Starting phenix.real_space_refine on Sun Feb 8 08:21:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd7_51249/02_2026/9gd7_51249.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd7_51249/02_2026/9gd7_51249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gd7_51249/02_2026/9gd7_51249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd7_51249/02_2026/9gd7_51249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gd7_51249/02_2026/9gd7_51249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd7_51249/02_2026/9gd7_51249.map" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 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 49 5.49 5 S 245 5.16 5 C 26606 2.51 5 N 7101 2.21 5 O 7716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41717 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1956 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 235} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5084 Classifications: {'peptide': 641} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 28, 'TRANS': 612} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 3, 'ASP:plan': 2, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "M" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 160 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 19} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 480 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 475 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 56} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 27773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3535, 27773 Classifications: {'peptide': 3535} Incomplete info: {'n_c_alpha_c_only': 3, 'truncation_to_alanine': 166} Link IDs: {'PTRANS': 146, 'TRANS': 3388} Chain breaks: 37 Unresolved chain link angles: 35 Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 791 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PHE:plan': 6, 'ARG:plan': 15, 'GLU:plan': 14, 'ASN:plan1': 6, 'ASP:plan': 9, 'GLN:plan1': 14, 'TYR:plan': 8, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 348 Chain: "T" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 4001 Classifications: {'peptide': 501} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 11} Link IDs: {'PTRANS': 28, 'TRANS': 472} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "i" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 510 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "j" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 764 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Time building chain proxies: 8.61, per 1000 atoms: 0.21 Number of scatterers: 41717 At special positions: 0 Unit cell: (133.008, 228.2, 221.68, 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 245 16.00 P 49 15.00 O 7716 8.00 N 7101 7.00 C 26606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.11 Conformation dependent library (CDL) restraints added in 2.2 seconds 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9886 Finding SS restraints... Secondary structure from input PDB file: 250 helices and 17 sheets defined 63.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'E' and resid 675 through 686 removed outlier: 3.780A pdb=" N GLU E 679 " --> pdb=" O LYS E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 715 Processing helix chain 'E' and resid 722 through 733 removed outlier: 4.180A pdb=" N LEU E 726 " --> pdb=" O LYS E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 758 removed outlier: 3.815A pdb=" N GLU E 757 " --> pdb=" O HIS E 753 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR E 758 " --> pdb=" O PHE E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 781 Processing helix chain 'E' and resid 788 through 804 removed outlier: 3.581A pdb=" N MET E 792 " --> pdb=" O THR E 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 844 Processing helix chain 'E' and resid 868 through 870 No H-bonds generated for 'chain 'E' and resid 868 through 870' Processing helix chain 'E' and resid 871 through 882 Processing helix chain 'L' and resid 29 through 49 Processing helix chain 'L' and resid 87 through 97 Processing helix chain 'L' and resid 106 through 122 removed outlier: 4.101A pdb=" N ALA L 110 " --> pdb=" O ASP L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 156 Processing helix chain 'L' and resid 198 through 216 Processing helix chain 'L' and resid 217 through 224 Processing helix chain 'L' and resid 237 through 241 removed outlier: 3.685A pdb=" N GLU L 241 " --> pdb=" O LYS L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 332 Processing helix chain 'L' and resid 352 through 356 Processing helix chain 'L' and resid 370 through 388 Processing helix chain 'L' and resid 441 through 445 removed outlier: 3.648A pdb=" N ALA L 445 " --> pdb=" O LYS L 442 " (cutoff:3.500A) Processing helix chain 'L' and resid 447 through 462 Processing helix chain 'L' and resid 484 through 500 removed outlier: 3.822A pdb=" N GLN L 488 " --> pdb=" O ASN L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 509 through 515 removed outlier: 3.690A pdb=" N TRP L 513 " --> pdb=" O GLN L 509 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 537 removed outlier: 3.860A pdb=" N THR L 523 " --> pdb=" O PRO L 519 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE L 528 " --> pdb=" O THR L 524 " (cutoff:3.500A) Proline residue: L 529 - end of helix Processing helix chain 'L' and resid 594 through 605 removed outlier: 3.661A pdb=" N LYS L 605 " --> pdb=" O LEU L 601 " (cutoff:3.500A) Processing helix chain 'L' and resid 609 through 622 removed outlier: 3.715A pdb=" N SER L 613 " --> pdb=" O PHE L 609 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN L 622 " --> pdb=" O ASN L 618 " (cutoff:3.500A) Processing helix chain 'L' and resid 628 through 649 removed outlier: 3.920A pdb=" N PHE L 649 " --> pdb=" O GLU L 645 " (cutoff:3.500A) Processing helix chain 'L' and resid 651 through 667 Processing helix chain 'L' and resid 675 through 681 Processing helix chain 'L' and resid 682 through 684 No H-bonds generated for 'chain 'L' and resid 682 through 684' Processing helix chain 'L' and resid 693 through 702 Processing helix chain 'P' and resid 146 through 198 removed outlier: 3.792A pdb=" N GLU P 170 " --> pdb=" O VAL P 166 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA P 171 " --> pdb=" O SER P 167 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL P 183 " --> pdb=" O ARG P 179 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN P 196 " --> pdb=" O ARG P 192 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS P 197 " --> pdb=" O SER P 193 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 201 removed outlier: 3.920A pdb=" N ALA Q 168 " --> pdb=" O LYS Q 164 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA Q 171 " --> pdb=" O SER Q 167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU Q 182 " --> pdb=" O LYS Q 178 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL Q 183 " --> pdb=" O ARG Q 179 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS Q 188 " --> pdb=" O LEU Q 184 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN Q 196 " --> pdb=" O ARG Q 192 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU Q 199 " --> pdb=" O HIS Q 195 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN Q 200 " --> pdb=" O ASN Q 196 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA Q 201 " --> pdb=" O LYS Q 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 21 Processing helix chain 'S' and resid 28 through 47 removed outlier: 4.241A pdb=" N SER S 47 " --> pdb=" O VAL S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 70 removed outlier: 3.953A pdb=" N THR S 55 " --> pdb=" O LEU S 51 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL S 58 " --> pdb=" O GLN S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 97 removed outlier: 3.836A pdb=" N CYS S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 102 No H-bonds generated for 'chain 'S' and resid 100 through 102' Processing helix chain 'S' and resid 103 through 117 Processing helix chain 'S' and resid 118 through 123 removed outlier: 3.751A pdb=" N CYS S 123 " --> pdb=" O ALA S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 124 through 141 Processing helix chain 'S' and resid 144 through 148 removed outlier: 3.989A pdb=" N PHE S 147 " --> pdb=" O MET S 144 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS S 148 " --> pdb=" O ASP S 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 144 through 148' Processing helix chain 'S' and resid 149 through 161 Processing helix chain 'S' and resid 170 through 172 No H-bonds generated for 'chain 'S' and resid 170 through 172' Processing helix chain 'S' and resid 173 through 178 Processing helix chain 'S' and resid 186 through 208 removed outlier: 4.435A pdb=" N GLU S 194 " --> pdb=" O ILE S 190 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASN S 195 " --> pdb=" O ASN S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 219 through 232 Processing helix chain 'S' and resid 240 through 253 removed outlier: 4.339A pdb=" N THR S 244 " --> pdb=" O GLU S 240 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU S 253 " --> pdb=" O PHE S 249 " (cutoff:3.500A) Processing helix chain 'S' and resid 265 through 279 Processing helix chain 'S' and resid 289 through 301 Processing helix chain 'S' and resid 305 through 330 removed outlier: 3.588A pdb=" N LYS S 309 " --> pdb=" O ASN S 305 " (cutoff:3.500A) Processing helix chain 'S' and resid 333 through 349 removed outlier: 5.332A pdb=" N MET S 342 " --> pdb=" O LEU S 338 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLU S 343 " --> pdb=" O GLN S 339 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE S 349 " --> pdb=" O PHE S 345 " (cutoff:3.500A) Processing helix chain 'S' and resid 357 through 369 Processing helix chain 'S' and resid 370 through 376 Processing helix chain 'S' and resid 377 through 397 removed outlier: 3.721A pdb=" N VAL S 381 " --> pdb=" O ASN S 377 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP S 382 " --> pdb=" O ALA S 378 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU S 397 " --> pdb=" O LYS S 393 " (cutoff:3.500A) Processing helix chain 'S' and resid 409 through 424 Processing helix chain 'S' and resid 428 through 430 No H-bonds generated for 'chain 'S' and resid 428 through 430' Processing helix chain 'S' and resid 431 through 445 Processing helix chain 'S' and resid 450 through 469 Processing helix chain 'S' and resid 471 through 493 removed outlier: 3.753A pdb=" N LYS S 493 " --> pdb=" O ARG S 489 " (cutoff:3.500A) Processing helix chain 'S' and resid 524 through 526 No H-bonds generated for 'chain 'S' and resid 524 through 526' Processing helix chain 'S' and resid 527 through 537 Processing helix chain 'S' and resid 537 through 547 removed outlier: 4.715A pdb=" N SER S 543 " --> pdb=" O GLN S 539 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP S 547 " --> pdb=" O SER S 543 " (cutoff:3.500A) Processing helix chain 'S' and resid 560 through 579 Processing helix chain 'S' and resid 616 through 634 Processing helix chain 'S' and resid 644 through 660 removed outlier: 4.791A pdb=" N SER S 648 " --> pdb=" O PRO S 644 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER S 650 " --> pdb=" O VAL S 646 " (cutoff:3.500A) Processing helix chain 'S' and resid 663 through 680 removed outlier: 3.642A pdb=" N TYR S 667 " --> pdb=" O ILE S 663 " (cutoff:3.500A) Processing helix chain 'S' and resid 698 through 718 Processing helix chain 'S' and resid 719 through 721 No H-bonds generated for 'chain 'S' and resid 719 through 721' Processing helix chain 'S' and resid 725 through 735 Processing helix chain 'S' and resid 739 through 743 removed outlier: 3.733A pdb=" N LEU S 743 " --> pdb=" O ILE S 740 " (cutoff:3.500A) Processing helix chain 'S' and resid 744 through 760 removed outlier: 4.123A pdb=" N TYR S 748 " --> pdb=" O ASP S 744 " (cutoff:3.500A) Proline residue: S 750 - end of helix Processing helix chain 'S' and resid 762 through 780 removed outlier: 3.691A pdb=" N ALA S 766 " --> pdb=" O TYR S 762 " (cutoff:3.500A) Processing helix chain 'S' and resid 788 through 793 Processing helix chain 'S' and resid 794 through 798 removed outlier: 3.561A pdb=" N GLY S 798 " --> pdb=" O CYS S 795 " (cutoff:3.500A) Processing helix chain 'S' and resid 834 through 839 removed outlier: 4.249A pdb=" N ASN S 839 " --> pdb=" O LYS S 836 " (cutoff:3.500A) Processing helix chain 'S' and resid 848 through 863 removed outlier: 3.819A pdb=" N GLY S 863 " --> pdb=" O LEU S 859 " (cutoff:3.500A) Processing helix chain 'S' and resid 863 through 868 Processing helix chain 'S' and resid 869 through 871 No H-bonds generated for 'chain 'S' and resid 869 through 871' Processing helix chain 'S' and resid 910 through 920 Processing helix chain 'S' and resid 923 through 948 Processing helix chain 'S' and resid 958 through 974 Proline residue: S 967 - end of helix removed outlier: 3.587A pdb=" N CYS S 974 " --> pdb=" O LEU S 970 " (cutoff:3.500A) Processing helix chain 'S' and resid 977 through 996 removed outlier: 3.713A pdb=" N ARG S 981 " --> pdb=" O ASP S 977 " (cutoff:3.500A) Proline residue: S 986 - end of helix Processing helix chain 'S' and resid 997 through 1001 Processing helix chain 'S' and resid 1004 through 1018 removed outlier: 3.588A pdb=" N ALA S1008 " --> pdb=" O GLN S1004 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY S1016 " --> pdb=" O ALA S1012 " (cutoff:3.500A) Processing helix chain 'S' and resid 1022 through 1044 Processing helix chain 'S' and resid 1045 through 1052 removed outlier: 3.535A pdb=" N GLN S1049 " --> pdb=" O THR S1045 " (cutoff:3.500A) Processing helix chain 'S' and resid 1055 through 1069 removed outlier: 3.556A pdb=" N LEU S1059 " --> pdb=" O ASN S1055 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU S1068 " --> pdb=" O TYR S1064 " (cutoff:3.500A) Processing helix chain 'S' and resid 1071 through 1090 removed outlier: 4.457A pdb=" N ARG S1087 " --> pdb=" O ASN S1083 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU S1088 " --> pdb=" O ASN S1084 " (cutoff:3.500A) Processing helix chain 'S' and resid 1093 through 1099 Processing helix chain 'S' and resid 1100 through 1118 Processing helix chain 'S' and resid 1122 through 1141 Processing helix chain 'S' and resid 1142 through 1147 Processing helix chain 'S' and resid 1164 through 1175 removed outlier: 3.584A pdb=" N LEU S1168 " --> pdb=" O CYS S1164 " (cutoff:3.500A) Processing helix chain 'S' and resid 1180 through 1195 Processing helix chain 'S' and resid 1196 through 1198 No H-bonds generated for 'chain 'S' and resid 1196 through 1198' Processing helix chain 'S' and resid 1204 through 1213 Processing helix chain 'S' and resid 1218 through 1223 removed outlier: 3.616A pdb=" N THR S1223 " --> pdb=" O PHE S1219 " (cutoff:3.500A) Processing helix chain 'S' and resid 1231 through 1238 removed outlier: 3.610A pdb=" N ILE S1235 " --> pdb=" O GLN S1231 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN S1238 " --> pdb=" O GLY S1234 " (cutoff:3.500A) Processing helix chain 'S' and resid 1250 through 1273 Processing helix chain 'S' and resid 1277 through 1281 Processing helix chain 'S' and resid 1288 through 1300 Processing helix chain 'S' and resid 1327 through 1352 Processing helix chain 'S' and resid 1357 through 1362 Processing helix chain 'S' and resid 1368 through 1378 removed outlier: 3.817A pdb=" N VAL S1373 " --> pdb=" O MET S1369 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLN S1374 " --> pdb=" O ARG S1370 " (cutoff:3.500A) Processing helix chain 'S' and resid 1389 through 1394 Processing helix chain 'S' and resid 1394 through 1409 removed outlier: 3.606A pdb=" N VAL S1398 " --> pdb=" O HIS S1394 " (cutoff:3.500A) Processing helix chain 'S' and resid 1411 through 1423 Processing helix chain 'S' and resid 1430 through 1434 removed outlier: 3.997A pdb=" N VAL S1434 " --> pdb=" O LEU S1431 " (cutoff:3.500A) Processing helix chain 'S' and resid 1442 through 1461 Processing helix chain 'S' and resid 1477 through 1492 removed outlier: 3.826A pdb=" N ILE S1491 " --> pdb=" O VAL S1487 " (cutoff:3.500A) Processing helix chain 'S' and resid 1504 through 1521 removed outlier: 3.756A pdb=" N PHE S1521 " --> pdb=" O LEU S1517 " (cutoff:3.500A) Processing helix chain 'S' and resid 1523 through 1533 removed outlier: 4.282A pdb=" N ARG S1527 " --> pdb=" O GLY S1523 " (cutoff:3.500A) Processing helix chain 'S' and resid 1555 through 1574 removed outlier: 6.936A pdb=" N GLU S1565 " --> pdb=" O SER S1561 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR S1566 " --> pdb=" O LEU S1562 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS S1573 " --> pdb=" O THR S1569 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN S1574 " --> pdb=" O GLU S1570 " (cutoff:3.500A) Processing helix chain 'S' and resid 1576 through 1586 Processing helix chain 'S' and resid 1590 through 1607 Processing helix chain 'S' and resid 1612 through 1625 removed outlier: 3.703A pdb=" N LEU S1616 " --> pdb=" O LYS S1612 " (cutoff:3.500A) Processing helix chain 'S' and resid 1638 through 1656 Processing helix chain 'S' and resid 1667 through 1680 Processing helix chain 'S' and resid 1685 through 1694 Processing helix chain 'S' and resid 1695 through 1699 removed outlier: 4.040A pdb=" N PHE S1698 " --> pdb=" O LEU S1695 " (cutoff:3.500A) Processing helix chain 'S' and resid 1708 through 1722 Processing helix chain 'S' and resid 1733 through 1754 Processing helix chain 'S' and resid 1755 through 1767 Processing helix chain 'S' and resid 1774 through 1787 removed outlier: 3.639A pdb=" N PHE S1778 " --> pdb=" O MET S1774 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG S1787 " --> pdb=" O ARG S1783 " (cutoff:3.500A) Processing helix chain 'S' and resid 1790 through 1805 Processing helix chain 'S' and resid 1816 through 1830 removed outlier: 4.207A pdb=" N VAL S1820 " --> pdb=" O ARG S1816 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU S1825 " --> pdb=" O ASP S1821 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N THR S1826 " --> pdb=" O ARG S1822 " (cutoff:3.500A) Processing helix chain 'S' and resid 1832 through 1849 removed outlier: 5.813A pdb=" N VAL S1845 " --> pdb=" O SER S1841 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP S1846 " --> pdb=" O THR S1842 " (cutoff:3.500A) Processing helix chain 'S' and resid 1863 through 1881 Processing helix chain 'S' and resid 1914 through 1921 Processing helix chain 'S' and resid 1935 through 1953 Processing helix chain 'S' and resid 2035 through 2048 Processing helix chain 'S' and resid 2094 through 2108 removed outlier: 3.525A pdb=" N THR S2098 " --> pdb=" O MET S2094 " (cutoff:3.500A) Processing helix chain 'S' and resid 2126 through 2135 removed outlier: 3.682A pdb=" N ASN S2135 " --> pdb=" O GLY S2131 " (cutoff:3.500A) Processing helix chain 'S' and resid 2139 through 2154 removed outlier: 3.550A pdb=" N ARG S2143 " --> pdb=" O PRO S2139 " (cutoff:3.500A) Processing helix chain 'S' and resid 2157 through 2159 No H-bonds generated for 'chain 'S' and resid 2157 through 2159' Processing helix chain 'S' and resid 2160 through 2173 removed outlier: 5.611A pdb=" N SER S2166 " --> pdb=" O LYS S2162 " (cutoff:3.500A) Proline residue: S2167 - end of helix Processing helix chain 'S' and resid 2181 through 2194 removed outlier: 3.760A pdb=" N MET S2185 " --> pdb=" O GLY S2181 " (cutoff:3.500A) Processing helix chain 'S' and resid 2205 through 2222 removed outlier: 3.762A pdb=" N GLU S2209 " --> pdb=" O VAL S2205 " (cutoff:3.500A) Processing helix chain 'S' and resid 2229 through 2245 Processing helix chain 'S' and resid 2254 through 2262 removed outlier: 4.116A pdb=" N GLU S2258 " --> pdb=" O ARG S2254 " (cutoff:3.500A) Processing helix chain 'S' and resid 2270 through 2282 removed outlier: 3.502A pdb=" N ILE S2274 " --> pdb=" O ASN S2270 " (cutoff:3.500A) Processing helix chain 'S' and resid 2300 through 2309 Processing helix chain 'S' and resid 2312 through 2329 removed outlier: 4.031A pdb=" N TYR S2316 " --> pdb=" O TYR S2312 " (cutoff:3.500A) Processing helix chain 'S' and resid 2330 through 2334 Processing helix chain 'S' and resid 2338 through 2351 Processing helix chain 'S' and resid 2359 through 2369 Processing helix chain 'S' and resid 2371 through 2377 removed outlier: 3.869A pdb=" N LEU S2374 " --> pdb=" O PHE S2371 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP S2376 " --> pdb=" O PRO S2373 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG S2377 " --> pdb=" O LEU S2374 " (cutoff:3.500A) Processing helix chain 'S' and resid 2378 through 2385 Processing helix chain 'S' and resid 2386 through 2389 removed outlier: 4.098A pdb=" N PHE S2389 " --> pdb=" O LEU S2386 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 2386 through 2389' Processing helix chain 'S' and resid 2391 through 2403 removed outlier: 3.673A pdb=" N THR S2395 " --> pdb=" O GLY S2391 " (cutoff:3.500A) Processing helix chain 'S' and resid 2411 through 2419 Processing helix chain 'S' and resid 2419 through 2426 removed outlier: 4.114A pdb=" N VAL S2423 " --> pdb=" O ASP S2419 " (cutoff:3.500A) Processing helix chain 'S' and resid 2428 through 2443 Processing helix chain 'S' and resid 2444 through 2446 No H-bonds generated for 'chain 'S' and resid 2444 through 2446' Processing helix chain 'S' and resid 2447 through 2460 removed outlier: 3.943A pdb=" N ASN S2456 " --> pdb=" O ARG S2452 " (cutoff:3.500A) Proline residue: S2457 - end of helix removed outlier: 4.468A pdb=" N GLU S2460 " --> pdb=" O ASN S2456 " (cutoff:3.500A) Processing helix chain 'S' and resid 2467 through 2484 Processing helix chain 'S' and resid 2492 through 2509 Processing helix chain 'S' and resid 2514 through 2527 removed outlier: 3.518A pdb=" N HIS S2527 " --> pdb=" O ASN S2523 " (cutoff:3.500A) Processing helix chain 'S' and resid 2534 through 2545 Processing helix chain 'S' and resid 2553 through 2565 removed outlier: 3.615A pdb=" N MET S2565 " --> pdb=" O PHE S2561 " (cutoff:3.500A) Processing helix chain 'S' and resid 2723 through 2730 removed outlier: 3.719A pdb=" N ARG S2727 " --> pdb=" O THR S2723 " (cutoff:3.500A) Processing helix chain 'S' and resid 2732 through 2736 removed outlier: 4.238A pdb=" N ASP S2735 " --> pdb=" O PHE S2732 " (cutoff:3.500A) Processing helix chain 'S' and resid 2737 through 2764 Processing helix chain 'S' and resid 2787 through 2801 Proline residue: S2793 - end of helix Processing helix chain 'S' and resid 2801 through 2821 removed outlier: 3.755A pdb=" N ALA S2805 " --> pdb=" O ASP S2801 " (cutoff:3.500A) Processing helix chain 'S' and resid 2825 through 2847 Processing helix chain 'S' and resid 2851 through 2864 Processing helix chain 'S' and resid 2865 through 2869 Processing helix chain 'S' and resid 2872 through 2884 Processing helix chain 'S' and resid 2885 through 2901 removed outlier: 3.784A pdb=" N GLY S2889 " --> pdb=" O GLN S2885 " (cutoff:3.500A) Processing helix chain 'S' and resid 2919 through 2934 Processing helix chain 'S' and resid 2936 through 2944 Processing helix chain 'S' and resid 2950 through 2961 removed outlier: 3.958A pdb=" N GLN S2954 " --> pdb=" O LYS S2950 " (cutoff:3.500A) Processing helix chain 'S' and resid 2964 through 2977 removed outlier: 3.658A pdb=" N ALA S2968 " --> pdb=" O ASP S2964 " (cutoff:3.500A) Processing helix chain 'S' and resid 2987 through 3005 Processing helix chain 'S' and resid 3007 through 3015 removed outlier: 3.677A pdb=" N LEU S3011 " --> pdb=" O GLU S3007 " (cutoff:3.500A) Processing helix chain 'S' and resid 3034 through 3054 Proline residue: S3042 - end of helix removed outlier: 3.751A pdb=" N GLN S3054 " --> pdb=" O LYS S3050 " (cutoff:3.500A) Processing helix chain 'S' and resid 3059 through 3070 removed outlier: 3.683A pdb=" N HIS S3070 " --> pdb=" O ASP S3066 " (cutoff:3.500A) Processing helix chain 'S' and resid 3071 through 3093 removed outlier: 3.642A pdb=" N SER S3083 " --> pdb=" O GLU S3079 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N GLN S3084 " --> pdb=" O LEU S3080 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU S3085 " --> pdb=" O HIS S3081 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU S3086 " --> pdb=" O TYR S3082 " (cutoff:3.500A) Processing helix chain 'S' and resid 3095 through 3117 Processing helix chain 'S' and resid 3121 through 3143 removed outlier: 3.740A pdb=" N ARG S3125 " --> pdb=" O LEU S3121 " (cutoff:3.500A) Processing helix chain 'S' and resid 3155 through 3162 removed outlier: 4.199A pdb=" N ARG S3159 " --> pdb=" O VAL S3155 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN S3162 " --> pdb=" O LYS S3158 " (cutoff:3.500A) Processing helix chain 'S' and resid 3162 through 3167 Processing helix chain 'S' and resid 3175 through 3197 removed outlier: 3.719A pdb=" N TRP S3179 " --> pdb=" O PRO S3175 " (cutoff:3.500A) Processing helix chain 'S' and resid 3227 through 3249 Processing helix chain 'S' and resid 3255 through 3265 Processing helix chain 'S' and resid 3269 through 3287 removed outlier: 3.535A pdb=" N LEU S3273 " --> pdb=" O ARG S3269 " (cutoff:3.500A) Processing helix chain 'S' and resid 3291 through 3299 Processing helix chain 'S' and resid 3304 through 3308 Processing helix chain 'S' and resid 3319 through 3344 removed outlier: 3.706A pdb=" N PHE S3323 " --> pdb=" O ASN S3319 " (cutoff:3.500A) Processing helix chain 'S' and resid 3347 through 3352 Processing helix chain 'S' and resid 3354 through 3364 Processing helix chain 'S' and resid 3369 through 3393 removed outlier: 3.607A pdb=" N GLU S3393 " --> pdb=" O VAL S3389 " (cutoff:3.500A) Processing helix chain 'S' and resid 3408 through 3428 removed outlier: 3.780A pdb=" N GLU S3428 " --> pdb=" O LEU S3424 " (cutoff:3.500A) Processing helix chain 'S' and resid 3442 through 3455 Processing helix chain 'S' and resid 3458 through 3463 Processing helix chain 'S' and resid 3464 through 3475 Processing helix chain 'S' and resid 3475 through 3480 Processing helix chain 'S' and resid 3481 through 3485 removed outlier: 4.172A pdb=" N THR S3484 " --> pdb=" O SER S3481 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS S3485 " --> pdb=" O LEU S3482 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 3481 through 3485' Processing helix chain 'S' and resid 3495 through 3497 No H-bonds generated for 'chain 'S' and resid 3495 through 3497' Processing helix chain 'S' and resid 3498 through 3508 removed outlier: 4.069A pdb=" N LYS S3508 " --> pdb=" O ALA S3504 " (cutoff:3.500A) Processing helix chain 'S' and resid 3512 through 3525 removed outlier: 3.801A pdb=" N HIS S3516 " --> pdb=" O VAL S3512 " (cutoff:3.500A) Processing helix chain 'S' and resid 3529 through 3536 Processing helix chain 'S' and resid 3547 through 3562 removed outlier: 3.685A pdb=" N ASN S3551 " --> pdb=" O THR S3547 " (cutoff:3.500A) Processing helix chain 'S' and resid 3564 through 3577 removed outlier: 3.857A pdb=" N ILE S3568 " --> pdb=" O GLN S3564 " (cutoff:3.500A) Processing helix chain 'S' and resid 3580 through 3595 removed outlier: 3.779A pdb=" N LEU S3584 " --> pdb=" O ASN S3580 " (cutoff:3.500A) Processing helix chain 'S' and resid 3605 through 3617 Processing helix chain 'S' and resid 3627 through 3644 removed outlier: 5.307A pdb=" N LYS S3638 " --> pdb=" O GLN S3634 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLU S3639 " --> pdb=" O THR S3635 " (cutoff:3.500A) Processing helix chain 'S' and resid 3658 through 3669 Processing helix chain 'S' and resid 3684 through 3689 Processing helix chain 'S' and resid 3759 through 3778 Processing helix chain 'S' and resid 3778 through 3784 Processing helix chain 'S' and resid 3812 through 3820 Processing helix chain 'S' and resid 3821 through 3831 removed outlier: 3.782A pdb=" N ASP S3831 " --> pdb=" O ALA S3827 " (cutoff:3.500A) Processing helix chain 'S' and resid 3833 through 3843 removed outlier: 5.912A pdb=" N LYS S3840 " --> pdb=" O PRO S3836 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASP S3841 " --> pdb=" O CYS S3837 " (cutoff:3.500A) Processing helix chain 'S' and resid 3853 through 3861 removed outlier: 4.410A pdb=" N LEU S3857 " --> pdb=" O GLY S3853 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET S3858 " --> pdb=" O ALA S3854 " (cutoff:3.500A) Processing helix chain 'S' and resid 3863 through 3878 Processing helix chain 'S' and resid 3881 through 3891 Processing helix chain 'S' and resid 3893 through 3918 Processing helix chain 'S' and resid 3924 through 3926 No H-bonds generated for 'chain 'S' and resid 3924 through 3926' Processing helix chain 'S' and resid 3947 through 3953 Processing helix chain 'S' and resid 3964 through 3969 Processing helix chain 'S' and resid 3978 through 3989 Processing helix chain 'S' and resid 3990 through 3991 No H-bonds generated for 'chain 'S' and resid 3990 through 3991' Processing helix chain 'S' and resid 3996 through 3996 No H-bonds generated for 'chain 'S' and resid 3996 through 3996' Processing helix chain 'S' and resid 3997 through 4003 removed outlier: 3.892A pdb=" N THR S4001 " --> pdb=" O LEU S3997 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP S4003 " --> pdb=" O THR S3999 " (cutoff:3.500A) Processing helix chain 'S' and resid 4039 through 4053 removed outlier: 3.902A pdb=" N LYS S4043 " --> pdb=" O TYR S4039 " (cutoff:3.500A) Processing helix chain 'S' and resid 4055 through 4065 Processing helix chain 'S' and resid 4073 through 4083 Processing helix chain 'S' and resid 4100 through 4110 Processing helix chain 'S' and resid 4112 through 4119 removed outlier: 4.084A pdb=" N ILE S4116 " --> pdb=" O THR S4112 " (cutoff:3.500A) Processing helix chain 'S' and resid 4121 through 4125 Processing helix chain 'T' and resid 58 through 79 removed outlier: 4.079A pdb=" N ASP T 79 " --> pdb=" O ILE T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 112 through 121 Processing helix chain 'T' and resid 123 through 135 Processing helix chain 'T' and resid 142 through 156 removed outlier: 3.550A pdb=" N VAL T 146 " --> pdb=" O SER T 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 179 through 196 Processing helix chain 'T' and resid 238 through 244 removed outlier: 3.540A pdb=" N ARG T 244 " --> pdb=" O GLU T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 330 through 339 Processing helix chain 'T' and resid 377 through 393 Processing helix chain 'T' and resid 455 through 469 Processing helix chain 'T' and resid 474 through 478 removed outlier: 3.735A pdb=" N SER T 477 " --> pdb=" O ARG T 474 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE T 478 " --> pdb=" O SER T 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 474 through 478' Processing helix chain 'T' and resid 480 through 495 Processing helix chain 'T' and resid 510 through 519 removed outlier: 3.522A pdb=" N MET T 514 " --> pdb=" O LYS T 510 " (cutoff:3.500A) Processing helix chain 'T' and resid 521 through 529 Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.246A pdb=" N SER A 43 " --> pdb=" O TRP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 112 through 122 Processing sheet with id=AA1, first strand: chain 'E' and resid 664 through 665 Processing sheet with id=AA2, first strand: chain 'L' and resid 77 through 79 removed outlier: 8.567A pdb=" N VAL L 57 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU L 12 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHE L 59 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N MET L 14 " --> pdb=" O PHE L 59 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA L 9 " --> pdb=" O HIS L 131 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N GLU L 133 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL L 11 " --> pdb=" O GLU L 133 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N PHE L 135 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N CYS L 13 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG L 130 " --> pdb=" O SER L 160 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N GLN L 162 " --> pdb=" O ARG L 130 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE L 132 " --> pdb=" O GLN L 162 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE L 164 " --> pdb=" O ILE L 132 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE L 134 " --> pdb=" O PHE L 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 247 through 253 removed outlier: 6.524A pdb=" N VAL L 361 " --> pdb=" O SER L 266 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLN L 360 " --> pdb=" O GLN L 423 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLN L 423 " --> pdb=" O GLN L 360 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU L 419 " --> pdb=" O VAL L 364 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L 408 " --> pdb=" O ALA L 391 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA L 391 " --> pdb=" O ALA L 408 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N MET L 389 " --> pdb=" O PRO L 410 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL L 390 " --> pdb=" O PHE L 345 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE L 345 " --> pdb=" O VAL L 390 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE L 392 " --> pdb=" O LEU L 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 277 through 279 Processing sheet with id=AA5, first strand: chain 'L' and resid 303 through 304 removed outlier: 4.119A pdb=" N CYS L 296 " --> pdb=" O LYS T 297 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS T 297 " --> pdb=" O CYS L 296 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 310 through 311 Processing sheet with id=AA7, first strand: chain 'L' and resid 313 through 315 Processing sheet with id=AA8, first strand: chain 'L' and resid 540 through 541 removed outlier: 3.623A pdb=" N ILE L 540 " --> pdb=" O ILE T 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 583 through 584 removed outlier: 3.615A pdb=" N HIS S 613 " --> pdb=" O GLU S 584 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 894 through 895 Processing sheet with id=AB2, first strand: chain 'S' and resid 2587 through 2588 Processing sheet with id=AB3, first strand: chain 'S' and resid 3727 through 3728 removed outlier: 3.692A pdb=" N THR S3727 " --> pdb=" O ARG S3737 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS S3736 " --> pdb=" O VAL S3752 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY S3801 " --> pdb=" O LYS S3753 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU S3800 " --> pdb=" O MET S3796 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 3810 through 3811 Processing sheet with id=AB5, first strand: chain 'T' and resid 103 through 109 removed outlier: 4.397A pdb=" N VAL T 104 " --> pdb=" O PHE T 87 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N PHE T 87 " --> pdb=" O VAL T 104 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU T 108 " --> pdb=" O LEU T 83 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU T 83 " --> pdb=" O LEU T 108 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP T 36 " --> pdb=" O LEU T 82 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA T 84 " --> pdb=" O ASP T 36 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU T 38 " --> pdb=" O ALA T 84 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL T 86 " --> pdb=" O LEU T 38 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE T 40 " --> pdb=" O VAL T 86 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N TYR T 88 " --> pdb=" O PHE T 40 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL T 42 " --> pdb=" O TYR T 88 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ARG T 35 " --> pdb=" O HIS T 163 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N ARG T 165 " --> pdb=" O ARG T 35 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER T 37 " --> pdb=" O ARG T 165 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N MET T 167 " --> pdb=" O SER T 37 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE T 39 " --> pdb=" O MET T 167 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N PHE T 169 " --> pdb=" O ILE T 39 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU T 41 " --> pdb=" O PHE T 169 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET T 203 " --> pdb=" O LEU T 168 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR T 170 " --> pdb=" O MET T 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 257 through 262 removed outlier: 3.949A pdb=" N SER T 257 " --> pdb=" O ILE T 273 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE T 273 " --> pdb=" O SER T 257 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE T 432 " --> pdb=" O VAL T 368 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL T 394 " --> pdb=" O PRO T 415 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ARG T 399 " --> pdb=" O LEU T 347 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU T 347 " --> pdb=" O ARG T 399 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR T 401 " --> pdb=" O LEU T 345 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU T 345 " --> pdb=" O THR T 401 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU T 345 " --> pdb=" O LYS T 260 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU T 347 " --> pdb=" O LYS T 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 419 through 420 removed outlier: 6.305A pdb=" N GLU T 419 " --> pdb=" O VAL T 427 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 47 through 48 removed outlier: 7.119A pdb=" N HIS A 47 " --> pdb=" O VAL A 84 " (cutoff:3.500A) 2253 hydrogen bonds defined for protein. 6630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.14 Time building geometry restraints manager: 5.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7674 1.33 - 1.45: 10229 1.45 - 1.57: 24249 1.57 - 1.69: 97 1.69 - 1.82: 380 Bond restraints: 42629 Sorted by residual: bond pdb=" C PRO S2372 " pdb=" N PRO S2373 " ideal model delta sigma weight residual 1.337 1.374 -0.037 9.80e-03 1.04e+04 1.43e+01 bond pdb=" N ASP S4012 " pdb=" CA ASP S4012 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.34e+00 bond pdb=" N LEU S 773 " pdb=" CA LEU S 773 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.16e-02 7.43e+03 5.97e+00 bond pdb=" N SER S4010 " pdb=" CA SER S4010 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.91e+00 bond pdb=" N GLU S 774 " pdb=" CA GLU S 774 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.27e-02 6.20e+03 5.56e+00 ... (remaining 42624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 56113 2.17 - 4.35: 1352 4.35 - 6.52: 274 6.52 - 8.70: 65 8.70 - 10.87: 11 Bond angle restraints: 57815 Sorted by residual: angle pdb=" C MET S1108 " pdb=" N GLU S1109 " pdb=" CA GLU S1109 " ideal model delta sigma weight residual 121.14 112.41 8.73 1.75e+00 3.27e-01 2.49e+01 angle pdb=" N GLN A 120 " pdb=" CA GLN A 120 " pdb=" CB GLN A 120 " ideal model delta sigma weight residual 110.20 117.40 -7.20 1.49e+00 4.50e-01 2.34e+01 angle pdb=" N GLN S3390 " pdb=" CA GLN S3390 " pdb=" CB GLN S3390 " ideal model delta sigma weight residual 110.28 117.61 -7.33 1.55e+00 4.16e-01 2.24e+01 angle pdb=" N GLU S3079 " pdb=" CA GLU S3079 " pdb=" CB GLU S3079 " ideal model delta sigma weight residual 110.20 117.08 -6.88 1.49e+00 4.50e-01 2.13e+01 angle pdb=" N GLN S3766 " pdb=" CA GLN S3766 " pdb=" CB GLN S3766 " ideal model delta sigma weight residual 110.22 117.21 -6.99 1.54e+00 4.22e-01 2.06e+01 ... (remaining 57810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.35: 24567 28.35 - 56.71: 1215 56.71 - 85.06: 159 85.06 - 113.41: 12 113.41 - 141.77: 2 Dihedral angle restraints: 25955 sinusoidal: 10821 harmonic: 15134 Sorted by residual: dihedral pdb=" CA TYR S 340 " pdb=" C TYR S 340 " pdb=" N PHE S 341 " pdb=" CA PHE S 341 " ideal model delta harmonic sigma weight residual -180.00 -152.45 -27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA PRO S3175 " pdb=" C PRO S3175 " pdb=" N MET S3176 " pdb=" CA MET S3176 " ideal model delta harmonic sigma weight residual 180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA LYS P 190 " pdb=" C LYS P 190 " pdb=" N ILE P 191 " pdb=" CA ILE P 191 " ideal model delta harmonic sigma weight residual 180.00 156.02 23.98 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 25952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 6154 0.093 - 0.185: 417 0.185 - 0.278: 6 0.278 - 0.370: 2 0.370 - 0.463: 1 Chirality restraints: 6580 Sorted by residual: chirality pdb=" P DT j 27 " pdb=" OP1 DT j 27 " pdb=" OP2 DT j 27 " pdb=" O5' DT j 27 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CB ILE S2804 " pdb=" CA ILE S2804 " pdb=" CG1 ILE S2804 " pdb=" CG2 ILE S2804 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CG LEU L 463 " pdb=" CB LEU L 463 " pdb=" CD1 LEU L 463 " pdb=" CD2 LEU L 463 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 6577 not shown) Planarity restraints: 7201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 776 " 0.029 2.00e-02 2.50e+03 2.95e-02 2.18e+01 pdb=" CG TRP S 776 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP S 776 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP S 776 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP S 776 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP S 776 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP S 776 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 776 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 776 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP S 776 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 241 " -0.046 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO S 242 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO S 242 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO S 242 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE S2420 " 0.008 2.00e-02 2.50e+03 2.04e-02 7.27e+00 pdb=" CG PHE S2420 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE S2420 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE S2420 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE S2420 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE S2420 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE S2420 " 0.004 2.00e-02 2.50e+03 ... (remaining 7198 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5538 2.75 - 3.29: 49133 3.29 - 3.82: 78434 3.82 - 4.36: 90843 4.36 - 4.90: 138725 Nonbonded interactions: 362673 Sorted by model distance: nonbonded pdb=" O SER S1657 " pdb=" OG SER S1660 " model vdw 2.211 3.040 nonbonded pdb=" O MET S3044 " pdb=" OG SER S3047 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR L 277 " pdb=" OG SER T 319 " model vdw 2.213 3.040 nonbonded pdb=" OG SER S3870 " pdb=" O LEU S4117 " model vdw 2.213 3.040 nonbonded pdb=" O GLU S1565 " pdb=" OG1 THR S1569 " model vdw 2.222 3.040 ... (remaining 362668 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 'P' and (resid 145 through 184 or (resid 185 and (name N or name CA or na \ me C or name O or name CB )) or resid 186 through 188 or (resid 189 and (name N \ or name CA or name C or name O or name CB )) or resid 190 through 201)) selection = chain 'Q' } 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 group one per residue 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 42.600 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.004 0.052 42629 Z= 0.182 Angle : 0.827 10.869 57815 Z= 0.426 Chirality : 0.048 0.463 6580 Planarity : 0.005 0.074 7201 Dihedral : 16.326 141.766 16069 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.25 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.12), residues: 5060 helix: 0.09 (0.09), residues: 3022 sheet: -1.10 (0.33), residues: 229 loop : -1.79 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG S 971 TYR 0.030 0.002 TYR S1874 PHE 0.037 0.002 PHE S3952 TRP 0.080 0.002 TRP S 776 HIS 0.011 0.001 HIS S3915 Details of bonding type rmsd covalent geometry : bond 0.00381 (42629) covalent geometry : angle 0.82746 (57815) hydrogen bonds : bond 0.14649 ( 2253) hydrogen bonds : angle 6.15267 ( 6630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 667 MET cc_start: 0.8529 (ppp) cc_final: 0.8289 (ppp) REVERT: E 792 MET cc_start: 0.3864 (ptm) cc_final: 0.2938 (ptm) REVERT: L 20 MET cc_start: 0.4333 (pmm) cc_final: 0.4110 (pmm) REVERT: L 389 MET cc_start: 0.8537 (tpp) cc_final: 0.8238 (tpp) REVERT: S 88 PHE cc_start: 0.7716 (m-10) cc_final: 0.7482 (m-10) REVERT: S 238 MET cc_start: 0.8016 (mmp) cc_final: 0.7770 (mmp) REVERT: S 275 PHE cc_start: 0.9039 (t80) cc_final: 0.8747 (t80) REVERT: S 707 PHE cc_start: 0.9521 (m-10) cc_final: 0.8830 (m-80) REVERT: S 718 MET cc_start: 0.9516 (ppp) cc_final: 0.9179 (ppp) REVERT: S 939 MET cc_start: 0.8956 (mtm) cc_final: 0.8440 (tpp) REVERT: S 966 PHE cc_start: 0.9040 (m-10) cc_final: 0.8706 (m-10) REVERT: S 1583 MET cc_start: 0.9557 (ttt) cc_final: 0.9344 (tpt) REVERT: S 1600 MET cc_start: 0.9272 (mmp) cc_final: 0.8788 (mmm) REVERT: S 1881 TYR cc_start: 0.7042 (m-10) cc_final: 0.6750 (m-80) REVERT: S 2443 MET cc_start: 0.9201 (ppp) cc_final: 0.8786 (ppp) REVERT: S 2565 MET cc_start: 0.9471 (ppp) cc_final: 0.9079 (ppp) REVERT: S 3110 PHE cc_start: 0.9333 (m-10) cc_final: 0.9107 (m-10) REVERT: S 3670 MET cc_start: 0.6648 (ppp) cc_final: 0.5906 (ppp) REVERT: S 3687 MET cc_start: 0.7745 (mmp) cc_final: 0.7449 (mmp) REVERT: S 3786 LEU cc_start: 0.8312 (mt) cc_final: 0.8032 (mt) REVERT: T 48 MET cc_start: 0.9581 (mpp) cc_final: 0.9343 (mpp) REVERT: T 62 MET cc_start: 0.9119 (ptp) cc_final: 0.8868 (ptp) REVERT: T 135 MET cc_start: 0.9057 (tpt) cc_final: 0.8738 (tpp) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2516 time to fit residues: 109.0159 Evaluate side-chains 193 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 50.0000 chunk 265 optimal weight: 9.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 0.7980 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 0.6980 chunk 142 optimal weight: 10.0000 overall best weight: 5.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 GLN ** L 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 680 GLN S 32 HIS S 54 GLN ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 771 ASN S1049 GLN ** S1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1611 GLN S1830 HIS S2306 ASN S2351 GLN S2508 GLN ** S3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3423 GLN ** S3549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 426 GLN ** T 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 489 ASN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.037742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.025530 restraints weight = 549868.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.026332 restraints weight = 354236.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.026878 restraints weight = 253817.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.027292 restraints weight = 197415.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.027576 restraints weight = 162396.600| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 42629 Z= 0.218 Angle : 0.685 10.565 57815 Z= 0.361 Chirality : 0.043 0.190 6580 Planarity : 0.005 0.070 7201 Dihedral : 13.252 141.219 6064 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.65 % Favored : 92.19 % Rotamer: Outliers : 0.29 % Allowed : 7.74 % Favored : 91.97 % 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: -0.75 (0.12), residues: 5060 helix: 0.28 (0.09), residues: 3068 sheet: -1.38 (0.33), residues: 232 loop : -1.68 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 971 TYR 0.019 0.002 TYR S3082 PHE 0.034 0.002 PHE S2420 TRP 0.038 0.002 TRP S 776 HIS 0.008 0.001 HIS S1418 Details of bonding type rmsd covalent geometry : bond 0.00434 (42629) covalent geometry : angle 0.68468 (57815) hydrogen bonds : bond 0.04157 ( 2253) hydrogen bonds : angle 5.19040 ( 6630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 224 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S2108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 20 MET cc_start: 0.4690 (pmm) cc_final: 0.4480 (pmm) REVERT: L 515 MET cc_start: 0.8199 (pmm) cc_final: 0.7943 (pmm) REVERT: S 238 MET cc_start: 0.8826 (mmp) cc_final: 0.8223 (mmp) REVERT: S 718 MET cc_start: 0.9385 (ppp) cc_final: 0.9178 (ppp) REVERT: S 754 MET cc_start: 0.9406 (tpt) cc_final: 0.8989 (tpp) REVERT: S 758 LEU cc_start: 0.9756 (mt) cc_final: 0.9406 (mt) REVERT: S 785 MET cc_start: 0.9139 (mmp) cc_final: 0.8863 (mmm) REVERT: S 939 MET cc_start: 0.9127 (mtm) cc_final: 0.8582 (tpp) REVERT: S 1369 MET cc_start: 0.9042 (ptm) cc_final: 0.8811 (ptm) REVERT: S 1600 MET cc_start: 0.9199 (mmp) cc_final: 0.8574 (mmm) REVERT: S 1881 TYR cc_start: 0.7357 (m-10) cc_final: 0.7113 (m-80) REVERT: S 2331 MET cc_start: 0.6087 (pmm) cc_final: 0.5483 (pmm) REVERT: S 2443 MET cc_start: 0.9140 (ppp) cc_final: 0.8920 (ppp) REVERT: S 2478 MET cc_start: 0.9280 (ptp) cc_final: 0.8810 (mtm) REVERT: S 2565 MET cc_start: 0.9492 (ppp) cc_final: 0.9204 (ppp) REVERT: S 3079 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.9081 (pp20) REVERT: S 3110 PHE cc_start: 0.8718 (m-10) cc_final: 0.8454 (m-10) REVERT: S 3111 MET cc_start: 0.9103 (ppp) cc_final: 0.8820 (ppp) REVERT: S 3238 MET cc_start: 0.9128 (mmp) cc_final: 0.8815 (mmm) REVERT: S 3242 MET cc_start: 0.9327 (tpp) cc_final: 0.9049 (tpt) REVERT: S 3414 MET cc_start: 0.9278 (mmt) cc_final: 0.9061 (mmp) REVERT: S 3670 MET cc_start: 0.6747 (ppp) cc_final: 0.6180 (ppp) REVERT: S 3687 MET cc_start: 0.7520 (mmp) cc_final: 0.7256 (mmp) REVERT: S 3786 LEU cc_start: 0.9177 (mt) cc_final: 0.8872 (mt) REVERT: S 3900 LEU cc_start: 0.9443 (pp) cc_final: 0.9208 (pp) REVERT: S 3984 MET cc_start: 0.9359 (mtm) cc_final: 0.9019 (mtp) REVERT: T 48 MET cc_start: 0.9378 (mpp) cc_final: 0.8993 (mpp) REVERT: T 135 MET cc_start: 0.9238 (tpt) cc_final: 0.8526 (tpp) REVERT: T 161 MET cc_start: 0.8773 (tmm) cc_final: 0.8482 (tmm) REVERT: T 446 MET cc_start: 0.8599 (pmm) cc_final: 0.8385 (pmm) outliers start: 13 outliers final: 2 residues processed: 237 average time/residue: 0.2244 time to fit residues: 90.0993 Evaluate side-chains 188 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 185 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 261 optimal weight: 0.0870 chunk 334 optimal weight: 5.9990 chunk 326 optimal weight: 10.0000 chunk 356 optimal weight: 9.9990 chunk 286 optimal weight: 4.9990 chunk 476 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 461 optimal weight: 5.9990 chunk 484 optimal weight: 8.9990 chunk 408 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 680 GLN S 32 HIS ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1049 GLN ** S1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2306 ASN S2351 GLN S2508 GLN ** S3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3908 HIS ** S3966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 426 GLN ** T 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.038022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.025705 restraints weight = 541898.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.026501 restraints weight = 346794.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.027066 restraints weight = 248432.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.027495 restraints weight = 192669.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.027790 restraints weight = 157881.079| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42629 Z= 0.167 Angle : 0.657 9.015 57815 Z= 0.341 Chirality : 0.042 0.215 6580 Planarity : 0.005 0.064 7201 Dihedral : 13.154 141.982 6064 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.09 % Favored : 92.79 % Rotamer: Outliers : 0.16 % Allowed : 5.54 % Favored : 94.30 % 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: -0.68 (0.12), residues: 5060 helix: 0.36 (0.09), residues: 3076 sheet: -1.47 (0.32), residues: 238 loop : -1.68 (0.16), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S3357 TYR 0.015 0.001 TYR S3082 PHE 0.025 0.002 PHE S2145 TRP 0.033 0.002 TRP S2245 HIS 0.009 0.001 HIS S1830 Details of bonding type rmsd covalent geometry : bond 0.00347 (42629) covalent geometry : angle 0.65696 (57815) hydrogen bonds : bond 0.03991 ( 2253) hydrogen bonds : angle 5.06509 ( 6630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 222 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S2108 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE S3991 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: E 792 MET cc_start: 0.6452 (ptm) cc_final: 0.6232 (ptm) REVERT: L 20 MET cc_start: 0.4730 (pmm) cc_final: 0.4520 (pmm) REVERT: S 138 PHE cc_start: 0.9228 (m-10) cc_final: 0.8932 (m-10) REVERT: S 238 MET cc_start: 0.8596 (mmp) cc_final: 0.8229 (mmp) REVERT: S 707 PHE cc_start: 0.9183 (m-80) cc_final: 0.8751 (m-80) REVERT: S 718 MET cc_start: 0.9364 (ppp) cc_final: 0.9152 (ppp) REVERT: S 754 MET cc_start: 0.9401 (tpt) cc_final: 0.8963 (tpp) REVERT: S 758 LEU cc_start: 0.9747 (mt) cc_final: 0.9350 (mt) REVERT: S 785 MET cc_start: 0.9155 (mmp) cc_final: 0.8918 (mmm) REVERT: S 939 MET cc_start: 0.9160 (mtm) cc_final: 0.8518 (tpp) REVERT: S 948 MET cc_start: 0.7961 (mmm) cc_final: 0.7608 (mmm) REVERT: S 1600 MET cc_start: 0.9188 (mmp) cc_final: 0.8597 (mmm) REVERT: S 2331 MET cc_start: 0.6213 (pmm) cc_final: 0.5743 (pmm) REVERT: S 2565 MET cc_start: 0.9454 (ppp) cc_final: 0.9223 (ppp) REVERT: S 3079 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.9072 (pp20) REVERT: S 3110 PHE cc_start: 0.8762 (m-10) cc_final: 0.8451 (m-10) REVERT: S 3111 MET cc_start: 0.9064 (ppp) cc_final: 0.8752 (ppp) REVERT: S 3238 MET cc_start: 0.9024 (mmp) cc_final: 0.8810 (mmm) REVERT: S 3242 MET cc_start: 0.9320 (tpp) cc_final: 0.8935 (tpt) REVERT: S 3670 MET cc_start: 0.6850 (ppp) cc_final: 0.6282 (ppp) REVERT: S 3687 MET cc_start: 0.7434 (mmp) cc_final: 0.7215 (mmp) REVERT: S 3786 LEU cc_start: 0.9154 (mt) cc_final: 0.8856 (mt) REVERT: S 3900 LEU cc_start: 0.9528 (pp) cc_final: 0.9324 (pp) REVERT: S 3984 MET cc_start: 0.9310 (mtm) cc_final: 0.8981 (mtp) REVERT: T 48 MET cc_start: 0.9425 (mpp) cc_final: 0.9051 (mpp) REVERT: T 135 MET cc_start: 0.9202 (tpt) cc_final: 0.8488 (tpp) outliers start: 7 outliers final: 3 residues processed: 229 average time/residue: 0.2495 time to fit residues: 96.8391 Evaluate side-chains 186 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 182 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 507 optimal weight: 20.0000 chunk 321 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 chunk 283 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 chunk 415 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 334 optimal weight: 0.6980 chunk 214 optimal weight: 0.0060 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 680 GLN S 32 HIS ** S 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 191 ASN ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 753 GLN S1049 GLN ** S1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2351 GLN S2508 GLN ** S3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 426 GLN T 433 GLN ** T 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.039103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.026505 restraints weight = 529617.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.027327 restraints weight = 338806.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.027913 restraints weight = 242045.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.028376 restraints weight = 187370.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.028716 restraints weight = 153342.270| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 42629 Z= 0.124 Angle : 0.651 9.142 57815 Z= 0.327 Chirality : 0.042 0.163 6580 Planarity : 0.004 0.064 7201 Dihedral : 13.012 141.199 6064 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.96 % Favored : 92.91 % Rotamer: Outliers : 0.18 % Allowed : 4.73 % Favored : 95.09 % 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: -0.53 (0.12), residues: 5060 helix: 0.49 (0.09), residues: 3070 sheet: -1.50 (0.33), residues: 229 loop : -1.64 (0.16), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 675 TYR 0.039 0.001 TYR T 71 PHE 0.027 0.001 PHE S2145 TRP 0.017 0.001 TRP S 776 HIS 0.009 0.001 HIS L 673 Details of bonding type rmsd covalent geometry : bond 0.00263 (42629) covalent geometry : angle 0.65078 (57815) hydrogen bonds : bond 0.03664 ( 2253) hydrogen bonds : angle 4.85155 ( 6630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 239 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S2108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE S3991 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 792 MET cc_start: 0.6407 (ptm) cc_final: 0.6152 (ptm) REVERT: L 20 MET cc_start: 0.4670 (pmm) cc_final: 0.4458 (pmm) REVERT: L 300 ASP cc_start: 0.8987 (t70) cc_final: 0.8622 (p0) REVERT: S 138 PHE cc_start: 0.9171 (m-10) cc_final: 0.8897 (m-10) REVERT: S 238 MET cc_start: 0.8542 (mmp) cc_final: 0.8110 (mmp) REVERT: S 531 PHE cc_start: 0.9416 (m-80) cc_final: 0.8940 (m-80) REVERT: S 707 PHE cc_start: 0.9142 (m-80) cc_final: 0.8609 (m-80) REVERT: S 754 MET cc_start: 0.9319 (tpt) cc_final: 0.8872 (tpp) REVERT: S 758 LEU cc_start: 0.9735 (mt) cc_final: 0.9324 (mt) REVERT: S 785 MET cc_start: 0.9147 (mmp) cc_final: 0.8801 (mmm) REVERT: S 879 MET cc_start: 0.6600 (tpp) cc_final: 0.5683 (tpp) REVERT: S 939 MET cc_start: 0.9087 (mtm) cc_final: 0.8490 (tpp) REVERT: S 948 MET cc_start: 0.7997 (mmm) cc_final: 0.7641 (mmm) REVERT: S 1600 MET cc_start: 0.9150 (mmp) cc_final: 0.8588 (mmm) REVERT: S 2331 MET cc_start: 0.6008 (pmm) cc_final: 0.5516 (pmm) REVERT: S 2565 MET cc_start: 0.9441 (ppp) cc_final: 0.9217 (ppp) REVERT: S 3079 GLU cc_start: 0.9429 (OUTLIER) cc_final: 0.9152 (pp20) REVERT: S 3110 PHE cc_start: 0.8695 (m-10) cc_final: 0.8354 (m-10) REVERT: S 3111 MET cc_start: 0.9032 (ppp) cc_final: 0.8663 (ppp) REVERT: S 3242 MET cc_start: 0.9364 (tpp) cc_final: 0.8985 (tpt) REVERT: S 3414 MET cc_start: 0.9332 (mmp) cc_final: 0.9117 (mmt) REVERT: S 3670 MET cc_start: 0.6570 (ppp) cc_final: 0.5750 (ppp) REVERT: S 3687 MET cc_start: 0.7501 (mmp) cc_final: 0.7266 (mmp) REVERT: S 3786 LEU cc_start: 0.9148 (mt) cc_final: 0.8855 (mt) REVERT: S 3900 LEU cc_start: 0.9500 (pp) cc_final: 0.9295 (pp) REVERT: S 3971 MET cc_start: 0.9558 (ppp) cc_final: 0.9331 (ppp) REVERT: S 3984 MET cc_start: 0.9233 (mtm) cc_final: 0.8903 (mtp) REVERT: T 48 MET cc_start: 0.9229 (mpp) cc_final: 0.8795 (mpp) REVERT: T 62 MET cc_start: 0.9024 (ptp) cc_final: 0.8788 (ptp) REVERT: T 135 MET cc_start: 0.9213 (tpt) cc_final: 0.8484 (tpp) REVERT: T 161 MET cc_start: 0.8630 (tmm) cc_final: 0.8406 (tmm) REVERT: T 498 MET cc_start: 0.9261 (pmm) cc_final: 0.9012 (tpt) outliers start: 8 outliers final: 6 residues processed: 247 average time/residue: 0.2345 time to fit residues: 97.7118 Evaluate side-chains 202 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 195 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 244 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 427 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 372 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 381 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 680 GLN S 32 HIS S 303 HIS ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1049 GLN ** S1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2306 ASN S2508 GLN ** S2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3251 ASN ** S3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3327 ASN ** S3549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 426 GLN ** T 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.038028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.025615 restraints weight = 539556.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.026441 restraints weight = 345477.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.027012 restraints weight = 245983.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.027420 restraints weight = 190910.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.027696 restraints weight = 157480.365| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 42629 Z= 0.180 Angle : 0.656 8.862 57815 Z= 0.342 Chirality : 0.042 0.182 6580 Planarity : 0.005 0.066 7201 Dihedral : 12.897 140.440 6064 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.33 % Favored : 92.55 % Rotamer: Outliers : 0.16 % Allowed : 3.53 % Favored : 96.31 % 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: -0.51 (0.12), residues: 5060 helix: 0.52 (0.09), residues: 3067 sheet: -1.58 (0.33), residues: 230 loop : -1.63 (0.16), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S4041 TYR 0.013 0.001 TYR Q 177 PHE 0.026 0.001 PHE S2145 TRP 0.060 0.002 TRP S 776 HIS 0.013 0.001 HIS S3915 Details of bonding type rmsd covalent geometry : bond 0.00373 (42629) covalent geometry : angle 0.65608 (57815) hydrogen bonds : bond 0.03691 ( 2253) hydrogen bonds : angle 4.95025 ( 6630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 225 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S 840 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S2108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE S3991 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 20 MET cc_start: 0.4854 (pmm) cc_final: 0.4622 (pmm) REVERT: L 300 ASP cc_start: 0.9084 (t70) cc_final: 0.8734 (p0) REVERT: S 138 PHE cc_start: 0.9250 (m-10) cc_final: 0.8980 (m-10) REVERT: S 238 MET cc_start: 0.8709 (mmp) cc_final: 0.8388 (mmp) REVERT: S 707 PHE cc_start: 0.9285 (m-80) cc_final: 0.8676 (m-80) REVERT: S 718 MET cc_start: 0.9358 (ppp) cc_final: 0.9123 (ppp) REVERT: S 754 MET cc_start: 0.9376 (tpt) cc_final: 0.8942 (tpp) REVERT: S 758 LEU cc_start: 0.9767 (mt) cc_final: 0.9395 (mt) REVERT: S 879 MET cc_start: 0.6646 (tpp) cc_final: 0.5700 (tpp) REVERT: S 948 MET cc_start: 0.8045 (mmm) cc_final: 0.7691 (mmm) REVERT: S 1600 MET cc_start: 0.9186 (mmp) cc_final: 0.8654 (mmm) REVERT: S 2236 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.8718 (tp30) REVERT: S 2331 MET cc_start: 0.6217 (pmm) cc_final: 0.5752 (pmm) REVERT: S 2443 MET cc_start: 0.9132 (ppp) cc_final: 0.8857 (ppp) REVERT: S 2742 MET cc_start: 0.7599 (tpt) cc_final: 0.7354 (tpt) REVERT: S 3110 PHE cc_start: 0.8776 (m-10) cc_final: 0.8427 (m-10) REVERT: S 3111 MET cc_start: 0.9090 (ppp) cc_final: 0.8688 (ppp) REVERT: S 3238 MET cc_start: 0.9100 (mmp) cc_final: 0.8819 (mmm) REVERT: S 3242 MET cc_start: 0.9434 (tpp) cc_final: 0.8964 (tpt) REVERT: S 3670 MET cc_start: 0.6800 (ppp) cc_final: 0.6019 (ppp) REVERT: S 3687 MET cc_start: 0.7569 (mmp) cc_final: 0.7352 (mmp) REVERT: S 3786 LEU cc_start: 0.9126 (mt) cc_final: 0.8845 (mt) REVERT: S 3984 MET cc_start: 0.9344 (mtm) cc_final: 0.8996 (mtp) REVERT: T 48 MET cc_start: 0.9368 (mpp) cc_final: 0.8933 (mpp) REVERT: T 62 MET cc_start: 0.9050 (ptp) cc_final: 0.8823 (ptp) REVERT: T 135 MET cc_start: 0.9232 (tpt) cc_final: 0.8503 (tpp) outliers start: 7 outliers final: 4 residues processed: 232 average time/residue: 0.2286 time to fit residues: 89.9919 Evaluate side-chains 191 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 186 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 164 optimal weight: 7.9990 chunk 228 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 3 optimal weight: 40.0000 chunk 203 optimal weight: 7.9990 chunk 229 optimal weight: 0.9980 chunk 487 optimal weight: 6.9990 chunk 445 optimal weight: 9.9990 chunk 270 optimal weight: 0.4980 chunk 190 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 680 GLN S 32 HIS S 303 HIS ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1049 GLN ** S1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2508 GLN ** S2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3423 GLN ** S3549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 426 GLN ** T 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.038507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.025950 restraints weight = 536217.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.026758 restraints weight = 340051.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.027345 restraints weight = 242193.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.027800 restraints weight = 187296.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.028116 restraints weight = 153431.805| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42629 Z= 0.136 Angle : 0.645 10.889 57815 Z= 0.329 Chirality : 0.042 0.165 6580 Planarity : 0.004 0.065 7201 Dihedral : 12.817 140.956 6064 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.13 % Favored : 92.75 % Rotamer: Outliers : 0.09 % Allowed : 3.05 % Favored : 96.85 % 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: -0.49 (0.12), residues: 5060 helix: 0.55 (0.09), residues: 3078 sheet: -1.55 (0.33), residues: 230 loop : -1.65 (0.16), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 782 TYR 0.016 0.001 TYR S1881 PHE 0.028 0.001 PHE S2145 TRP 0.044 0.001 TRP S 776 HIS 0.014 0.001 HIS S3915 Details of bonding type rmsd covalent geometry : bond 0.00291 (42629) covalent geometry : angle 0.64453 (57815) hydrogen bonds : bond 0.03555 ( 2253) hydrogen bonds : angle 4.84987 ( 6630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 223 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S 840 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S2108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE S3991 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 792 MET cc_start: 0.6288 (ptm) cc_final: 0.6026 (ptm) REVERT: L 20 MET cc_start: 0.4697 (pmm) cc_final: 0.4469 (pmm) REVERT: L 300 ASP cc_start: 0.9113 (t70) cc_final: 0.8770 (p0) REVERT: L 515 MET cc_start: 0.8293 (pmm) cc_final: 0.8034 (pmm) REVERT: S 138 PHE cc_start: 0.9213 (m-10) cc_final: 0.8934 (m-10) REVERT: S 238 MET cc_start: 0.8742 (mmp) cc_final: 0.8442 (mmp) REVERT: S 707 PHE cc_start: 0.9306 (m-80) cc_final: 0.8818 (m-80) REVERT: S 718 MET cc_start: 0.9322 (ppp) cc_final: 0.9088 (ppp) REVERT: S 754 MET cc_start: 0.9349 (tpt) cc_final: 0.8911 (tpp) REVERT: S 758 LEU cc_start: 0.9738 (mt) cc_final: 0.9357 (mt) REVERT: S 879 MET cc_start: 0.6683 (tpp) cc_final: 0.5723 (tpp) REVERT: S 948 MET cc_start: 0.8033 (mmm) cc_final: 0.7668 (mmm) REVERT: S 1600 MET cc_start: 0.9185 (mmp) cc_final: 0.8603 (mmm) REVERT: S 2104 MET cc_start: 0.9061 (mmm) cc_final: 0.8817 (mmm) REVERT: S 2331 MET cc_start: 0.6134 (pmm) cc_final: 0.5612 (pmm) REVERT: S 2565 MET cc_start: 0.9510 (ppp) cc_final: 0.9231 (ppp) REVERT: S 3110 PHE cc_start: 0.8721 (m-10) cc_final: 0.8423 (m-10) REVERT: S 3111 MET cc_start: 0.9090 (ppp) cc_final: 0.8686 (ppp) REVERT: S 3238 MET cc_start: 0.9024 (mmp) cc_final: 0.8820 (mmm) REVERT: S 3242 MET cc_start: 0.9418 (tpp) cc_final: 0.8902 (tpt) REVERT: S 3414 MET cc_start: 0.9380 (mmp) cc_final: 0.9166 (mmt) REVERT: S 3670 MET cc_start: 0.6654 (ppp) cc_final: 0.5842 (ppp) REVERT: S 3687 MET cc_start: 0.7429 (mmp) cc_final: 0.7228 (mmp) REVERT: S 3786 LEU cc_start: 0.9158 (mt) cc_final: 0.8877 (mt) REVERT: S 3984 MET cc_start: 0.9319 (mtm) cc_final: 0.8972 (mtp) REVERT: T 48 MET cc_start: 0.9338 (mpp) cc_final: 0.8965 (mpp) REVERT: T 135 MET cc_start: 0.9184 (tpt) cc_final: 0.8442 (tpp) outliers start: 4 outliers final: 4 residues processed: 227 average time/residue: 0.2523 time to fit residues: 97.3154 Evaluate side-chains 192 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 68 optimal weight: 7.9990 chunk 372 optimal weight: 3.9990 chunk 377 optimal weight: 10.0000 chunk 316 optimal weight: 0.9990 chunk 271 optimal weight: 10.0000 chunk 363 optimal weight: 0.1980 chunk 158 optimal weight: 9.9990 chunk 336 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 469 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 22 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 680 GLN S 32 HIS S 303 HIS ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1049 GLN ** S1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2508 GLN ** S3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3510 GLN ** S3549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 426 GLN ** T 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.038247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.025721 restraints weight = 537495.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.026564 restraints weight = 340455.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.027157 restraints weight = 242377.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.027583 restraints weight = 187253.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.027894 restraints weight = 154017.842| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42629 Z= 0.151 Angle : 0.655 9.263 57815 Z= 0.337 Chirality : 0.042 0.261 6580 Planarity : 0.004 0.065 7201 Dihedral : 12.741 140.573 6064 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.31 % Favored : 92.57 % Rotamer: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.33 % 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: -0.47 (0.12), residues: 5060 helix: 0.55 (0.09), residues: 3070 sheet: -1.56 (0.33), residues: 230 loop : -1.62 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 708 TYR 0.018 0.001 TYR Q 177 PHE 0.042 0.001 PHE S 251 TRP 0.033 0.001 TRP S 776 HIS 0.012 0.001 HIS S3915 Details of bonding type rmsd covalent geometry : bond 0.00320 (42629) covalent geometry : angle 0.65452 (57815) hydrogen bonds : bond 0.03556 ( 2253) hydrogen bonds : angle 4.90579 ( 6630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S 840 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S2108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE S3991 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 792 MET cc_start: 0.6565 (ptm) cc_final: 0.6355 (ptm) REVERT: L 20 MET cc_start: 0.4673 (pmm) cc_final: 0.4434 (pmm) REVERT: L 300 ASP cc_start: 0.9127 (t70) cc_final: 0.8783 (p0) REVERT: S 138 PHE cc_start: 0.9175 (m-10) cc_final: 0.8905 (m-10) REVERT: S 238 MET cc_start: 0.8652 (mmp) cc_final: 0.8418 (mmp) REVERT: S 453 MET cc_start: 0.9205 (pmm) cc_final: 0.8996 (pmm) REVERT: S 707 PHE cc_start: 0.9313 (m-80) cc_final: 0.8809 (m-80) REVERT: S 754 MET cc_start: 0.9344 (tpt) cc_final: 0.8904 (tpp) REVERT: S 758 LEU cc_start: 0.9746 (mt) cc_final: 0.9370 (mt) REVERT: S 879 MET cc_start: 0.6722 (tpp) cc_final: 0.5749 (tpp) REVERT: S 948 MET cc_start: 0.8017 (mmm) cc_final: 0.7649 (mmm) REVERT: S 1600 MET cc_start: 0.9185 (mmp) cc_final: 0.8620 (mmm) REVERT: S 2331 MET cc_start: 0.6050 (pmm) cc_final: 0.5450 (pmm) REVERT: S 2565 MET cc_start: 0.9503 (ppp) cc_final: 0.9212 (ppp) REVERT: S 2742 MET cc_start: 0.7532 (tpt) cc_final: 0.7282 (tpt) REVERT: S 3110 PHE cc_start: 0.8749 (m-10) cc_final: 0.8514 (m-10) REVERT: S 3111 MET cc_start: 0.9106 (ppp) cc_final: 0.8699 (ppp) REVERT: S 3242 MET cc_start: 0.9453 (tpp) cc_final: 0.8873 (tpt) REVERT: S 3414 MET cc_start: 0.9403 (mmp) cc_final: 0.9150 (mmt) REVERT: S 3670 MET cc_start: 0.6673 (ppp) cc_final: 0.5848 (ppp) REVERT: S 3687 MET cc_start: 0.7467 (mmp) cc_final: 0.7263 (mmp) REVERT: S 3786 LEU cc_start: 0.9158 (mt) cc_final: 0.8915 (mt) REVERT: S 3984 MET cc_start: 0.9357 (mtm) cc_final: 0.8999 (mtp) REVERT: T 48 MET cc_start: 0.9383 (mpp) cc_final: 0.9016 (mpp) REVERT: T 135 MET cc_start: 0.9212 (tpt) cc_final: 0.8398 (tpp) outliers start: 4 outliers final: 4 residues processed: 226 average time/residue: 0.2455 time to fit residues: 94.4157 Evaluate side-chains 190 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 186 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 185 optimal weight: 0.9990 chunk 278 optimal weight: 5.9990 chunk 331 optimal weight: 8.9990 chunk 452 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 157 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 680 GLN S 32 HIS S 303 HIS ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1049 GLN ** S1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2508 GLN ** S2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 426 GLN ** T 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.038253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.025757 restraints weight = 536961.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.026581 restraints weight = 338915.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.027076 restraints weight = 242098.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.027566 restraints weight = 190029.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.027887 restraints weight = 155877.636| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42629 Z= 0.150 Angle : 0.658 10.310 57815 Z= 0.338 Chirality : 0.042 0.230 6580 Planarity : 0.004 0.066 7201 Dihedral : 12.674 140.667 6064 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.27 % Favored : 92.61 % Rotamer: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.94 % 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: -0.47 (0.12), residues: 5060 helix: 0.56 (0.09), residues: 3069 sheet: -1.49 (0.33), residues: 230 loop : -1.66 (0.16), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S1608 TYR 0.015 0.001 TYR Q 177 PHE 0.027 0.001 PHE S2145 TRP 0.029 0.001 TRP S 776 HIS 0.011 0.001 HIS S3915 Details of bonding type rmsd covalent geometry : bond 0.00319 (42629) covalent geometry : angle 0.65826 (57815) hydrogen bonds : bond 0.03558 ( 2253) hydrogen bonds : angle 4.88358 ( 6630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S 840 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S2108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE S3991 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 667 MET cc_start: 0.7803 (ppp) cc_final: 0.7434 (ppp) REVERT: L 20 MET cc_start: 0.4634 (pmm) cc_final: 0.4391 (pmm) REVERT: L 300 ASP cc_start: 0.9146 (t70) cc_final: 0.8827 (p0) REVERT: S 138 PHE cc_start: 0.9186 (m-10) cc_final: 0.8919 (m-10) REVERT: S 531 PHE cc_start: 0.9490 (m-80) cc_final: 0.8991 (m-80) REVERT: S 707 PHE cc_start: 0.9322 (m-80) cc_final: 0.8844 (m-80) REVERT: S 754 MET cc_start: 0.9343 (tpt) cc_final: 0.8915 (tpp) REVERT: S 758 LEU cc_start: 0.9770 (mt) cc_final: 0.9384 (mt) REVERT: S 879 MET cc_start: 0.6751 (tpp) cc_final: 0.5873 (tpp) REVERT: S 948 MET cc_start: 0.8022 (mmm) cc_final: 0.7565 (mmm) REVERT: S 1369 MET cc_start: 0.9033 (ptp) cc_final: 0.8217 (ttp) REVERT: S 1600 MET cc_start: 0.9171 (mmp) cc_final: 0.8612 (mmm) REVERT: S 2331 MET cc_start: 0.6176 (pmm) cc_final: 0.5778 (pmm) REVERT: S 2443 MET cc_start: 0.9078 (ppp) cc_final: 0.8336 (ppp) REVERT: S 2478 MET cc_start: 0.9095 (mtm) cc_final: 0.8879 (ptp) REVERT: S 2565 MET cc_start: 0.9507 (ppp) cc_final: 0.9178 (ppp) REVERT: S 2742 MET cc_start: 0.8065 (tpt) cc_final: 0.7801 (tpt) REVERT: S 3110 PHE cc_start: 0.8732 (m-10) cc_final: 0.8485 (m-10) REVERT: S 3111 MET cc_start: 0.9111 (ppp) cc_final: 0.8700 (ppp) REVERT: S 3238 MET cc_start: 0.9176 (mmp) cc_final: 0.8811 (mmm) REVERT: S 3242 MET cc_start: 0.9494 (tpp) cc_final: 0.8881 (tpt) REVERT: S 3414 MET cc_start: 0.9425 (mmp) cc_final: 0.9215 (mmt) REVERT: S 3613 MET cc_start: 0.9337 (tmm) cc_final: 0.9095 (tmm) REVERT: S 3670 MET cc_start: 0.6765 (ppp) cc_final: 0.5944 (ppp) REVERT: S 3687 MET cc_start: 0.7479 (mmp) cc_final: 0.7275 (mmp) REVERT: S 3786 LEU cc_start: 0.9154 (mt) cc_final: 0.8919 (mt) REVERT: S 3984 MET cc_start: 0.9310 (mtm) cc_final: 0.8968 (mtp) REVERT: T 48 MET cc_start: 0.9366 (mpp) cc_final: 0.9001 (mpp) outliers start: 3 outliers final: 3 residues processed: 228 average time/residue: 0.2439 time to fit residues: 95.1569 Evaluate side-chains 189 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 186 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 209 optimal weight: 0.6980 chunk 6 optimal weight: 0.0030 chunk 507 optimal weight: 6.9990 chunk 436 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 120 optimal weight: 0.0030 chunk 52 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 331 optimal weight: 0.9990 chunk 488 optimal weight: 30.0000 chunk 252 optimal weight: 9.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 680 GLN S 32 HIS S 289 ASN S 415 GLN S 738 HIS S 869 ASN ** S 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1457 GLN S1830 HIS S1946 ASN S2508 GLN ** S3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 426 GLN ** T 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.039291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.026560 restraints weight = 521973.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.027394 restraints weight = 331253.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.028014 restraints weight = 235841.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.028389 restraints weight = 182218.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.028745 restraints weight = 151521.705| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 42629 Z= 0.130 Angle : 0.696 12.249 57815 Z= 0.348 Chirality : 0.044 0.691 6580 Planarity : 0.005 0.091 7201 Dihedral : 12.553 139.995 6064 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.78 % Favored : 93.10 % Rotamer: Outliers : 0.09 % Allowed : 1.15 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.12), residues: 5060 helix: 0.54 (0.09), residues: 3082 sheet: -1.34 (0.33), residues: 230 loop : -1.65 (0.16), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T 252 TYR 0.029 0.001 TYR S1881 PHE 0.037 0.001 PHE S 251 TRP 0.030 0.001 TRP S 776 HIS 0.012 0.001 HIS S3915 Details of bonding type rmsd covalent geometry : bond 0.00275 (42629) covalent geometry : angle 0.69572 (57815) hydrogen bonds : bond 0.03540 ( 2253) hydrogen bonds : angle 4.81746 ( 6630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 235 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S 840 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S2108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE S3991 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 667 MET cc_start: 0.7679 (ppp) cc_final: 0.7333 (ppp) REVERT: E 837 ARG cc_start: 0.8132 (ptp90) cc_final: 0.7851 (ptm160) REVERT: L 300 ASP cc_start: 0.9067 (t70) cc_final: 0.8727 (p0) REVERT: L 345 PHE cc_start: 0.9258 (m-10) cc_final: 0.9053 (m-10) REVERT: S 138 PHE cc_start: 0.9191 (m-10) cc_final: 0.8911 (m-10) REVERT: S 531 PHE cc_start: 0.9468 (m-80) cc_final: 0.8936 (m-80) REVERT: S 707 PHE cc_start: 0.9368 (m-80) cc_final: 0.8845 (m-80) REVERT: S 718 MET cc_start: 0.9334 (ppp) cc_final: 0.9060 (ppp) REVERT: S 754 MET cc_start: 0.9370 (tpt) cc_final: 0.8927 (tpp) REVERT: S 758 LEU cc_start: 0.9755 (mt) cc_final: 0.9359 (mt) REVERT: S 879 MET cc_start: 0.6759 (tpp) cc_final: 0.5863 (tpp) REVERT: S 948 MET cc_start: 0.7926 (mmm) cc_final: 0.7528 (mmm) REVERT: S 1342 MET cc_start: 0.9493 (ppp) cc_final: 0.9239 (ppp) REVERT: S 1369 MET cc_start: 0.8883 (ptp) cc_final: 0.7981 (ttp) REVERT: S 1600 MET cc_start: 0.9201 (mmp) cc_final: 0.8600 (mmm) REVERT: S 2331 MET cc_start: 0.6307 (pmm) cc_final: 0.5862 (pmm) REVERT: S 2424 MET cc_start: 0.9077 (ppp) cc_final: 0.8715 (ppp) REVERT: S 2443 MET cc_start: 0.8975 (ppp) cc_final: 0.8278 (ppp) REVERT: S 2478 MET cc_start: 0.9123 (mtm) cc_final: 0.8918 (ptp) REVERT: S 2565 MET cc_start: 0.9505 (ppp) cc_final: 0.9118 (ppp) REVERT: S 2742 MET cc_start: 0.8320 (tpt) cc_final: 0.8004 (tpt) REVERT: S 3110 PHE cc_start: 0.8711 (m-10) cc_final: 0.8428 (m-10) REVERT: S 3111 MET cc_start: 0.9115 (ppp) cc_final: 0.8689 (ppp) REVERT: S 3176 MET cc_start: 0.8928 (pmm) cc_final: 0.8712 (pmm) REVERT: S 3238 MET cc_start: 0.9087 (mmp) cc_final: 0.8810 (mmm) REVERT: S 3242 MET cc_start: 0.9523 (tpp) cc_final: 0.8990 (tpt) REVERT: S 3414 MET cc_start: 0.9403 (mmp) cc_final: 0.9164 (mmt) REVERT: S 3483 MET cc_start: 0.8791 (ttt) cc_final: 0.8202 (ptm) REVERT: S 3670 MET cc_start: 0.7060 (ppp) cc_final: 0.6212 (ppp) REVERT: S 3687 MET cc_start: 0.7435 (mmp) cc_final: 0.7234 (mmp) REVERT: S 3984 MET cc_start: 0.9319 (mtm) cc_final: 0.8950 (mtp) REVERT: T 48 MET cc_start: 0.9334 (mpp) cc_final: 0.8971 (mpp) REVERT: T 135 MET cc_start: 0.9437 (mmm) cc_final: 0.8766 (mmm) REVERT: T 446 MET cc_start: 0.8066 (pmm) cc_final: 0.7839 (pmm) outliers start: 4 outliers final: 4 residues processed: 239 average time/residue: 0.2383 time to fit residues: 97.3780 Evaluate side-chains 200 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 196 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 437 optimal weight: 0.9990 chunk 364 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 356 optimal weight: 8.9990 chunk 223 optimal weight: 0.0670 chunk 495 optimal weight: 9.9990 chunk 185 optimal weight: 0.9990 chunk 6 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 253 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 680 GLN S 32 HIS S 303 HIS ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1049 GLN ** S1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2508 GLN ** S2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 426 GLN ** T 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.038977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.026388 restraints weight = 527845.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.027212 restraints weight = 337213.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.027817 restraints weight = 241746.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.028174 restraints weight = 187167.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.028537 restraints weight = 155403.346| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 42629 Z= 0.128 Angle : 0.668 10.988 57815 Z= 0.337 Chirality : 0.043 0.462 6580 Planarity : 0.004 0.072 7201 Dihedral : 12.465 139.079 6064 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.82 % Favored : 93.06 % Rotamer: Outliers : 0.07 % Allowed : 0.61 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.12), residues: 5060 helix: 0.59 (0.09), residues: 3081 sheet: -1.24 (0.33), residues: 240 loop : -1.66 (0.16), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T 252 TYR 0.012 0.001 TYR Q 177 PHE 0.034 0.001 PHE S 251 TRP 0.027 0.001 TRP S 776 HIS 0.011 0.001 HIS S3915 Details of bonding type rmsd covalent geometry : bond 0.00279 (42629) covalent geometry : angle 0.66809 (57815) hydrogen bonds : bond 0.03454 ( 2253) hydrogen bonds : angle 4.78727 ( 6630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 228 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S 840 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S2108 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE S3991 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S4128 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 667 MET cc_start: 0.8135 (ppp) cc_final: 0.7760 (ppp) REVERT: E 837 ARG cc_start: 0.8148 (ptp90) cc_final: 0.7731 (ptm160) REVERT: L 300 ASP cc_start: 0.9128 (t70) cc_final: 0.8790 (p0) REVERT: L 345 PHE cc_start: 0.9254 (m-10) cc_final: 0.9014 (m-10) REVERT: Q 157 ASP cc_start: 0.7742 (t70) cc_final: 0.7475 (m-30) REVERT: S 138 PHE cc_start: 0.9181 (m-10) cc_final: 0.8893 (m-10) REVERT: S 238 MET cc_start: 0.8559 (mmp) cc_final: 0.7459 (mmt) REVERT: S 453 MET cc_start: 0.9114 (pmm) cc_final: 0.8879 (pmm) REVERT: S 531 PHE cc_start: 0.9459 (m-80) cc_final: 0.8941 (m-80) REVERT: S 707 PHE cc_start: 0.9351 (m-80) cc_final: 0.8853 (m-80) REVERT: S 718 MET cc_start: 0.9254 (ppp) cc_final: 0.9049 (ppp) REVERT: S 754 MET cc_start: 0.9355 (tpt) cc_final: 0.8913 (tpp) REVERT: S 758 LEU cc_start: 0.9744 (mt) cc_final: 0.9324 (mt) REVERT: S 879 MET cc_start: 0.6766 (tpp) cc_final: 0.5860 (tpp) REVERT: S 948 MET cc_start: 0.7922 (mmm) cc_final: 0.7533 (mmm) REVERT: S 1342 MET cc_start: 0.9475 (ppp) cc_final: 0.9202 (ppp) REVERT: S 1369 MET cc_start: 0.8841 (ptp) cc_final: 0.7969 (ttp) REVERT: S 1600 MET cc_start: 0.9193 (mmp) cc_final: 0.8605 (mmm) REVERT: S 2443 MET cc_start: 0.9032 (ppp) cc_final: 0.8316 (ppp) REVERT: S 2478 MET cc_start: 0.9121 (mtm) cc_final: 0.8896 (ptp) REVERT: S 2565 MET cc_start: 0.9489 (ppp) cc_final: 0.9123 (ppp) REVERT: S 2742 MET cc_start: 0.8092 (tpt) cc_final: 0.7767 (tpt) REVERT: S 3110 PHE cc_start: 0.8659 (m-10) cc_final: 0.8392 (m-10) REVERT: S 3111 MET cc_start: 0.9121 (ppp) cc_final: 0.8696 (ppp) REVERT: S 3238 MET cc_start: 0.9032 (mmp) cc_final: 0.8755 (mmm) REVERT: S 3242 MET cc_start: 0.9524 (tpp) cc_final: 0.9027 (tpt) REVERT: S 3414 MET cc_start: 0.9390 (mmp) cc_final: 0.9152 (mmt) REVERT: S 3483 MET cc_start: 0.8790 (ttt) cc_final: 0.8249 (ptm) REVERT: S 3670 MET cc_start: 0.6957 (ppp) cc_final: 0.6096 (ppp) REVERT: S 3786 LEU cc_start: 0.9355 (mt) cc_final: 0.9053 (mt) REVERT: S 3900 LEU cc_start: 0.9490 (pp) cc_final: 0.9289 (pp) REVERT: S 3984 MET cc_start: 0.9323 (mtm) cc_final: 0.8956 (mtp) REVERT: T 48 MET cc_start: 0.9279 (mpp) cc_final: 0.8889 (mpp) REVERT: T 135 MET cc_start: 0.9300 (mmm) cc_final: 0.8394 (mmm) REVERT: T 446 MET cc_start: 0.8057 (pmm) cc_final: 0.7826 (pmm) outliers start: 3 outliers final: 3 residues processed: 231 average time/residue: 0.2485 time to fit residues: 98.2509 Evaluate side-chains 196 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 229 optimal weight: 0.8980 chunk 349 optimal weight: 2.9990 chunk 422 optimal weight: 2.9990 chunk 388 optimal weight: 8.9990 chunk 415 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 298 optimal weight: 0.7980 chunk 224 optimal weight: 10.0000 chunk 461 optimal weight: 5.9990 chunk 462 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 680 GLN S 32 HIS S 303 HIS ** S 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1049 GLN ** S1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2508 GLN ** S2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 426 GLN ** T 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.038945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.026257 restraints weight = 527818.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.027109 restraints weight = 336353.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.027714 restraints weight = 241210.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.028086 restraints weight = 186696.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.028439 restraints weight = 155369.588| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42629 Z= 0.126 Angle : 0.664 10.601 57815 Z= 0.335 Chirality : 0.042 0.358 6580 Planarity : 0.004 0.064 7201 Dihedral : 12.387 139.177 6064 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.86 % Favored : 93.00 % Rotamer: Outliers : 0.07 % Allowed : 0.81 % Favored : 99.12 % 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: -0.38 (0.12), residues: 5060 helix: 0.63 (0.09), residues: 3080 sheet: -1.26 (0.33), residues: 241 loop : -1.64 (0.16), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 252 TYR 0.012 0.001 TYR S 959 PHE 0.033 0.001 PHE S 251 TRP 0.026 0.001 TRP S 776 HIS 0.011 0.001 HIS S3915 Details of bonding type rmsd covalent geometry : bond 0.00274 (42629) covalent geometry : angle 0.66367 (57815) hydrogen bonds : bond 0.03401 ( 2253) hydrogen bonds : angle 4.73594 ( 6630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9390.32 seconds wall clock time: 163 minutes 11.56 seconds (9791.56 seconds total)