 153 LYS cc_start: 0.5531 (OUTLIER) cc_final: 0.3387 (tptt) REVERT: H 177 GLU cc_start: 0.8555 (tp30) cc_final: 0.8328 (tp30) REVERT: H 178 LYS cc_start: 0.8544 (mmtp) cc_final: 0.8105 (mtpt) REVERT: f 238 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8549 (mtmt) REVERT: f 249 ASP cc_start: 0.8235 (m-30) cc_final: 0.7999 (m-30) REVERT: f 270 ASN cc_start: 0.5107 (OUTLIER) cc_final: 0.3958 (t0) REVERT: f 365 ASP cc_start: 0.8490 (t0) cc_final: 0.8166 (t0) REVERT: f 389 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7665 (ttmt) outliers start: 72 outliers final: 52 residues processed: 321 average time/residue: 0.1520 time to fit residues: 73.9437 Evaluate side-chains 328 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 263 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 945 LYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 272 VAL Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 196 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 137 optimal weight: 0.9990 chunk 73 optimal weight: 0.0470 chunk 54 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 116 optimal weight: 0.6980 chunk 200 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 GLN G 36 HIS ** G 134 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 = 0.4082 r_free = 0.4082 target = 0.164437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112152 restraints weight = 28355.377| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.21 r_work: 0.3056 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21183 Z= 0.144 Angle : 0.561 8.548 29063 Z= 0.303 Chirality : 0.041 0.271 3241 Planarity : 0.004 0.066 3397 Dihedral : 18.324 153.482 3540 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.84 % Allowed : 15.79 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2300 helix: 1.35 (0.16), residues: 1124 sheet: -0.18 (0.31), residues: 274 loop : -0.97 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG f 320 TYR 0.015 0.001 TYR F 281 PHE 0.022 0.001 PHE G 130 TRP 0.013 0.001 TRP A 932 HIS 0.008 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (21182) covalent geometry : angle 0.56085 / 0.30 (29061) SS BOND : bond 0.00617 / 0.32 ( 1) SS BOND : angle 1.76695 / 0.95 ( 2) hydrogen bonds : bond 0.03660 / 2.39 ( 1048) hydrogen bonds : angle 4.09653 / 2.83 ( 2961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 272 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7290 (tp30) REVERT: A 481 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: A 501 THR cc_start: 0.8543 (p) cc_final: 0.8343 (p) REVERT: A 511 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7141 (mt) REVERT: A 639 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7624 (pp) REVERT: A 692 MET cc_start: 0.8874 (mtp) cc_final: 0.8491 (mtm) REVERT: A 744 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7729 (tp30) REVERT: B 41 GLN cc_start: 0.8198 (mp10) cc_final: 0.7963 (mp10) REVERT: B 71 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7735 (ttt90) REVERT: B 120 ASP cc_start: 0.7950 (m-30) cc_final: 0.7320 (m-30) REVERT: B 145 LYS cc_start: 0.8776 (mttt) cc_final: 0.8332 (mtpp) REVERT: B 212 MET cc_start: 0.8886 (mtt) cc_final: 0.8646 (mtt) REVERT: B 295 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8211 (mt) REVERT: B 298 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8010 (mmt-90) REVERT: B 437 HIS cc_start: 0.8181 (t-90) cc_final: 0.7832 (m90) REVERT: B 469 MET cc_start: 0.9050 (tpt) cc_final: 0.8820 (tpp) REVERT: B 492 MET cc_start: 0.8251 (mmm) cc_final: 0.7973 (mmt) REVERT: B 520 LYS cc_start: 0.8937 (tttt) cc_final: 0.8668 (ttmm) REVERT: B 581 ILE cc_start: 0.8460 (mt) cc_final: 0.8236 (mm) REVERT: B 582 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7958 (mm-30) REVERT: B 798 MET cc_start: 0.8707 (mmm) cc_final: 0.8374 (mtp) REVERT: B 892 GLU cc_start: 0.8983 (tt0) cc_final: 0.8704 (mt-10) REVERT: F 215 GLU cc_start: 0.7492 (pm20) cc_final: 0.7262 (tt0) REVERT: F 219 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.4850 (pp20) REVERT: F 252 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7651 (tt) REVERT: F 259 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7831 (t80) REVERT: F 281 TYR cc_start: 0.7378 (m-80) cc_final: 0.7052 (m-80) REVERT: F 287 LYS cc_start: 0.8714 (tptp) cc_final: 0.8132 (ttmt) REVERT: F 295 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7524 (pp) REVERT: F 327 TRP cc_start: 0.4764 (OUTLIER) cc_final: 0.4403 (t-100) REVERT: F 335 ARG cc_start: 0.8141 (ppt170) cc_final: 0.7442 (ttp-170) REVERT: F 342 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8477 (tttt) REVERT: F 352 GLN cc_start: 0.8754 (tt0) cc_final: 0.8500 (mp10) REVERT: F 361 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7675 (mttt) REVERT: F 389 LYS cc_start: 0.8454 (tptm) cc_final: 0.8102 (tppt) REVERT: F 391 LEU cc_start: 0.8398 (tp) cc_final: 0.7922 (tt) REVERT: F 398 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8472 (tp40) REVERT: G 55 ILE cc_start: 0.8782 (mt) cc_final: 0.8453 (tp) REVERT: G 153 LYS cc_start: 0.5583 (OUTLIER) cc_final: 0.3425 (tptt) REVERT: H 177 GLU cc_start: 0.8523 (tp30) cc_final: 0.8298 (tp30) REVERT: H 178 LYS cc_start: 0.8508 (mmtp) cc_final: 0.8081 (mtpt) REVERT: f 238 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8515 (mtmt) REVERT: f 249 ASP cc_start: 0.8229 (m-30) cc_final: 0.7992 (m-30) REVERT: f 270 ASN cc_start: 0.5066 (OUTLIER) cc_final: 0.3930 (t0) REVERT: f 340 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8288 (tt) REVERT: f 365 ASP cc_start: 0.8511 (t0) cc_final: 0.8220 (t0) REVERT: f 389 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7666 (ttmt) REVERT: f 402 ARG cc_start: 0.7337 (tmm-80) cc_final: 0.6977 (tmm-80) outliers start: 78 outliers final: 55 residues processed: 329 average time/residue: 0.1658 time to fit residues: 82.4870 Evaluate side-chains 333 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 263 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 945 CYS Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 259 PHE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 272 VAL Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 337 VAL Chi-restraints excluded: chain f residue 340 ILE Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 65 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 223 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 238 optimal weight: 10.0000 chunk 225 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 HIS B 137 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN F 339 GLN ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 326 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 = 0.4070 r_free = 0.4070 target = 0.163373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110578 restraints weight = 28265.319| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.42 r_work: 0.3013 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 21183 Z= 0.209 Angle : 0.603 8.486 29063 Z= 0.323 Chirality : 0.043 0.272 3241 Planarity : 0.004 0.050 3397 Dihedral : 18.363 153.872 3540 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.89 % Allowed : 16.38 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.17), residues: 2300 helix: 1.30 (0.16), residues: 1121 sheet: -0.19 (0.30), residues: 274 loop : -1.00 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG f 404 TYR 0.014 0.001 TYR F 281 PHE 0.021 0.002 PHE B 190 TRP 0.015 0.002 TRP A 341 HIS 0.009 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (21182) covalent geometry : angle 0.60315 / 0.32 (29061) SS BOND : bond 0.00812 / 0.43 ( 1) SS BOND : angle 2.05127 / 1.11 ( 2) hydrogen bonds : bond 0.04056 / 2.65 ( 1048) hydrogen bonds : angle 4.14500 / 2.87 ( 2961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 268 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: A 481 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: A 511 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7100 (mt) REVERT: A 639 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7490 (pp) REVERT: A 692 MET cc_start: 0.8888 (mtp) cc_final: 0.8479 (mtm) REVERT: A 744 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7811 (tp30) REVERT: A 1058 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.6501 (t70) REVERT: A 1220 MET cc_start: 0.9144 (ppp) cc_final: 0.8923 (pmm) REVERT: B 41 GLN cc_start: 0.8264 (mp10) cc_final: 0.8012 (mp10) REVERT: B 71 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7787 (ttt90) REVERT: B 120 ASP cc_start: 0.8010 (m-30) cc_final: 0.7396 (m-30) REVERT: B 145 LYS cc_start: 0.8800 (mttt) cc_final: 0.8360 (mtpp) REVERT: B 212 MET cc_start: 0.8917 (mtt) cc_final: 0.8682 (mtt) REVERT: B 295 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8321 (mt) REVERT: B 437 HIS cc_start: 0.8212 (t-90) cc_final: 0.7889 (m90) REVERT: B 469 MET cc_start: 0.9086 (tpt) cc_final: 0.8861 (tpp) REVERT: B 520 LYS cc_start: 0.8936 (tttt) cc_final: 0.8670 (ttmm) REVERT: B 581 ILE cc_start: 0.8578 (mt) cc_final: 0.8331 (mm) REVERT: B 582 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8026 (mm-30) REVERT: B 797 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8587 (mm-30) REVERT: B 798 MET cc_start: 0.8773 (mmm) cc_final: 0.8382 (mtp) REVERT: B 892 GLU cc_start: 0.8987 (tt0) cc_final: 0.8734 (mt-10) REVERT: B 913 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8967 (mtt) REVERT: F 215 GLU cc_start: 0.7548 (pm20) cc_final: 0.7305 (tt0) REVERT: F 219 GLU cc_start: 0.5907 (OUTLIER) cc_final: 0.4934 (pp20) REVERT: F 252 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7711 (tt) REVERT: F 281 TYR cc_start: 0.7480 (m-80) cc_final: 0.7157 (m-80) REVERT: F 287 LYS cc_start: 0.8790 (tptp) cc_final: 0.8209 (ttmt) REVERT: F 295 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7512 (pp) REVERT: F 327 TRP cc_start: 0.4775 (OUTLIER) cc_final: 0.4511 (t-100) REVERT: F 335 ARG cc_start: 0.8162 (ppt170) cc_final: 0.7516 (ttp-170) REVERT: F 342 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8555 (tttt) REVERT: F 352 GLN cc_start: 0.8750 (tt0) cc_final: 0.8505 (mp10) REVERT: F 361 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7669 (mttt) REVERT: F 389 LYS cc_start: 0.8451 (tptm) cc_final: 0.8111 (tppt) REVERT: F 391 LEU cc_start: 0.8409 (tp) cc_final: 0.7909 (tt) REVERT: F 398 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8490 (tp40) REVERT: G 55 ILE cc_start: 0.8773 (mt) cc_final: 0.8437 (tp) REVERT: G 153 LYS cc_start: 0.5647 (OUTLIER) cc_final: 0.3438 (tptt) REVERT: H 177 GLU cc_start: 0.8582 (tp30) cc_final: 0.8355 (tp30) REVERT: H 178 LYS cc_start: 0.8557 (mmtp) cc_final: 0.8125 (mtpt) REVERT: f 238 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8526 (mtmt) REVERT: f 249 ASP cc_start: 0.8327 (m-30) cc_final: 0.8097 (m-30) REVERT: f 340 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8333 (tt) REVERT: f 365 ASP cc_start: 0.8500 (t0) cc_final: 0.8191 (t0) REVERT: f 389 LYS cc_start: 0.8286 (mtpt) cc_final: 0.8027 (tttt) outliers start: 79 outliers final: 53 residues processed: 325 average time/residue: 0.1616 time to fit residues: 79.5605 Evaluate side-chains 331 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 263 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 945 CYS Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 272 VAL Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 337 VAL Chi-restraints excluded: chain f residue 340 ILE Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 50 optimal weight: 20.0000 chunk 125 optimal weight: 0.3980 chunk 108 optimal weight: 0.5980 chunk 112 optimal weight: 0.4980 chunk 43 optimal weight: 0.0060 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 182 optimal weight: 30.0000 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN F 339 GLN G 53 HIS ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 326 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 = 0.4067 r_free = 0.4067 target = 0.163029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112675 restraints weight = 28109.442| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.61 r_work: 0.3003 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21183 Z= 0.197 Angle : 0.600 12.941 29063 Z= 0.320 Chirality : 0.043 0.278 3241 Planarity : 0.004 0.047 3397 Dihedral : 18.369 153.872 3538 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.64 % Allowed : 16.58 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.17), residues: 2300 helix: 1.32 (0.16), residues: 1121 sheet: -0.18 (0.30), residues: 274 loop : -1.02 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG f 404 TYR 0.019 0.001 TYR B 283 PHE 0.023 0.002 PHE B 190 TRP 0.016 0.002 TRP A 341 HIS 0.008 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (21182) covalent geometry : angle 0.59949 / 0.32 (29061) SS BOND : bond 0.00701 / 0.37 ( 1) SS BOND : angle 1.97035 / 1.06 ( 2) hydrogen bonds : bond 0.03949 / 2.58 ( 1048) hydrogen bonds : angle 4.15635 / 2.88 ( 2961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 265 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: A 481 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: A 501 THR cc_start: 0.8326 (p) cc_final: 0.7845 (t) REVERT: A 511 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7092 (mt) REVERT: A 639 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7428 (pp) REVERT: A 692 MET cc_start: 0.8882 (mtp) cc_final: 0.8452 (mtm) REVERT: A 744 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7803 (tp30) REVERT: A 1032 MET cc_start: 0.7989 (mmp) cc_final: 0.7365 (ppp) REVERT: A 1058 HIS cc_start: 0.7529 (OUTLIER) cc_final: 0.6500 (t70) REVERT: A 1220 MET cc_start: 0.9133 (ppp) cc_final: 0.8932 (pmm) REVERT: B 41 GLN cc_start: 0.8254 (mp10) cc_final: 0.7985 (mp10) REVERT: B 71 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7759 (ttt90) REVERT: B 120 ASP cc_start: 0.7965 (m-30) cc_final: 0.7298 (m-30) REVERT: B 145 LYS cc_start: 0.8808 (mttt) cc_final: 0.8332 (mtpp) REVERT: B 212 MET cc_start: 0.8906 (mtt) cc_final: 0.8668 (mtt) REVERT: B 295 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8274 (mt) REVERT: B 298 ARG cc_start: 0.8553 (mmm-85) cc_final: 0.8041 (mmt-90) REVERT: B 361 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8585 (ttp-170) REVERT: B 437 HIS cc_start: 0.8225 (t-90) cc_final: 0.7830 (m90) REVERT: B 520 LYS cc_start: 0.8938 (tttt) cc_final: 0.8635 (ttmm) REVERT: B 581 ILE cc_start: 0.8586 (mt) cc_final: 0.8356 (mm) REVERT: B 582 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7946 (mm-30) REVERT: B 797 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8637 (mm-30) REVERT: B 798 MET cc_start: 0.8762 (mmm) cc_final: 0.8329 (mtp) REVERT: B 892 GLU cc_start: 0.9017 (tt0) cc_final: 0.8735 (mt-10) REVERT: B 913 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.9043 (mtt) REVERT: F 215 GLU cc_start: 0.7691 (pm20) cc_final: 0.7374 (tt0) REVERT: F 219 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.4904 (pp20) REVERT: F 252 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7641 (tt) REVERT: F 281 TYR cc_start: 0.7526 (m-80) cc_final: 0.7218 (m-80) REVERT: F 287 LYS cc_start: 0.8767 (tptp) cc_final: 0.8176 (ttmt) REVERT: F 295 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7469 (pp) REVERT: F 335 ARG cc_start: 0.8169 (ppt170) cc_final: 0.7501 (ttp-170) REVERT: F 342 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8531 (tttt) REVERT: F 352 GLN cc_start: 0.8778 (tt0) cc_final: 0.8544 (mp10) REVERT: F 361 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7572 (mttt) REVERT: F 389 LYS cc_start: 0.8439 (tptm) cc_final: 0.8117 (tppt) REVERT: F 398 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8499 (tp40) REVERT: F 421 ASP cc_start: 0.8297 (p0) cc_final: 0.7940 (p0) REVERT: G 36 HIS cc_start: 0.7323 (p90) cc_final: 0.6713 (p90) REVERT: G 55 ILE cc_start: 0.8782 (mt) cc_final: 0.8450 (tp) REVERT: G 153 LYS cc_start: 0.5691 (OUTLIER) cc_final: 0.3453 (tptt) REVERT: H 177 GLU cc_start: 0.8593 (tp30) cc_final: 0.8364 (tp30) REVERT: H 178 LYS cc_start: 0.8543 (mmtp) cc_final: 0.8038 (mtpt) REVERT: f 238 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8492 (mtmt) REVERT: f 249 ASP cc_start: 0.8437 (m-30) cc_final: 0.8222 (m-30) REVERT: f 340 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8270 (tt) REVERT: f 365 ASP cc_start: 0.8455 (t0) cc_final: 0.8153 (t0) REVERT: f 389 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7597 (ttmm) REVERT: f 421 ASP cc_start: 0.7815 (p0) cc_final: 0.7165 (t0) outliers start: 74 outliers final: 54 residues processed: 323 average time/residue: 0.1570 time to fit residues: 76.3957 Evaluate side-chains 331 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 262 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 945 CYS Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 272 VAL Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 337 VAL Chi-restraints excluded: chain f residue 340 ILE Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 71 optimal weight: 0.6980 chunk 174 optimal weight: 6.9990 chunk 220 optimal weight: 0.7980 chunk 96 optimal weight: 0.2980 chunk 118 optimal weight: 0.2980 chunk 124 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 chunk 235 optimal weight: 0.7980 chunk 237 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 232 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN F 339 GLN ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 326 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 = 0.4080 r_free = 0.4080 target = 0.164156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112564 restraints weight = 28313.304| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.60 r_work: 0.3010 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21183 Z= 0.159 Angle : 0.582 12.076 29063 Z= 0.312 Chirality : 0.042 0.281 3241 Planarity : 0.004 0.068 3397 Dihedral : 18.316 153.835 3538 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.69 % Allowed : 16.53 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.18), residues: 2300 helix: 1.43 (0.16), residues: 1122 sheet: -0.17 (0.31), residues: 273 loop : -0.96 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG f 404 TYR 0.021 0.001 TYR B 283 PHE 0.021 0.001 PHE B 190 TRP 0.017 0.001 TRP F 370 HIS 0.008 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (21182) covalent geometry : angle 0.58170 / 0.31 (29061) SS BOND : bond 0.00641 / 0.34 ( 1) SS BOND : angle 1.93279 / 1.04 ( 2) hydrogen bonds : bond 0.03734 / 2.44 ( 1048) hydrogen bonds : angle 4.09455 / 2.84 ( 2961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 268 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: A 481 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: A 511 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7102 (mt) REVERT: A 639 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7567 (pp) REVERT: A 692 MET cc_start: 0.8880 (mtp) cc_final: 0.8466 (mtm) REVERT: A 744 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7836 (tp30) REVERT: A 1058 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6476 (t70) REVERT: B 41 GLN cc_start: 0.8256 (mp10) cc_final: 0.8001 (mp10) REVERT: B 71 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7817 (ttt90) REVERT: B 120 ASP cc_start: 0.8008 (m-30) cc_final: 0.7369 (m-30) REVERT: B 137 HIS cc_start: 0.8373 (t-90) cc_final: 0.8143 (t70) REVERT: B 145 LYS cc_start: 0.8841 (mttt) cc_final: 0.8394 (mtpp) REVERT: B 212 MET cc_start: 0.8911 (mtt) cc_final: 0.8669 (mtt) REVERT: B 295 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8175 (mt) REVERT: B 361 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8513 (ttp-170) REVERT: B 437 HIS cc_start: 0.8228 (t-90) cc_final: 0.7891 (m90) REVERT: B 469 MET cc_start: 0.9083 (tpt) cc_final: 0.8855 (tpp) REVERT: B 520 LYS cc_start: 0.8978 (tttt) cc_final: 0.8696 (ttmm) REVERT: B 581 ILE cc_start: 0.8556 (mt) cc_final: 0.8339 (mm) REVERT: B 582 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7898 (mm-30) REVERT: B 798 MET cc_start: 0.8780 (mmm) cc_final: 0.8401 (mtp) REVERT: B 892 GLU cc_start: 0.8946 (tt0) cc_final: 0.8720 (mt-10) REVERT: B 913 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.9022 (mtt) REVERT: F 215 GLU cc_start: 0.7698 (pm20) cc_final: 0.7385 (tt0) REVERT: F 219 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.4962 (pp20) REVERT: F 252 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7627 (tt) REVERT: F 281 TYR cc_start: 0.7521 (m-80) cc_final: 0.7216 (m-80) REVERT: F 287 LYS cc_start: 0.8802 (tptp) cc_final: 0.8240 (ttmt) REVERT: F 295 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7507 (pp) REVERT: F 335 ARG cc_start: 0.8111 (ppt170) cc_final: 0.7475 (ttp-170) REVERT: F 342 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8544 (tttt) REVERT: F 352 GLN cc_start: 0.8786 (tt0) cc_final: 0.8555 (mp10) REVERT: F 361 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7592 (mttt) REVERT: F 389 LYS cc_start: 0.8456 (tptm) cc_final: 0.8160 (tppt) REVERT: F 394 PRO cc_start: 0.7960 (Cg_exo) cc_final: 0.7746 (Cg_endo) REVERT: F 398 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8362 (tp-100) REVERT: G 55 ILE cc_start: 0.8852 (mt) cc_final: 0.8574 (tp) REVERT: G 153 LYS cc_start: 0.5712 (OUTLIER) cc_final: 0.3465 (tptt) REVERT: H 177 GLU cc_start: 0.8608 (tp30) cc_final: 0.8396 (tp30) REVERT: H 178 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8113 (mtpt) REVERT: f 238 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8529 (mtmt) REVERT: f 249 ASP cc_start: 0.8442 (m-30) cc_final: 0.8239 (m-30) REVERT: f 340 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8301 (tt) REVERT: f 365 ASP cc_start: 0.8506 (t0) cc_final: 0.8219 (t0) REVERT: f 389 LYS cc_start: 0.8265 (mtpt) cc_final: 0.7649 (ttmm) REVERT: f 421 ASP cc_start: 0.7894 (p0) cc_final: 0.7255 (t0) outliers start: 75 outliers final: 54 residues processed: 324 average time/residue: 0.1612 time to fit residues: 78.3152 Evaluate side-chains 332 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 262 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 945 CYS Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain F residue 339 GLN Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 272 VAL Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 337 VAL Chi-restraints excluded: chain f residue 340 ILE Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 188 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 239 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.0030 chunk 237 optimal weight: 0.0370 overall best weight: 0.4468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN F 339 GLN ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN G 48 HIS ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 220 GLN ** f 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.163582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111503 restraints weight = 28143.324| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.18 r_work: 0.3042 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21183 Z= 0.152 Angle : 0.586 12.644 29063 Z= 0.314 Chirality : 0.042 0.282 3241 Planarity : 0.004 0.062 3397 Dihedral : 18.292 153.805 3538 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.59 % Allowed : 16.82 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2300 helix: 1.43 (0.16), residues: 1125 sheet: -0.14 (0.31), residues: 273 loop : -0.93 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG f 404 TYR 0.022 0.001 TYR B 283 PHE 0.026 0.001 PHE F 344 TRP 0.016 0.001 TRP F 370 HIS 0.007 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (21182) covalent geometry : angle 0.58580 / 0.31 (29061) SS BOND : bond 0.00607 / 0.32 ( 1) SS BOND : angle 1.87451 / 1.01 ( 2) hydrogen bonds : bond 0.03683 / 2.41 ( 1048) hydrogen bonds : angle 4.09779 / 2.84 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7571.30 seconds wall clock time: 129 minutes 49.82 seconds (7789.82 seconds total)