Starting phenix.real_space_refine on Thu Mar 5 08:00:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7egh_31117/03_2026/7egh_31117.cif Found real_map, /net/cci-nas-00/data/ceres_data/7egh_31117/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7egh_31117/03_2026/7egh_31117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7egh_31117/03_2026/7egh_31117.map" model { file = "/net/cci-nas-00/data/ceres_data/7egh_31117/03_2026/7egh_31117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7egh_31117/03_2026/7egh_31117.cif" } 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-dev-5986/lib/python3.9/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: 4.24, per 1000 atoms: 0.21 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: 1.70 Conformation dependent library (CDL) restraints added in 779.0 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: 2.68 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: 4.33 Time building geometry restraints manager: 2.26 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: 26935 2.28 - 4.55: 1876 4.55 - 6.83: 194 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: 2888 0.132 - 0.263: 313 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: 10.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.180 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 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= 0.546 Angle : 1.242 38.137 29063 Z= 0.817 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 covalent geometry : bond 0.00914 (21182) covalent geometry : angle 1.20954 (29061) SS BOND : bond 0.19687 ( 1) SS BOND : angle 34.11467 ( 2) hydrogen bonds : bond 0.14179 ( 1048) hydrogen bonds : angle 6.42313 ( 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 : 0.764 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: 0.1834 time to fit residues: 119.7305 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 : 0.698 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 415 HIS 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 33 GLN G 48 HIS f 343 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.164635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112583 restraints weight = 28429.055| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.21 r_work: 0.3062 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21183 Z= 0.168 Angle : 0.634 10.049 29063 Z= 0.338 Chirality : 0.042 0.252 3241 Planarity : 0.005 0.053 3397 Dihedral : 18.407 150.375 3582 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.66 % Allowed : 12.99 % Favored : 84.36 % 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: -0.81 (0.17), residues: 2300 helix: 0.27 (0.15), residues: 1118 sheet: -0.79 (0.30), residues: 275 loop : -1.40 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1233 TYR 0.012 0.001 TYR A 683 PHE 0.022 0.001 PHE B 190 TRP 0.018 0.002 TRP A 932 HIS 0.007 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00382 (21182) covalent geometry : angle 0.63291 (29061) SS BOND : bond 0.00640 ( 1) SS BOND : angle 3.84109 ( 2) hydrogen bonds : bond 0.04270 ( 1048) hydrogen bonds : angle 4.49501 ( 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 338 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 284 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 ARG cc_start: 0.5762 (OUTLIER) cc_final: 0.4988 (tmm160) REVERT: A 404 MET cc_start: 0.8582 (mmm) cc_final: 0.8003 (mmm) REVERT: A 481 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: A 511 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7152 (mt) REVERT: A 625 PHE cc_start: 0.8113 (p90) cc_final: 0.7862 (p90) REVERT: A 691 MET cc_start: 0.8822 (tpp) cc_final: 0.8520 (tpp) REVERT: A 692 MET cc_start: 0.8953 (mtp) cc_final: 0.8638 (mtm) REVERT: A 744 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7823 (tp30) REVERT: A 786 CYS cc_start: 0.8539 (m) cc_final: 0.8261 (m) REVERT: A 945 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7150 (mtpp) REVERT: A 1058 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.6902 (t-170) REVERT: A 1061 ARG cc_start: 0.8132 (ttp-110) cc_final: 0.7740 (mtm110) REVERT: A 1071 ASP cc_start: 0.7920 (t0) cc_final: 0.7656 (m-30) REVERT: A 1220 MET cc_start: 0.9452 (tpp) cc_final: 0.9180 (mmm) REVERT: B 80 LEU cc_start: 0.8600 (mt) cc_final: 0.8390 (mt) REVERT: B 120 ASP cc_start: 0.7969 (m-30) cc_final: 0.7332 (m-30) REVERT: B 145 LYS cc_start: 0.8792 (mttt) cc_final: 0.8309 (mtpp) REVERT: B 212 MET cc_start: 0.8867 (mtt) cc_final: 0.8629 (mtt) REVERT: B 262 MET cc_start: 0.8558 (ttm) cc_final: 0.8282 (mtm) REVERT: B 295 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8157 (mt) REVERT: B 352 GLN cc_start: 0.8700 (mt0) cc_final: 0.8500 (mt0) REVERT: B 437 HIS cc_start: 0.8034 (t-90) cc_final: 0.7804 (m90) REVERT: B 448 MET cc_start: 0.9384 (mmt) cc_final: 0.9069 (mmt) REVERT: B 492 MET cc_start: 0.8298 (mmm) cc_final: 0.8020 (mmt) REVERT: B 520 LYS cc_start: 0.8899 (tttt) cc_final: 0.8640 (ttmm) REVERT: B 615 ASP cc_start: 0.8394 (t0) cc_final: 0.8180 (t0) REVERT: B 683 ASP cc_start: 0.8591 (m-30) cc_final: 0.8160 (m-30) REVERT: B 798 MET cc_start: 0.8791 (mmm) cc_final: 0.8409 (mtp) REVERT: B 892 GLU cc_start: 0.8986 (tt0) cc_final: 0.8737 (mt-10) REVERT: B 916 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.8738 (p0) REVERT: F 259 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7661 (t80) REVERT: F 295 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7552 (pp) REVERT: F 327 TRP cc_start: 0.4883 (OUTLIER) cc_final: 0.4451 (t-100) REVERT: F 352 GLN cc_start: 0.8807 (tt0) cc_final: 0.8383 (mp10) REVERT: F 391 LEU cc_start: 0.8386 (tp) cc_final: 0.8041 (tt) REVERT: F 398 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8409 (tp-100) REVERT: H 177 GLU cc_start: 0.8470 (tp30) cc_final: 0.8124 (tp30) REVERT: H 178 LYS cc_start: 0.8587 (mmtp) cc_final: 0.8140 (mmmm) REVERT: H 184 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8384 (mtp85) REVERT: f 238 LYS cc_start: 0.8862 (mtpt) cc_final: 0.8601 (mtmt) REVERT: f 249 ASP cc_start: 0.8040 (m-30) cc_final: 0.7806 (m-30) REVERT: f 270 ASN cc_start: 0.5073 (OUTLIER) cc_final: 0.3888 (t0) REVERT: f 365 ASP cc_start: 0.8314 (t0) cc_final: 0.8086 (t0) REVERT: f 389 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7820 (mtpp) REVERT: f 402 ARG cc_start: 0.7432 (tmm-80) cc_final: 0.7132 (tmm-80) outliers start: 54 outliers final: 27 residues processed: 328 average time/residue: 0.1717 time to fit residues: 83.3305 Evaluate side-chains 301 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 263 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 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 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 596 SER 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 147 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 172 optimal weight: 5.9990 chunk 186 optimal weight: 0.0570 chunk 19 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 217 optimal weight: 0.1980 chunk 166 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN A1058 HIS B 137 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.164861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.112091 restraints weight = 28506.664| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.40 r_work: 0.3046 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21183 Z= 0.164 Angle : 0.584 8.108 29063 Z= 0.312 Chirality : 0.041 0.181 3241 Planarity : 0.004 0.043 3397 Dihedral : 18.141 150.167 3541 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.74 % Allowed : 13.77 % Favored : 82.49 % 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: -0.29 (0.17), residues: 2300 helix: 0.79 (0.15), residues: 1121 sheet: -0.59 (0.30), residues: 270 loop : -1.24 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 298 TYR 0.032 0.001 TYR F 281 PHE 0.020 0.001 PHE B 190 TRP 0.014 0.001 TRP A 932 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00381 (21182) covalent geometry : angle 0.58340 (29061) SS BOND : bond 0.00598 ( 1) SS BOND : angle 2.50573 ( 2) hydrogen bonds : bond 0.03891 ( 1048) hydrogen bonds : angle 4.28607 ( 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 356 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 280 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.4992 (tmm160) REVERT: A 404 MET cc_start: 0.8563 (mmm) cc_final: 0.7994 (mmm) REVERT: A 481 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: A 511 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7045 (mt) REVERT: A 625 PHE cc_start: 0.8259 (p90) cc_final: 0.8021 (p90) REVERT: A 692 MET cc_start: 0.8938 (mtp) cc_final: 0.8501 (mtm) REVERT: A 744 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7802 (tp30) REVERT: A 945 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7324 (mtpp) REVERT: A 1058 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.6549 (t70) REVERT: A 1220 MET cc_start: 0.9489 (tpp) cc_final: 0.9194 (mmm) REVERT: A 1233 ARG cc_start: 0.9105 (ttp-110) cc_final: 0.8655 (ptt90) REVERT: B 41 GLN cc_start: 0.8228 (mp10) cc_final: 0.7967 (mp10) REVERT: B 71 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7728 (ttt90) REVERT: B 120 ASP cc_start: 0.7996 (m-30) cc_final: 0.7416 (m-30) REVERT: B 145 LYS cc_start: 0.8823 (mttt) cc_final: 0.8389 (mtpp) REVERT: B 212 MET cc_start: 0.8879 (mtt) cc_final: 0.8645 (mtt) REVERT: B 263 HIS cc_start: 0.8578 (m90) cc_final: 0.8361 (m-70) REVERT: B 295 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8217 (mt) REVERT: B 437 HIS cc_start: 0.8187 (t-90) cc_final: 0.7873 (m90) REVERT: B 448 MET cc_start: 0.9404 (mmt) cc_final: 0.9089 (mmt) REVERT: B 469 MET cc_start: 0.9070 (tpt) cc_final: 0.8835 (tpp) REVERT: B 492 MET cc_start: 0.8349 (mmm) cc_final: 0.8086 (mmt) REVERT: B 520 LYS cc_start: 0.8970 (tttt) cc_final: 0.8713 (ttmm) REVERT: B 582 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8069 (mm-30) REVERT: B 615 ASP cc_start: 0.8414 (t0) cc_final: 0.8177 (t0) REVERT: B 683 ASP cc_start: 0.8571 (m-30) cc_final: 0.8138 (m-30) REVERT: B 797 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8643 (mm-30) REVERT: B 798 MET cc_start: 0.8743 (mmm) cc_final: 0.8402 (mtp) REVERT: B 892 GLU cc_start: 0.9001 (tt0) cc_final: 0.8742 (mt-10) REVERT: F 252 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7665 (tt) REVERT: F 259 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7736 (t80) REVERT: F 281 TYR cc_start: 0.7409 (m-80) cc_final: 0.7048 (m-80) REVERT: F 287 LYS cc_start: 0.8817 (tptp) cc_final: 0.8114 (ttmt) REVERT: F 295 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7565 (pp) REVERT: F 327 TRP cc_start: 0.4837 (OUTLIER) cc_final: 0.4376 (t-100) REVERT: F 342 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8376 (tttt) REVERT: F 361 LYS cc_start: 0.8308 (ptpp) cc_final: 0.8105 (mttm) REVERT: F 389 LYS cc_start: 0.8508 (tptm) cc_final: 0.8075 (tppt) REVERT: F 391 LEU cc_start: 0.8378 (tp) cc_final: 0.8021 (tt) REVERT: F 398 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8252 (tp-100) REVERT: G 46 GLU cc_start: 0.7236 (tt0) cc_final: 0.6555 (tt0) REVERT: H 177 GLU cc_start: 0.8521 (tp30) cc_final: 0.8217 (tp30) REVERT: H 178 LYS cc_start: 0.8580 (mmtp) cc_final: 0.8103 (mtpt) REVERT: H 184 ARG cc_start: 0.8655 (mmm-85) cc_final: 0.8404 (mtp85) REVERT: f 238 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8565 (mtmt) REVERT: f 249 ASP cc_start: 0.8240 (m-30) cc_final: 0.7998 (m-30) REVERT: f 365 ASP cc_start: 0.8424 (t0) cc_final: 0.8124 (t0) REVERT: f 389 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7832 (mtpp) REVERT: f 402 ARG cc_start: 0.7427 (tmm-80) cc_final: 0.6322 (tmm-80) REVERT: f 424 GLN cc_start: 0.8000 (tt0) cc_final: 0.7532 (tt0) outliers start: 76 outliers final: 42 residues processed: 335 average time/residue: 0.1719 time to fit residues: 85.6114 Evaluate side-chains 317 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 262 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ARG 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 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 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 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 611 GLU Chi-restraints excluded: chain B residue 674 THR 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 236 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 121 optimal weight: 0.2980 chunk 138 optimal weight: 0.6980 chunk 214 optimal weight: 0.1980 chunk 231 optimal weight: 0.0670 chunk 149 optimal weight: 0.2980 chunk 157 optimal weight: 0.6980 chunk 235 optimal weight: 0.7980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 343 HIS H 201 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.165779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113973 restraints weight = 28530.046| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.22 r_work: 0.3071 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21183 Z= 0.132 Angle : 0.555 9.720 29063 Z= 0.296 Chirality : 0.040 0.167 3241 Planarity : 0.004 0.039 3397 Dihedral : 17.996 150.339 3541 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.44 % Allowed : 15.15 % Favored : 81.41 % 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: 0.16 (0.17), residues: 2300 helix: 1.19 (0.15), residues: 1121 sheet: -0.38 (0.30), residues: 274 loop : -1.08 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 335 TYR 0.026 0.001 TYR F 281 PHE 0.020 0.001 PHE B 190 TRP 0.013 0.001 TRP A 932 HIS 0.014 0.001 HIS F 343 Details of bonding type rmsd covalent geometry : bond 0.00299 (21182) covalent geometry : angle 0.55442 (29061) SS BOND : bond 0.00514 ( 1) SS BOND : angle 1.90140 ( 2) hydrogen bonds : bond 0.03457 ( 1048) hydrogen bonds : angle 4.12245 ( 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 353 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 283 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.4991 (tmm160) REVERT: A 400 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7004 (tp30) REVERT: A 481 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: A 511 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6979 (mt) REVERT: A 639 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7658 (pp) REVERT: A 692 MET cc_start: 0.8897 (mtp) cc_final: 0.8427 (mtm) REVERT: A 744 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7706 (tp30) REVERT: A 945 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7252 (mtpp) REVERT: A 1058 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.6571 (t70) REVERT: A 1220 MET cc_start: 0.9466 (tpp) cc_final: 0.9140 (mmm) REVERT: A 1233 ARG cc_start: 0.9076 (ttp-110) cc_final: 0.8642 (ptt90) REVERT: B 41 GLN cc_start: 0.8210 (mp10) cc_final: 0.7915 (mp10) REVERT: B 71 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7703 (ttt90) REVERT: B 120 ASP cc_start: 0.7922 (m-30) cc_final: 0.7302 (m-30) REVERT: B 145 LYS cc_start: 0.8770 (mttt) cc_final: 0.8316 (mtpp) REVERT: B 212 MET cc_start: 0.8870 (mtt) cc_final: 0.8635 (mtt) REVERT: B 295 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8171 (mt) REVERT: B 298 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.7995 (mmt-90) REVERT: B 437 HIS cc_start: 0.8141 (t-90) cc_final: 0.7764 (m90) REVERT: B 492 MET cc_start: 0.8323 (mmm) cc_final: 0.8031 (mmt) REVERT: B 520 LYS cc_start: 0.8941 (tttt) cc_final: 0.8661 (ttmm) REVERT: B 581 ILE cc_start: 0.8404 (mt) cc_final: 0.8119 (mm) REVERT: B 582 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7985 (mm-30) REVERT: B 615 ASP cc_start: 0.8374 (t0) cc_final: 0.8119 (t0) REVERT: B 798 MET cc_start: 0.8710 (mmm) cc_final: 0.8333 (mtp) REVERT: B 892 GLU cc_start: 0.9000 (tt0) cc_final: 0.8642 (mt-10) REVERT: B 916 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8829 (p0) REVERT: F 215 GLU cc_start: 0.7450 (pm20) cc_final: 0.7215 (tt0) REVERT: F 252 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7658 (tt) REVERT: F 259 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7733 (t80) REVERT: F 281 TYR cc_start: 0.7321 (m-80) cc_final: 0.6948 (m-80) REVERT: F 287 LYS cc_start: 0.8765 (tptp) cc_final: 0.8127 (ttmt) REVERT: F 295 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7573 (pp) REVERT: F 327 TRP cc_start: 0.4736 (OUTLIER) cc_final: 0.4353 (t-100) REVERT: F 335 ARG cc_start: 0.7399 (ttp-170) cc_final: 0.7017 (ttp-170) REVERT: F 389 LYS cc_start: 0.8446 (tptm) cc_final: 0.8077 (tppt) REVERT: F 391 LEU cc_start: 0.8364 (tp) cc_final: 0.7989 (tt) REVERT: F 398 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8429 (tp40) REVERT: F 421 ASP cc_start: 0.8230 (p0) cc_final: 0.7988 (p0) REVERT: G 55 ILE cc_start: 0.8753 (mt) cc_final: 0.8421 (tp) REVERT: H 177 GLU cc_start: 0.8508 (tp30) cc_final: 0.8262 (tp30) REVERT: H 178 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8037 (mtpt) REVERT: H 184 ARG cc_start: 0.8584 (mmm-85) cc_final: 0.8333 (mtp85) REVERT: f 238 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8536 (mtmt) REVERT: f 249 ASP cc_start: 0.8240 (m-30) cc_final: 0.7964 (m-30) REVERT: f 270 ASN cc_start: 0.5037 (OUTLIER) cc_final: 0.3900 (t0) REVERT: f 365 ASP cc_start: 0.8439 (t0) cc_final: 0.8136 (t0) REVERT: f 389 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7585 (ttmt) REVERT: f 402 ARG cc_start: 0.7471 (tmm-80) cc_final: 0.6892 (tmm-80) REVERT: f 424 GLN cc_start: 0.7919 (tt0) cc_final: 0.7663 (tt0) outliers start: 70 outliers final: 41 residues processed: 334 average time/residue: 0.1675 time to fit residues: 83.4195 Evaluate side-chains 330 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 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 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 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 582 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 674 THR 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 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 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 F residue 343 HIS Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL 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: 0.7980 chunk 154 optimal weight: 0.9990 chunk 151 optimal weight: 0.0970 chunk 209 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 218 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 343 HIS G 36 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.164948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112161 restraints weight = 28355.483| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.36 r_work: 0.3047 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.004 0.049 21183 Z= 0.157 Angle : 0.558 8.082 29063 Z= 0.297 Chirality : 0.041 0.173 3241 Planarity : 0.004 0.040 3397 Dihedral : 17.936 150.481 3538 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.49 % Allowed : 15.40 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2300 helix: 1.33 (0.16), residues: 1123 sheet: -0.22 (0.30), residues: 274 loop : -1.01 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 320 TYR 0.021 0.001 TYR F 281 PHE 0.020 0.001 PHE B 190 TRP 0.013 0.001 TRP A 932 HIS 0.008 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00367 (21182) covalent geometry : angle 0.55781 (29061) SS BOND : bond 0.00641 ( 1) SS BOND : angle 1.85096 ( 2) hydrogen bonds : bond 0.03566 ( 1048) hydrogen bonds : angle 4.09865 ( 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 350 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 279 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7242 (tp30) REVERT: A 481 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: A 511 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7101 (mt) REVERT: A 639 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7640 (pp) REVERT: A 692 MET cc_start: 0.8872 (mtp) cc_final: 0.8401 (mtm) REVERT: A 744 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7759 (tp30) REVERT: A 1058 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.6558 (t70) REVERT: B 71 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7743 (ttt90) REVERT: B 120 ASP cc_start: 0.7972 (m-30) cc_final: 0.7356 (m-30) REVERT: B 145 LYS cc_start: 0.8796 (mttt) cc_final: 0.8346 (mtpp) REVERT: B 212 MET cc_start: 0.8895 (mtt) cc_final: 0.8667 (mtt) REVERT: B 295 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8192 (mt) REVERT: B 298 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8086 (mmt-90) REVERT: B 437 HIS cc_start: 0.8188 (t-90) cc_final: 0.7838 (m90) REVERT: B 469 MET cc_start: 0.9046 (tpt) cc_final: 0.8824 (tpp) REVERT: B 492 MET cc_start: 0.8330 (mmm) cc_final: 0.8056 (mmt) REVERT: B 520 LYS cc_start: 0.8959 (tttt) cc_final: 0.8698 (ttmm) REVERT: B 581 ILE cc_start: 0.8495 (mt) cc_final: 0.8250 (mm) REVERT: B 582 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8010 (mm-30) REVERT: B 615 ASP cc_start: 0.8395 (t0) cc_final: 0.8069 (t0) REVERT: B 798 MET cc_start: 0.8693 (mmm) cc_final: 0.8372 (mtp) REVERT: B 892 GLU cc_start: 0.8986 (tt0) cc_final: 0.8702 (mt-10) REVERT: F 215 GLU cc_start: 0.7469 (pm20) cc_final: 0.7237 (tt0) REVERT: F 252 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7665 (tt) REVERT: F 281 TYR cc_start: 0.7353 (m-80) cc_final: 0.7020 (m-80) REVERT: F 287 LYS cc_start: 0.8706 (tptp) cc_final: 0.8140 (ttmt) REVERT: F 295 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7554 (pp) REVERT: F 327 TRP cc_start: 0.4959 (OUTLIER) cc_final: 0.4611 (t-100) REVERT: F 335 ARG cc_start: 0.7391 (ttp-170) cc_final: 0.7035 (ttp-170) REVERT: F 389 LYS cc_start: 0.8436 (tptm) cc_final: 0.8078 (tppt) REVERT: F 391 LEU cc_start: 0.8363 (tp) cc_final: 0.7987 (tt) REVERT: F 398 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8440 (tp40) REVERT: G 46 GLU cc_start: 0.7500 (tt0) cc_final: 0.6486 (tt0) REVERT: G 55 ILE cc_start: 0.8743 (mt) cc_final: 0.8434 (tp) REVERT: H 177 GLU cc_start: 0.8553 (tp30) cc_final: 0.8318 (tp30) REVERT: H 178 LYS cc_start: 0.8518 (mmtp) cc_final: 0.8077 (mtpt) REVERT: H 184 ARG cc_start: 0.8622 (mmm-85) cc_final: 0.8371 (mtp85) REVERT: f 238 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8534 (mtmt) REVERT: f 249 ASP cc_start: 0.8311 (m-30) cc_final: 0.8059 (m-30) REVERT: f 270 ASN cc_start: 0.5075 (OUTLIER) cc_final: 0.3929 (t0) REVERT: f 365 ASP cc_start: 0.8477 (t0) cc_final: 0.8167 (t0) REVERT: f 389 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7651 (ttmt) REVERT: f 402 ARG cc_start: 0.7512 (tmm-80) cc_final: 0.6767 (tmm-80) REVERT: f 424 GLN cc_start: 0.7958 (tt0) cc_final: 0.7523 (tt0) outliers start: 71 outliers final: 48 residues processed: 331 average time/residue: 0.1694 time to fit residues: 83.6512 Evaluate side-chains 333 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 274 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ARG 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 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 674 THR 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 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 G residue 98 THR 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: 0.0030 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 151 optimal weight: 0.3980 chunk 198 optimal weight: 6.9990 chunk 195 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 229 optimal weight: 0.2980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN G 33 GLN G 36 HIS ** 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 = 0.4083 r_free = 0.4083 target = 0.164380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113567 restraints weight = 28244.336| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.65 r_work: 0.3032 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21183 Z= 0.156 Angle : 0.553 7.474 29063 Z= 0.295 Chirality : 0.040 0.171 3241 Planarity : 0.004 0.039 3397 Dihedral : 17.883 150.562 3538 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.69 % Allowed : 15.35 % Favored : 80.96 % 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: 0.50 (0.18), residues: 2300 helix: 1.45 (0.16), residues: 1123 sheet: -0.10 (0.31), residues: 274 loop : -0.94 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1224 TYR 0.017 0.001 TYR F 281 PHE 0.020 0.001 PHE B 190 TRP 0.013 0.001 TRP A 341 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00365 (21182) covalent geometry : angle 0.55312 (29061) SS BOND : bond 0.00632 ( 1) SS BOND : angle 1.79199 ( 2) hydrogen bonds : bond 0.03515 ( 1048) hydrogen bonds : angle 4.04138 ( 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 360 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 285 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5016 (tmm160) REVERT: A 400 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: A 481 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: A 511 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7075 (mt) REVERT: A 639 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7752 (pp) REVERT: A 692 MET cc_start: 0.8864 (mtp) cc_final: 0.8456 (mtm) REVERT: A 744 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7786 (tp30) REVERT: A 945 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7291 (mtpp) REVERT: A 1058 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.6664 (t70) REVERT: B 41 GLN cc_start: 0.8224 (mp10) cc_final: 0.8013 (mp10) REVERT: B 71 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7781 (ttt90) REVERT: B 86 TYR cc_start: 0.8495 (t80) cc_final: 0.8228 (t80) REVERT: B 120 ASP cc_start: 0.7968 (m-30) cc_final: 0.7323 (m-30) REVERT: B 145 LYS cc_start: 0.8812 (mttt) cc_final: 0.8373 (mtpp) REVERT: B 212 MET cc_start: 0.8904 (mtt) cc_final: 0.8682 (mtt) REVERT: B 295 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8227 (mt) REVERT: B 298 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8110 (mmt-90) REVERT: B 437 HIS cc_start: 0.8207 (t-90) cc_final: 0.7874 (m90) REVERT: B 469 MET cc_start: 0.9065 (tpt) cc_final: 0.8835 (tpp) REVERT: B 520 LYS cc_start: 0.8987 (tttt) cc_final: 0.8731 (ttmm) REVERT: B 582 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7998 (mm-30) REVERT: B 615 ASP cc_start: 0.8397 (t0) cc_final: 0.8072 (t0) REVERT: B 798 MET cc_start: 0.8725 (mmm) cc_final: 0.8402 (mtp) REVERT: B 892 GLU cc_start: 0.9012 (tt0) cc_final: 0.8737 (mt-10) REVERT: F 215 GLU cc_start: 0.7497 (pm20) cc_final: 0.7272 (tt0) REVERT: F 252 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7732 (tt) REVERT: F 281 TYR cc_start: 0.7453 (m-80) cc_final: 0.7124 (m-80) REVERT: F 287 LYS cc_start: 0.8795 (tptp) cc_final: 0.8171 (ttmt) REVERT: F 295 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7480 (pp) REVERT: F 327 TRP cc_start: 0.4683 (OUTLIER) cc_final: 0.4458 (t-100) REVERT: F 335 ARG cc_start: 0.7458 (ttp-170) cc_final: 0.7151 (ttp-170) REVERT: F 389 LYS cc_start: 0.8436 (tptm) cc_final: 0.8101 (tppt) REVERT: F 391 LEU cc_start: 0.8412 (tp) cc_final: 0.7928 (tt) REVERT: F 398 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8452 (tp40) REVERT: G 46 GLU cc_start: 0.7573 (tt0) cc_final: 0.7029 (tt0) REVERT: G 55 ILE cc_start: 0.8817 (mt) cc_final: 0.8519 (tp) REVERT: G 153 LYS cc_start: 0.5578 (OUTLIER) cc_final: 0.3360 (tptt) REVERT: H 177 GLU cc_start: 0.8611 (tp30) cc_final: 0.8388 (tp30) REVERT: H 178 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8139 (mtpt) REVERT: H 184 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8394 (mtp85) REVERT: f 238 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8536 (mtmt) REVERT: f 249 ASP cc_start: 0.8371 (m-30) cc_final: 0.8102 (m-30) REVERT: f 270 ASN cc_start: 0.5001 (OUTLIER) cc_final: 0.3876 (t0) REVERT: f 365 ASP cc_start: 0.8538 (t0) cc_final: 0.8261 (t0) REVERT: f 389 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7689 (ttmt) REVERT: f 424 GLN cc_start: 0.8045 (tt0) cc_final: 0.7593 (tt0) outliers start: 75 outliers final: 50 residues processed: 341 average time/residue: 0.1644 time to fit residues: 83.6644 Evaluate side-chains 339 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 274 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ARG 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 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 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 582 GLU 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 674 THR 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 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 326 HIS Chi-restraints excluded: chain F residue 327 TRP 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 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: 2.9990 chunk 104 optimal weight: 0.0870 chunk 137 optimal weight: 0.7980 chunk 73 optimal weight: 0.0980 chunk 54 optimal weight: 0.6980 chunk 233 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 200 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN G 33 GLN ** 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 = 0.4094 r_free = 0.4094 target = 0.165376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114250 restraints weight = 28274.487| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.62 r_work: 0.3049 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21183 Z= 0.126 Angle : 0.537 7.789 29063 Z= 0.286 Chirality : 0.040 0.161 3241 Planarity : 0.004 0.039 3397 Dihedral : 17.790 150.449 3536 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.49 % Allowed : 16.04 % 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: 0.66 (0.18), residues: 2300 helix: 1.59 (0.16), residues: 1124 sheet: 0.02 (0.31), residues: 274 loop : -0.88 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1224 TYR 0.015 0.001 TYR F 281 PHE 0.021 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 covalent geometry : bond 0.00286 (21182) covalent geometry : angle 0.53701 (29061) SS BOND : bond 0.00485 ( 1) SS BOND : angle 1.62053 ( 2) hydrogen bonds : bond 0.03242 ( 1048) hydrogen bonds : angle 3.97422 ( 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 353 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 282 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.4961 (tmm160) REVERT: A 400 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7245 (tp30) REVERT: A 481 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: A 511 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7052 (mt) REVERT: A 639 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7694 (pp) REVERT: A 692 MET cc_start: 0.8818 (mtp) cc_final: 0.8394 (mtm) REVERT: A 744 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7788 (tp30) REVERT: A 1058 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.6723 (t70) REVERT: B 41 GLN cc_start: 0.8224 (mp10) cc_final: 0.7979 (mp10) REVERT: B 71 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7818 (ttt-90) REVERT: B 86 TYR cc_start: 0.8457 (t80) cc_final: 0.8192 (t80) REVERT: B 120 ASP cc_start: 0.7856 (m-30) cc_final: 0.7239 (m-30) REVERT: B 145 LYS cc_start: 0.8794 (mttt) cc_final: 0.8417 (mtpp) REVERT: B 212 MET cc_start: 0.8890 (mtt) cc_final: 0.8662 (mtt) REVERT: B 295 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8139 (mt) REVERT: B 298 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8123 (mmt-90) REVERT: B 303 CYS cc_start: 0.8856 (m) cc_final: 0.8332 (t) REVERT: B 437 HIS cc_start: 0.8196 (t-90) cc_final: 0.7861 (m90) REVERT: B 448 MET cc_start: 0.9415 (mmt) cc_final: 0.9093 (mmt) REVERT: B 520 LYS cc_start: 0.8989 (tttt) cc_final: 0.8706 (ttmm) REVERT: B 798 MET cc_start: 0.8681 (mmm) cc_final: 0.8387 (mtp) REVERT: B 892 GLU cc_start: 0.8983 (tt0) cc_final: 0.8721 (mt-10) REVERT: B 916 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8821 (p0) REVERT: F 215 GLU cc_start: 0.7509 (pm20) cc_final: 0.7284 (tt0) REVERT: F 281 TYR cc_start: 0.7467 (m-80) cc_final: 0.7209 (m-80) REVERT: F 287 LYS cc_start: 0.8753 (tptp) cc_final: 0.8158 (ttmt) REVERT: F 295 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7417 (pp) REVERT: F 327 TRP cc_start: 0.4644 (OUTLIER) cc_final: 0.4255 (t-100) REVERT: F 389 LYS cc_start: 0.8462 (tptm) cc_final: 0.8172 (tppt) REVERT: F 391 LEU cc_start: 0.8376 (tp) cc_final: 0.7890 (tt) REVERT: F 398 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8457 (tp40) REVERT: G 46 GLU cc_start: 0.7665 (tt0) cc_final: 0.7115 (tt0) REVERT: G 55 ILE cc_start: 0.8811 (mt) cc_final: 0.8499 (tp) REVERT: G 153 LYS cc_start: 0.5589 (OUTLIER) cc_final: 0.3388 (tptt) REVERT: H 177 GLU cc_start: 0.8622 (tp30) cc_final: 0.8407 (tp30) REVERT: H 178 LYS cc_start: 0.8587 (mmtp) cc_final: 0.8144 (mtpt) REVERT: H 184 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.8337 (mtp85) REVERT: f 225 LYS cc_start: 0.8897 (ttpp) cc_final: 0.8690 (ttpt) REVERT: f 238 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8519 (mtmt) REVERT: f 249 ASP cc_start: 0.8345 (m-30) cc_final: 0.8098 (m-30) REVERT: f 270 ASN cc_start: 0.4948 (OUTLIER) cc_final: 0.3845 (t0) REVERT: f 365 ASP cc_start: 0.8543 (t0) cc_final: 0.8289 (t0) REVERT: f 389 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7682 (ttmt) outliers start: 71 outliers final: 50 residues processed: 334 average time/residue: 0.1786 time to fit residues: 88.8498 Evaluate side-chains 328 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 265 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ARG 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 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 674 THR 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 234 SER Chi-restraints excluded: chain F residue 243 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 326 HIS Chi-restraints excluded: chain F residue 327 TRP 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 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: 0.7980 chunk 140 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 198 optimal weight: 50.0000 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 223 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 225 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 HIS ** 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 = 0.4078 r_free = 0.4078 target = 0.163994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.113053 restraints weight = 28202.910| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.63 r_work: 0.3009 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21183 Z= 0.184 Angle : 0.583 14.075 29063 Z= 0.307 Chirality : 0.041 0.176 3241 Planarity : 0.004 0.054 3397 Dihedral : 17.821 150.727 3536 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.74 % Allowed : 15.99 % Favored : 80.28 % 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: 0.60 (0.18), residues: 2300 helix: 1.51 (0.16), residues: 1124 sheet: 0.04 (0.31), residues: 274 loop : -0.89 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 539 TYR 0.020 0.001 TYR B 283 PHE 0.021 0.001 PHE B 190 TRP 0.013 0.001 TRP F 370 HIS 0.008 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00436 (21182) covalent geometry : angle 0.58299 (29061) SS BOND : bond 0.00697 ( 1) SS BOND : angle 1.94651 ( 2) hydrogen bonds : bond 0.03690 ( 1048) hydrogen bonds : angle 4.03927 ( 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 345 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 269 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 ARG cc_start: 0.6267 (OUTLIER) cc_final: 0.5044 (tmm160) REVERT: A 400 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: A 481 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: A 511 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7117 (mt) REVERT: A 639 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7622 (pp) REVERT: A 692 MET cc_start: 0.8880 (mtp) cc_final: 0.8431 (mtm) REVERT: A 744 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7900 (tt0) REVERT: A 1058 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.6607 (t70) REVERT: B 41 GLN cc_start: 0.8257 (mp10) cc_final: 0.7998 (mp10) REVERT: B 71 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7806 (ttt90) REVERT: B 120 ASP cc_start: 0.7957 (m-30) cc_final: 0.7321 (m-30) REVERT: B 133 GLU cc_start: 0.8401 (pm20) cc_final: 0.8122 (pm20) REVERT: B 145 LYS cc_start: 0.8825 (mttt) cc_final: 0.8373 (mtpp) REVERT: B 212 MET cc_start: 0.8919 (mtt) cc_final: 0.8695 (mtt) REVERT: B 295 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8126 (mt) REVERT: B 303 CYS cc_start: 0.8907 (m) cc_final: 0.8356 (t) REVERT: B 437 HIS cc_start: 0.8232 (t-90) cc_final: 0.7895 (m90) REVERT: B 520 LYS cc_start: 0.8990 (tttt) cc_final: 0.8731 (ttmm) REVERT: B 798 MET cc_start: 0.8750 (mmm) cc_final: 0.8404 (mtp) REVERT: B 892 GLU cc_start: 0.9021 (tt0) cc_final: 0.8733 (mt-10) REVERT: B 916 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8836 (p0) REVERT: F 215 GLU cc_start: 0.7561 (pm20) cc_final: 0.7308 (tt0) REVERT: F 281 TYR cc_start: 0.7518 (m-80) cc_final: 0.7243 (m-80) REVERT: F 287 LYS cc_start: 0.8809 (tptp) cc_final: 0.8188 (ttmt) REVERT: F 295 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7395 (pp) REVERT: F 391 LEU cc_start: 0.8339 (tp) cc_final: 0.7863 (tt) REVERT: F 398 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8309 (tp-100) REVERT: G 36 HIS cc_start: 0.7289 (p90) cc_final: 0.6707 (p-80) REVERT: G 46 GLU cc_start: 0.7758 (tt0) cc_final: 0.7024 (tt0) REVERT: G 55 ILE cc_start: 0.8876 (mt) cc_final: 0.8585 (tp) REVERT: G 153 LYS cc_start: 0.5622 (OUTLIER) cc_final: 0.3407 (tptt) REVERT: H 177 GLU cc_start: 0.8646 (tp30) cc_final: 0.8428 (tp30) REVERT: H 178 LYS cc_start: 0.8590 (mmtp) cc_final: 0.8137 (mtpt) REVERT: f 238 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8521 (mtmt) REVERT: f 249 ASP cc_start: 0.8393 (m-30) cc_final: 0.8160 (m-30) REVERT: f 340 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8327 (tt) REVERT: f 365 ASP cc_start: 0.8542 (t0) cc_final: 0.8271 (t0) REVERT: f 389 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7714 (ttmt) REVERT: f 421 ASP cc_start: 0.7986 (p0) cc_final: 0.7280 (t0) outliers start: 76 outliers final: 55 residues processed: 326 average time/residue: 0.1778 time to fit residues: 86.0686 Evaluate side-chains 328 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 261 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ARG 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 628 LEU 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 B residue 21 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 674 THR 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 50 optimal weight: 9.9990 chunk 125 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 112 optimal weight: 0.0870 chunk 43 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.163848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112172 restraints weight = 28174.454| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.66 r_work: 0.3008 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21183 Z= 0.184 Angle : 0.595 14.035 29063 Z= 0.314 Chirality : 0.041 0.175 3241 Planarity : 0.004 0.057 3397 Dihedral : 17.833 150.747 3536 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.69 % Allowed : 16.13 % Favored : 80.18 % 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: 0.58 (0.18), residues: 2300 helix: 1.49 (0.16), residues: 1123 sheet: 0.08 (0.31), residues: 271 loop : -0.90 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1233 TYR 0.020 0.001 TYR B 283 PHE 0.027 0.001 PHE F 344 TRP 0.014 0.001 TRP F 370 HIS 0.008 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00435 (21182) covalent geometry : angle 0.59517 (29061) SS BOND : bond 0.00647 ( 1) SS BOND : angle 1.89073 ( 2) hydrogen bonds : bond 0.03696 ( 1048) hydrogen bonds : angle 4.07350 ( 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 329 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 254 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 ARG cc_start: 0.6244 (OUTLIER) cc_final: 0.5014 (tmm160) REVERT: A 400 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7261 (tp30) REVERT: A 481 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: A 511 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7123 (mt) REVERT: A 639 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.7623 (pp) REVERT: A 692 MET cc_start: 0.8868 (mtp) cc_final: 0.8415 (mtm) REVERT: A 744 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7817 (tp30) REVERT: A 1058 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.6608 (t70) REVERT: B 71 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7812 (ttt90) REVERT: B 120 ASP cc_start: 0.7901 (m-30) cc_final: 0.7277 (m-30) REVERT: B 133 GLU cc_start: 0.8408 (pm20) cc_final: 0.8207 (pm20) REVERT: B 137 HIS cc_start: 0.8393 (t-90) cc_final: 0.8162 (t70) REVERT: B 145 LYS cc_start: 0.8823 (mttt) cc_final: 0.8367 (mtpp) REVERT: B 212 MET cc_start: 0.8918 (mtt) cc_final: 0.8689 (mtt) REVERT: B 295 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8112 (mt) REVERT: B 298 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.7956 (mmt-90) REVERT: B 303 CYS cc_start: 0.8905 (m) cc_final: 0.8343 (t) REVERT: B 437 HIS cc_start: 0.8244 (t-90) cc_final: 0.7922 (m90) REVERT: B 520 LYS cc_start: 0.9001 (tttt) cc_final: 0.8739 (ttmm) REVERT: B 798 MET cc_start: 0.8763 (mmm) cc_final: 0.8402 (mtp) REVERT: B 892 GLU cc_start: 0.8990 (tt0) cc_final: 0.8736 (mt-10) REVERT: F 215 GLU cc_start: 0.7560 (pm20) cc_final: 0.7313 (tt0) REVERT: F 281 TYR cc_start: 0.7544 (m-80) cc_final: 0.7271 (m-80) REVERT: F 295 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7366 (pp) REVERT: F 398 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8304 (tp-100) REVERT: G 46 GLU cc_start: 0.7763 (tt0) cc_final: 0.7025 (tt0) REVERT: G 55 ILE cc_start: 0.8904 (mt) cc_final: 0.8612 (tp) REVERT: G 153 LYS cc_start: 0.5578 (OUTLIER) cc_final: 0.3388 (tptt) REVERT: H 178 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8135 (mtpt) REVERT: f 238 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8519 (mtmt) REVERT: f 340 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8320 (tt) REVERT: f 365 ASP cc_start: 0.8537 (t0) cc_final: 0.8270 (t0) REVERT: f 389 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7704 (ttmt) REVERT: f 421 ASP cc_start: 0.7826 (p0) cc_final: 0.7161 (t0) outliers start: 75 outliers final: 57 residues processed: 312 average time/residue: 0.1644 time to fit residues: 77.6132 Evaluate side-chains 320 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 252 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ARG 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 624 SER Chi-restraints excluded: chain A residue 628 LEU 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 1019 LYS 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 674 THR 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 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 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 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 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: 0.2980 chunk 174 optimal weight: 7.9990 chunk 220 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 104 optimal weight: 0.0980 chunk 235 optimal weight: 0.8980 chunk 237 optimal weight: 0.0170 chunk 113 optimal weight: 0.6980 chunk 232 optimal weight: 0.8980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.164435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113748 restraints weight = 28136.229| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.53 r_work: 0.3042 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21183 Z= 0.136 Angle : 0.565 10.209 29063 Z= 0.299 Chirality : 0.040 0.163 3241 Planarity : 0.004 0.068 3397 Dihedral : 17.751 150.573 3536 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.30 % Allowed : 16.53 % Favored : 80.18 % 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: 0.70 (0.18), residues: 2300 helix: 1.57 (0.16), residues: 1131 sheet: 0.15 (0.31), residues: 271 loop : -0.85 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1233 TYR 0.021 0.001 TYR F 374 PHE 0.027 0.001 PHE F 344 TRP 0.014 0.001 TRP F 370 HIS 0.007 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00314 (21182) covalent geometry : angle 0.56478 (29061) SS BOND : bond 0.00470 ( 1) SS BOND : angle 1.68869 ( 2) hydrogen bonds : bond 0.03356 ( 1048) hydrogen bonds : angle 3.99943 ( 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 329 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 262 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.5019 (tmm160) REVERT: A 400 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7158 (tp30) REVERT: A 481 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: A 511 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7137 (mt) REVERT: A 639 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7669 (pp) REVERT: A 692 MET cc_start: 0.8789 (mtp) cc_final: 0.8340 (mtm) REVERT: A 744 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7763 (tp30) REVERT: A 1032 MET cc_start: 0.7959 (mmp) cc_final: 0.7437 (ppp) REVERT: A 1058 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.6640 (t70) REVERT: B 71 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7782 (ttt90) REVERT: B 120 ASP cc_start: 0.7796 (m-30) cc_final: 0.7148 (m-30) REVERT: B 145 LYS cc_start: 0.8804 (mttt) cc_final: 0.8364 (mtpp) REVERT: B 212 MET cc_start: 0.8887 (mtt) cc_final: 0.8658 (mtt) REVERT: B 295 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8137 (mt) REVERT: B 303 CYS cc_start: 0.8799 (m) cc_final: 0.8301 (t) REVERT: B 437 HIS cc_start: 0.8218 (t-90) cc_final: 0.7893 (m90) REVERT: B 520 LYS cc_start: 0.8974 (tttt) cc_final: 0.8710 (ttmm) REVERT: B 798 MET cc_start: 0.8691 (mmm) cc_final: 0.8370 (mtp) REVERT: B 892 GLU cc_start: 0.8975 (tt0) cc_final: 0.8726 (mt-10) REVERT: F 215 GLU cc_start: 0.7541 (pm20) cc_final: 0.7289 (tt0) REVERT: F 252 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7750 (tt) REVERT: F 281 TYR cc_start: 0.7482 (m-80) cc_final: 0.7250 (m-80) REVERT: F 295 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7394 (pp) REVERT: F 394 PRO cc_start: 0.7923 (Cg_exo) cc_final: 0.7692 (Cg_endo) REVERT: F 398 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8370 (tp-100) REVERT: G 55 ILE cc_start: 0.8897 (mt) cc_final: 0.8643 (tp) REVERT: G 153 LYS cc_start: 0.5543 (OUTLIER) cc_final: 0.3396 (tptt) REVERT: H 178 LYS cc_start: 0.8568 (mmtp) cc_final: 0.8071 (mtpt) REVERT: f 238 LYS cc_start: 0.8827 (mtpt) cc_final: 0.8497 (mtmt) REVERT: f 339 GLN cc_start: 0.8384 (tt0) cc_final: 0.8046 (tp40) REVERT: f 365 ASP cc_start: 0.8569 (t0) cc_final: 0.8319 (t0) REVERT: f 389 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7719 (ttmt) REVERT: f 421 ASP cc_start: 0.7906 (p0) cc_final: 0.7326 (t0) outliers start: 67 outliers final: 49 residues processed: 313 average time/residue: 0.1675 time to fit residues: 79.2234 Evaluate side-chains 313 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 253 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 624 SER 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 1019 LYS 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 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 625 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 705 ILE 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 945 CYS 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 326 HIS Chi-restraints excluded: chain F residue 327 TRP 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 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 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: 3.9990 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 239 optimal weight: 6.9990 chunk 110 optimal weight: 0.0980 chunk 194 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.0570 chunk 237 optimal weight: 9.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.164671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112967 restraints weight = 28174.103| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.51 r_work: 0.3046 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21183 Z= 0.136 Angle : 0.563 12.183 29063 Z= 0.298 Chirality : 0.040 0.165 3241 Planarity : 0.004 0.058 3397 Dihedral : 17.688 150.604 3532 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.20 % Allowed : 17.02 % 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: 0.79 (0.18), residues: 2300 helix: 1.64 (0.16), residues: 1126 sheet: 0.23 (0.31), residues: 271 loop : -0.80 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1233 TYR 0.020 0.001 TYR F 374 PHE 0.024 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 covalent geometry : bond 0.00312 (21182) covalent geometry : angle 0.56317 (29061) SS BOND : bond 0.00472 ( 1) SS BOND : angle 1.70109 ( 2) hydrogen bonds : bond 0.03368 ( 1048) hydrogen bonds : angle 3.95537 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8337.29 seconds wall clock time: 142 minutes 23.36 seconds (8543.36 seconds total)