Starting phenix.real_space_refine on Wed Aug 27 00:08:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8esc_28575/08_2025/8esc_28575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8esc_28575/08_2025/8esc_28575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8esc_28575/08_2025/8esc_28575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8esc_28575/08_2025/8esc_28575.map" model { file = "/net/cci-nas-00/data/ceres_data/8esc_28575/08_2025/8esc_28575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8esc_28575/08_2025/8esc_28575.cif" } resolution = 3.1 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 180 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 179 5.16 5 C 27835 2.51 5 N 7275 2.21 5 O 7985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43279 Number of models: 1 Model: "" Number of chains: 7 Chain: "Z" Number of atoms: 28974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3543, 28974 Classifications: {'peptide': 3543} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 150, 'TRANS': 3391} Chain breaks: 11 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3311 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 396} Chain breaks: 1 Chain: "A" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2814 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 1 Chain: "P" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2281 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain breaks: 2 Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3645 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 27, 'TRANS': 412} Chain breaks: 2 Chain: "S" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2221 Classifications: {'peptide': 268} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 12, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.93, per 1000 atoms: 0.18 Number of scatterers: 43279 At special positions: 0 Unit cell: (199.72, 227.868, 167.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 179 16.00 P 3 15.00 Mg 2 11.99 O 7985 8.00 N 7275 7.00 C 27835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10272 Finding SS restraints... Secondary structure from input PDB file: 276 helices and 22 sheets defined 66.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'Z' and resid 5 through 16 removed outlier: 4.140A pdb=" N GLN Z 9 " --> pdb=" O GLU Z 5 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP Z 16 " --> pdb=" O SER Z 12 " (cutoff:3.500A) Processing helix chain 'Z' and resid 20 through 30 removed outlier: 4.114A pdb=" N GLU Z 30 " --> pdb=" O SER Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 30 through 38 Processing helix chain 'Z' and resid 40 through 62 Proline residue: Z 53 - end of helix removed outlier: 3.856A pdb=" N ASN Z 57 " --> pdb=" O PRO Z 53 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN Z 58 " --> pdb=" O LEU Z 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU Z 61 " --> pdb=" O ASN Z 57 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL Z 62 " --> pdb=" O GLN Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 80 removed outlier: 3.772A pdb=" N SER Z 78 " --> pdb=" O LYS Z 74 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU Z 80 " --> pdb=" O ARG Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 86 Processing helix chain 'Z' and resid 89 through 94 Proline residue: Z 94 - end of helix Processing helix chain 'Z' and resid 95 through 107 removed outlier: 3.516A pdb=" N VAL Z 99 " --> pdb=" O TYR Z 95 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE Z 102 " --> pdb=" O GLU Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 110 No H-bonds generated for 'chain 'Z' and resid 108 through 110' Processing helix chain 'Z' and resid 112 through 128 removed outlier: 3.740A pdb=" N ILE Z 116 " --> pdb=" O GLU Z 112 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU Z 117 " --> pdb=" O GLU Z 113 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU Z 122 " --> pdb=" O CYS Z 118 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR Z 124 " --> pdb=" O LYS Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 136 through 149 removed outlier: 4.467A pdb=" N PHE Z 140 " --> pdb=" O LYS Z 136 " (cutoff:3.500A) Processing helix chain 'Z' and resid 153 through 160 removed outlier: 4.047A pdb=" N GLN Z 157 " --> pdb=" O ASN Z 153 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR Z 158 " --> pdb=" O LEU Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 222 through 225 Processing helix chain 'Z' and resid 226 through 237 removed outlier: 3.839A pdb=" N MET Z 231 " --> pdb=" O CYS Z 227 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR Z 233 " --> pdb=" O ILE Z 229 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU Z 234 " --> pdb=" O THR Z 230 " (cutoff:3.500A) Processing helix chain 'Z' and resid 241 through 259 Proline residue: Z 247 - end of helix Proline residue: Z 251 - end of helix removed outlier: 3.542A pdb=" N LEU Z 257 " --> pdb=" O ILE Z 253 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE Z 259 " --> pdb=" O ASN Z 255 " (cutoff:3.500A) Processing helix chain 'Z' and resid 261 through 273 removed outlier: 4.021A pdb=" N GLU Z 266 " --> pdb=" O LYS Z 262 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA Z 267 " --> pdb=" O GLN Z 263 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG Z 268 " --> pdb=" O GLN Z 264 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU Z 269 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA Z 271 " --> pdb=" O ALA Z 267 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 311 removed outlier: 3.644A pdb=" N TYR Z 307 " --> pdb=" O SER Z 303 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG Z 311 " --> pdb=" O TYR Z 307 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 324 removed outlier: 3.834A pdb=" N PHE Z 324 " --> pdb=" O ASP Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 324 through 335 Processing helix chain 'Z' and resid 341 through 357 removed outlier: 3.994A pdb=" N GLU Z 346 " --> pdb=" O SER Z 342 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR Z 357 " --> pdb=" O HIS Z 353 " (cutoff:3.500A) Processing helix chain 'Z' and resid 358 through 364 removed outlier: 3.955A pdb=" N LYS Z 361 " --> pdb=" O ASN Z 358 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE Z 363 " --> pdb=" O LYS Z 360 " (cutoff:3.500A) Processing helix chain 'Z' and resid 366 through 372 removed outlier: 3.546A pdb=" N LEU Z 370 " --> pdb=" O LYS Z 366 " (cutoff:3.500A) Processing helix chain 'Z' and resid 380 through 386 removed outlier: 3.720A pdb=" N HIS Z 384 " --> pdb=" O GLY Z 380 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR Z 386 " --> pdb=" O THR Z 382 " (cutoff:3.500A) Processing helix chain 'Z' and resid 387 through 402 Processing helix chain 'Z' and resid 407 through 424 removed outlier: 3.831A pdb=" N ILE Z 411 " --> pdb=" O GLN Z 407 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS Z 413 " --> pdb=" O SER Z 409 " (cutoff:3.500A) Processing helix chain 'Z' and resid 428 through 442 removed outlier: 3.602A pdb=" N GLN Z 432 " --> pdb=" O ALA Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 442 through 451 Processing helix chain 'Z' and resid 456 through 480 removed outlier: 3.669A pdb=" N ILE Z 467 " --> pdb=" O LEU Z 463 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE Z 468 " --> pdb=" O LEU Z 464 " (cutoff:3.500A) Processing helix chain 'Z' and resid 481 through 504 removed outlier: 3.556A pdb=" N LYS Z 487 " --> pdb=" O ASP Z 483 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU Z 498 " --> pdb=" O THR Z 494 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS Z 499 " --> pdb=" O HIS Z 495 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU Z 503 " --> pdb=" O LYS Z 499 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS Z 504 " --> pdb=" O ALA Z 500 " (cutoff:3.500A) Processing helix chain 'Z' and resid 512 through 522 removed outlier: 3.840A pdb=" N GLU Z 516 " --> pdb=" O LYS Z 512 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE Z 517 " --> pdb=" O GLU Z 513 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL Z 521 " --> pdb=" O PHE Z 517 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU Z 522 " --> pdb=" O MET Z 518 " (cutoff:3.500A) Processing helix chain 'Z' and resid 563 through 567 removed outlier: 3.731A pdb=" N TYR Z 566 " --> pdb=" O ILE Z 563 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA Z 567 " --> pdb=" O LYS Z 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 563 through 567' Processing helix chain 'Z' and resid 578 through 596 removed outlier: 3.736A pdb=" N ASP Z 582 " --> pdb=" O ASP Z 578 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA Z 583 " --> pdb=" O PRO Z 579 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR Z 596 " --> pdb=" O SER Z 592 " (cutoff:3.500A) Processing helix chain 'Z' and resid 599 through 605 removed outlier: 4.028A pdb=" N LYS Z 602 " --> pdb=" O HIS Z 599 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL Z 603 " --> pdb=" O ASP Z 600 " (cutoff:3.500A) Processing helix chain 'Z' and resid 615 through 620 removed outlier: 3.794A pdb=" N ALA Z 620 " --> pdb=" O PRO Z 616 " (cutoff:3.500A) Processing helix chain 'Z' and resid 627 through 647 removed outlier: 3.511A pdb=" N VAL Z 633 " --> pdb=" O GLU Z 629 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE Z 634 " --> pdb=" O GLU Z 630 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS Z 646 " --> pdb=" O ILE Z 642 " (cutoff:3.500A) Processing helix chain 'Z' and resid 676 through 690 removed outlier: 3.547A pdb=" N LEU Z 682 " --> pdb=" O ASP Z 678 " (cutoff:3.500A) Processing helix chain 'Z' and resid 698 through 716 removed outlier: 3.540A pdb=" N ILE Z 702 " --> pdb=" O PHE Z 698 " (cutoff:3.500A) Proline residue: Z 707 - end of helix removed outlier: 3.790A pdb=" N GLU Z 715 " --> pdb=" O GLU Z 711 " (cutoff:3.500A) Processing helix chain 'Z' and resid 719 through 729 removed outlier: 3.820A pdb=" N ALA Z 723 " --> pdb=" O LEU Z 719 " (cutoff:3.500A) Processing helix chain 'Z' and resid 732 through 749 removed outlier: 3.675A pdb=" N GLY Z 738 " --> pdb=" O PRO Z 734 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY Z 746 " --> pdb=" O ARG Z 742 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS Z 749 " --> pdb=" O LYS Z 745 " (cutoff:3.500A) Processing helix chain 'Z' and resid 755 through 776 removed outlier: 3.646A pdb=" N VAL Z 773 " --> pdb=" O SER Z 769 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN Z 774 " --> pdb=" O PHE Z 770 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU Z 775 " --> pdb=" O MET Z 771 " (cutoff:3.500A) Processing helix chain 'Z' and resid 776 through 801 removed outlier: 3.765A pdb=" N GLU Z 781 " --> pdb=" O PRO Z 777 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL Z 782 " --> pdb=" O ASN Z 778 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL Z 783 " --> pdb=" O ILE Z 779 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU Z 784 " --> pdb=" O ASN Z 780 " (cutoff:3.500A) Proline residue: Z 786 - end of helix removed outlier: 3.999A pdb=" N ASN Z 789 " --> pdb=" O LEU Z 785 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP Z 790 " --> pdb=" O PRO Z 786 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU Z 793 " --> pdb=" O ASN Z 789 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR Z 800 " --> pdb=" O LEU Z 796 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR Z 801 " --> pdb=" O LYS Z 797 " (cutoff:3.500A) Processing helix chain 'Z' and resid 805 through 820 removed outlier: 3.628A pdb=" N PHE Z 809 " --> pdb=" O PRO Z 805 " (cutoff:3.500A) Processing helix chain 'Z' and resid 824 through 848 removed outlier: 3.825A pdb=" N SER Z 830 " --> pdb=" O ASN Z 826 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS Z 832 " --> pdb=" O TYR Z 828 " (cutoff:3.500A) Proline residue: Z 833 - end of helix removed outlier: 4.542A pdb=" N GLN Z 836 " --> pdb=" O LYS Z 832 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL Z 837 " --> pdb=" O PRO Z 833 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN Z 844 " --> pdb=" O GLN Z 840 " (cutoff:3.500A) Processing helix chain 'Z' and resid 853 through 864 removed outlier: 3.819A pdb=" N LEU Z 857 " --> pdb=" O HIS Z 853 " (cutoff:3.500A) Processing helix chain 'Z' and resid 872 through 874 No H-bonds generated for 'chain 'Z' and resid 872 through 874' Processing helix chain 'Z' and resid 875 through 889 removed outlier: 3.566A pdb=" N LEU Z 879 " --> pdb=" O TYR Z 875 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS Z 881 " --> pdb=" O PRO Z 877 " (cutoff:3.500A) Proline residue: Z 882 - end of helix Processing helix chain 'Z' and resid 890 through 892 No H-bonds generated for 'chain 'Z' and resid 890 through 892' Processing helix chain 'Z' and resid 893 through 908 removed outlier: 3.656A pdb=" N THR Z 900 " --> pdb=" O GLN Z 896 " (cutoff:3.500A) Processing helix chain 'Z' and resid 913 through 918 Processing helix chain 'Z' and resid 920 through 932 removed outlier: 3.773A pdb=" N LYS Z 926 " --> pdb=" O ASP Z 922 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU Z 932 " --> pdb=" O LEU Z 928 " (cutoff:3.500A) Processing helix chain 'Z' and resid 938 through 952 removed outlier: 3.616A pdb=" N ASN Z 944 " --> pdb=" O ALA Z 940 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU Z 952 " --> pdb=" O ILE Z 948 " (cutoff:3.500A) Processing helix chain 'Z' and resid 996 through 1005 removed outlier: 3.851A pdb=" N LEU Z1001 " --> pdb=" O ILE Z 997 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1010 through 1029 Processing helix chain 'Z' and resid 1030 through 1034 removed outlier: 3.637A pdb=" N GLU Z1034 " --> pdb=" O SER Z1031 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1038 through 1048 Processing helix chain 'Z' and resid 1068 through 1090 removed outlier: 5.627A pdb=" N ASN Z1074 " --> pdb=" O ARG Z1070 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE Z1087 " --> pdb=" O LEU Z1083 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1095 through 1125 removed outlier: 3.808A pdb=" N VAL Z1115 " --> pdb=" O CYS Z1111 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN Z1116 " --> pdb=" O LEU Z1112 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR Z1117 " --> pdb=" O LEU Z1113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1143 through 1154 Proline residue: Z1150 - end of helix Processing helix chain 'Z' and resid 1157 through 1180 Processing helix chain 'Z' and resid 1180 through 1187 removed outlier: 3.591A pdb=" N ALA Z1184 " --> pdb=" O GLY Z1180 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU Z1185 " --> pdb=" O GLU Z1181 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER Z1186 " --> pdb=" O GLU Z1182 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1188 through 1201 removed outlier: 4.101A pdb=" N GLU Z1192 " --> pdb=" O SER Z1188 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS Z1201 " --> pdb=" O PHE Z1197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1205 through 1223 removed outlier: 3.668A pdb=" N VAL Z1218 " --> pdb=" O LEU Z1214 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN Z1222 " --> pdb=" O VAL Z1218 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1228 through 1247 removed outlier: 3.773A pdb=" N LYS Z1232 " --> pdb=" O VAL Z1228 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR Z1235 " --> pdb=" O LYS Z1231 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN Z1236 " --> pdb=" O LYS Z1232 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1254 through 1272 Processing helix chain 'Z' and resid 1282 through 1295 removed outlier: 3.709A pdb=" N THR Z1288 " --> pdb=" O VAL Z1284 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU Z1295 " --> pdb=" O ASP Z1291 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1300 through 1319 removed outlier: 3.963A pdb=" N ALA Z1306 " --> pdb=" O LYS Z1302 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU Z1317 " --> pdb=" O THR Z1313 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1321 through 1326 removed outlier: 3.547A pdb=" N MET Z1326 " --> pdb=" O ILE Z1322 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1329 through 1340 Proline residue: Z1336 - end of helix removed outlier: 3.669A pdb=" N LYS Z1340 " --> pdb=" O PRO Z1336 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1346 through 1362 removed outlier: 3.809A pdb=" N ILE Z1351 " --> pdb=" O PHE Z1347 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY Z1352 " --> pdb=" O THR Z1348 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL Z1354 " --> pdb=" O GLN Z1350 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER Z1362 " --> pdb=" O THR Z1358 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1371 through 1378 removed outlier: 3.788A pdb=" N PHE Z1375 " --> pdb=" O ASN Z1371 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1384 through 1390 removed outlier: 3.583A pdb=" N ASP Z1389 " --> pdb=" O ALA Z1385 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1403 through 1423 Processing helix chain 'Z' and resid 1437 through 1447 removed outlier: 3.552A pdb=" N LEU Z1441 " --> pdb=" O ARG Z1437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1454 through 1469 removed outlier: 3.520A pdb=" N GLU Z1461 " --> pdb=" O ASN Z1457 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU Z1469 " --> pdb=" O GLY Z1465 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1474 through 1482 removed outlier: 3.653A pdb=" N LEU Z1478 " --> pdb=" O PRO Z1474 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN Z1480 " --> pdb=" O GLU Z1476 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1482 through 1488 removed outlier: 3.586A pdb=" N ASN Z1488 " --> pdb=" O PRO Z1484 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1496 through 1510 removed outlier: 3.850A pdb=" N LEU Z1503 " --> pdb=" O GLY Z1499 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU Z1508 " --> pdb=" O SER Z1504 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU Z1509 " --> pdb=" O LYS Z1505 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1516 through 1529 removed outlier: 3.980A pdb=" N ARG Z1520 " --> pdb=" O VAL Z1516 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS Z1525 " --> pdb=" O LYS Z1521 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA Z1528 " --> pdb=" O ASP Z1524 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1531 through 1538 removed outlier: 3.581A pdb=" N LEU Z1535 " --> pdb=" O ARG Z1531 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR Z1537 " --> pdb=" O GLU Z1533 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU Z1538 " --> pdb=" O VAL Z1534 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1546 through 1558 removed outlier: 3.748A pdb=" N LYS Z1550 " --> pdb=" O GLN Z1546 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE Z1558 " --> pdb=" O SER Z1554 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1569 through 1584 removed outlier: 3.505A pdb=" N LEU Z1574 " --> pdb=" O LEU Z1570 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU Z1575 " --> pdb=" O ASN Z1571 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1592 through 1603 removed outlier: 4.018A pdb=" N LEU Z1596 " --> pdb=" O PHE Z1592 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR Z1599 " --> pdb=" O PRO Z1595 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1604 through 1614 removed outlier: 3.836A pdb=" N LYS Z1613 " --> pdb=" O GLU Z1609 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN Z1614 " --> pdb=" O TYR Z1610 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1617 through 1629 removed outlier: 3.634A pdb=" N VAL Z1621 " --> pdb=" O LEU Z1617 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU Z1622 " --> pdb=" O ARG Z1618 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE Z1623 " --> pdb=" O GLN Z1619 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN Z1629 " --> pdb=" O CYS Z1625 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1635 through 1640 removed outlier: 3.870A pdb=" N ASP Z1639 " --> pdb=" O GLU Z1635 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1643 through 1659 Proline residue: Z1656 - end of helix removed outlier: 3.639A pdb=" N GLN Z1659 " --> pdb=" O ILE Z1655 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1661 through 1681 removed outlier: 4.233A pdb=" N THR Z1679 " --> pdb=" O THR Z1675 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1681 through 1687 removed outlier: 3.994A pdb=" N LEU Z1685 " --> pdb=" O GLY Z1681 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS Z1686 " --> pdb=" O ASP Z1682 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS Z1687 " --> pdb=" O GLU Z1683 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 1681 through 1687' Processing helix chain 'Z' and resid 1689 through 1710 removed outlier: 4.074A pdb=" N LEU Z1693 " --> pdb=" O GLY Z1689 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP Z1697 " --> pdb=" O LEU Z1693 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET Z1698 " --> pdb=" O LYS Z1694 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1714 through 1735 removed outlier: 3.749A pdb=" N LEU Z1735 " --> pdb=" O ARG Z1731 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1739 through 1753 removed outlier: 3.748A pdb=" N LEU Z1743 " --> pdb=" O ASP Z1739 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU Z1744 " --> pdb=" O GLN Z1740 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1761 through 1770 Processing helix chain 'Z' and resid 1776 through 1791 Processing helix chain 'Z' and resid 1795 through 1805 removed outlier: 3.669A pdb=" N LEU Z1803 " --> pdb=" O ARG Z1799 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1807 through 1817 removed outlier: 3.507A pdb=" N LEU Z1811 " --> pdb=" O ILE Z1807 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1834 through 1839 Processing helix chain 'Z' and resid 1844 through 1849 removed outlier: 3.590A pdb=" N ILE Z1848 " --> pdb=" O ASN Z1844 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1858 through 1874 removed outlier: 3.637A pdb=" N LEU Z1865 " --> pdb=" O ARG Z1861 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE Z1871 " --> pdb=" O LEU Z1867 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE Z1872 " --> pdb=" O SER Z1868 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1875 through 1881 removed outlier: 3.810A pdb=" N ALA Z1880 " --> pdb=" O GLU Z1877 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU Z1881 " --> pdb=" O ILE Z1878 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1882 through 1891 removed outlier: 3.878A pdb=" N ILE Z1886 " --> pdb=" O ILE Z1882 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS Z1890 " --> pdb=" O ILE Z1886 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1892 through 1896 Processing helix chain 'Z' and resid 1900 through 1916 removed outlier: 3.705A pdb=" N PHE Z1912 " --> pdb=" O VAL Z1908 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE Z1913 " --> pdb=" O THR Z1909 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER Z1914 " --> pdb=" O SER Z1910 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1919 through 1933 Processing helix chain 'Z' and resid 1938 through 1957 removed outlier: 3.680A pdb=" N VAL Z1942 " --> pdb=" O ALA Z1938 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS Z1943 " --> pdb=" O ARG Z1939 " (cutoff:3.500A) Proline residue: Z1951 - end of helix removed outlier: 3.969A pdb=" N GLU Z1955 " --> pdb=" O PRO Z1951 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG Z1956 " --> pdb=" O VAL Z1952 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1964 through 1977 removed outlier: 3.545A pdb=" N VAL Z1975 " --> pdb=" O LYS Z1971 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN Z1977 " --> pdb=" O VAL Z1973 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1981 through 1988 removed outlier: 3.977A pdb=" N TYR Z1986 " --> pdb=" O ASN Z1982 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN Z1987 " --> pdb=" O ASN Z1983 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2003 through 2016 removed outlier: 3.760A pdb=" N HIS Z2009 " --> pdb=" O SER Z2005 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR Z2015 " --> pdb=" O MET Z2011 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE Z2016 " --> pdb=" O ASN Z2012 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2021 through 2043 removed outlier: 3.895A pdb=" N LEU Z2027 " --> pdb=" O ASP Z2023 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA Z2028 " --> pdb=" O SER Z2024 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE Z2029 " --> pdb=" O HIS Z2025 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR Z2042 " --> pdb=" O TRP Z2038 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU Z2043 " --> pdb=" O GLU Z2039 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2093 through 2104 Processing helix chain 'Z' and resid 2114 through 2129 Processing helix chain 'Z' and resid 2139 through 2142 Processing helix chain 'Z' and resid 2143 through 2148 Processing helix chain 'Z' and resid 2156 through 2175 removed outlier: 4.147A pdb=" N VAL Z2167 " --> pdb=" O ASN Z2163 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2176 through 2183 removed outlier: 3.623A pdb=" N ILE Z2180 " --> pdb=" O THR Z2176 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET Z2181 " --> pdb=" O LYS Z2177 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU Z2182 " --> pdb=" O GLU Z2178 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN Z2183 " --> pdb=" O TRP Z2179 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 2176 through 2183' Processing helix chain 'Z' and resid 2183 through 2191 removed outlier: 3.530A pdb=" N ILE Z2187 " --> pdb=" O ASN Z2183 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2191 through 2197 Processing helix chain 'Z' and resid 2201 through 2221 removed outlier: 4.193A pdb=" N ALA Z2205 " --> pdb=" O ASP Z2201 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS Z2208 " --> pdb=" O GLU Z2204 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL Z2209 " --> pdb=" O ALA Z2205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA Z2219 " --> pdb=" O LYS Z2215 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN Z2220 " --> pdb=" O ALA Z2216 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2232 through 2248 removed outlier: 4.195A pdb=" N ILE Z2236 " --> pdb=" O GLY Z2232 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN Z2248 " --> pdb=" O THR Z2244 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2249 through 2251 No H-bonds generated for 'chain 'Z' and resid 2249 through 2251' Processing helix chain 'Z' and resid 2252 through 2267 removed outlier: 3.543A pdb=" N GLY Z2256 " --> pdb=" O SER Z2252 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL Z2257 " --> pdb=" O VAL Z2253 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR Z2258 " --> pdb=" O THR Z2254 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET Z2265 " --> pdb=" O TRP Z2261 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN Z2266 " --> pdb=" O VAL Z2262 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2268 through 2271 removed outlier: 3.584A pdb=" N ILE Z2271 " --> pdb=" O PRO Z2268 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 2268 through 2271' Processing helix chain 'Z' and resid 2275 through 2291 removed outlier: 3.931A pdb=" N SER Z2291 " --> pdb=" O LYS Z2287 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2298 through 2320 removed outlier: 3.522A pdb=" N ALA Z2304 " --> pdb=" O ALA Z2300 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG Z2305 " --> pdb=" O LEU Z2301 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR Z2308 " --> pdb=" O ALA Z2304 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS Z2313 " --> pdb=" O LYS Z2309 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU Z2320 " --> pdb=" O TYR Z2316 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2328 through 2342 Processing helix chain 'Z' and resid 2347 through 2362 removed outlier: 3.893A pdb=" N LYS Z2351 " --> pdb=" O ASN Z2347 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE Z2352 " --> pdb=" O PHE Z2348 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER Z2358 " --> pdb=" O ASN Z2354 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP Z2359 " --> pdb=" O MET Z2355 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2370 through 2379 Processing helix chain 'Z' and resid 2381 through 2386 Processing helix chain 'Z' and resid 2387 through 2404 removed outlier: 3.524A pdb=" N VAL Z2398 " --> pdb=" O PHE Z2394 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN Z2404 " --> pdb=" O LYS Z2400 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2413 through 2415 No H-bonds generated for 'chain 'Z' and resid 2413 through 2415' Processing helix chain 'Z' and resid 2416 through 2424 Processing helix chain 'Z' and resid 2428 through 2442 Processing helix chain 'Z' and resid 2446 through 2456 Processing helix chain 'Z' and resid 2459 through 2464 removed outlier: 4.180A pdb=" N PHE Z2462 " --> pdb=" O ASN Z2459 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2468 through 2478 Processing helix chain 'Z' and resid 2498 through 2503 removed outlier: 3.754A pdb=" N GLU Z2502 " --> pdb=" O SER Z2498 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2516 through 2534 removed outlier: 3.576A pdb=" N GLY Z2532 " --> pdb=" O ALA Z2528 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2537 through 2550 removed outlier: 3.827A pdb=" N PHE Z2541 " --> pdb=" O ILE Z2537 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU Z2547 " --> pdb=" O ASP Z2543 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR Z2550 " --> pdb=" O ILE Z2546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2552 through 2569 removed outlier: 3.879A pdb=" N ILE Z2556 " --> pdb=" O ASP Z2552 " (cutoff:3.500A) Proline residue: Z2565 - end of helix removed outlier: 3.708A pdb=" N LYS Z2569 " --> pdb=" O PRO Z2565 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2575 through 2588 Processing helix chain 'Z' and resid 2601 through 2612 removed outlier: 3.754A pdb=" N LYS Z2612 " --> pdb=" O ASP Z2608 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2619 through 2630 Processing helix chain 'Z' and resid 2632 through 2642 Processing helix chain 'Z' and resid 2651 through 2670 removed outlier: 3.514A pdb=" N ILE Z2655 " --> pdb=" O ASN Z2651 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA Z2661 " --> pdb=" O ALA Z2657 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2671 through 2683 Processing helix chain 'Z' and resid 2685 through 2698 removed outlier: 3.781A pdb=" N ASN Z2689 " --> pdb=" O TYR Z2685 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2699 through 2714 Processing helix chain 'Z' and resid 2722 through 2740 Processing helix chain 'Z' and resid 2742 through 2754 removed outlier: 4.274A pdb=" N GLU Z2748 " --> pdb=" O ASP Z2744 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2755 through 2764 Processing helix chain 'Z' and resid 2772 through 2784 Processing helix chain 'Z' and resid 2788 through 2806 removed outlier: 3.580A pdb=" N PHE Z2794 " --> pdb=" O ARG Z2790 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2809 through 2831 removed outlier: 3.654A pdb=" N VAL Z2813 " --> pdb=" O GLY Z2809 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER Z2830 " --> pdb=" O ILE Z2826 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2837 through 2863 removed outlier: 4.334A pdb=" N TRP Z2841 " --> pdb=" O PRO Z2837 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU Z2842 " --> pdb=" O ALA Z2838 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU Z2853 " --> pdb=" O TYR Z2849 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2874 through 2887 Processing helix chain 'Z' and resid 2894 through 2915 removed outlier: 3.508A pdb=" N ILE Z2912 " --> pdb=" O ALA Z2908 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2939 through 2957 removed outlier: 3.542A pdb=" N ALA Z2944 " --> pdb=" O TYR Z2940 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP Z2945 " --> pdb=" O HIS Z2941 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2959 through 2969 removed outlier: 3.622A pdb=" N CYS Z2963 " --> pdb=" O MET Z2959 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG Z2969 " --> pdb=" O SER Z2965 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2977 through 2994 removed outlier: 4.029A pdb=" N GLN Z2994 " --> pdb=" O LYS Z2990 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2999 through 3009 removed outlier: 4.085A pdb=" N LEU Z3003 " --> pdb=" O LEU Z2999 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR Z3009 " --> pdb=" O VAL Z3005 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3015 through 3033 Processing helix chain 'Z' and resid 3037 through 3051 Processing helix chain 'Z' and resid 3053 through 3071 Processing helix chain 'Z' and resid 3074 through 3090 Processing helix chain 'Z' and resid 3096 through 3109 removed outlier: 3.651A pdb=" N LEU Z3100 " --> pdb=" O LYS Z3096 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG Z3103 " --> pdb=" O GLU Z3099 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER Z3109 " --> pdb=" O LEU Z3105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3117 through 3123 removed outlier: 3.537A pdb=" N PHE Z3121 " --> pdb=" O LEU Z3117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3130 through 3135 removed outlier: 3.917A pdb=" N THR Z3135 " --> pdb=" O TYR Z3132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3136 through 3143 Processing helix chain 'Z' and resid 3144 through 3146 No H-bonds generated for 'chain 'Z' and resid 3144 through 3146' Processing helix chain 'Z' and resid 3148 through 3163 removed outlier: 4.344A pdb=" N VAL Z3152 " --> pdb=" O GLU Z3148 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS Z3154 " --> pdb=" O ASN Z3150 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE Z3155 " --> pdb=" O MET Z3151 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3163 through 3182 removed outlier: 4.053A pdb=" N LEU Z3167 " --> pdb=" O TYR Z3163 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N PHE Z3169 " --> pdb=" O GLN Z3165 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLN Z3170 " --> pdb=" O ALA Z3166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3203 through 3218 Processing helix chain 'Z' and resid 3219 through 3237 removed outlier: 3.501A pdb=" N LEU Z3224 " --> pdb=" O PRO Z3220 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3240 through 3261 Processing helix chain 'Z' and resid 3273 through 3285 removed outlier: 3.720A pdb=" N THR Z3285 " --> pdb=" O VAL Z3281 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3292 through 3300 Processing helix chain 'Z' and resid 3308 through 3327 Processing helix chain 'Z' and resid 3333 through 3338 Processing helix chain 'Z' and resid 3338 through 3343 removed outlier: 3.593A pdb=" N SER Z3342 " --> pdb=" O CYS Z3338 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3344 through 3347 Processing helix chain 'Z' and resid 3413 through 3425 Processing helix chain 'Z' and resid 3426 through 3433 Processing helix chain 'Z' and resid 3433 through 3439 removed outlier: 3.939A pdb=" N ARG Z3439 " --> pdb=" O GLU Z3435 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3467 through 3479 Processing helix chain 'Z' and resid 3483 through 3496 removed outlier: 3.658A pdb=" N ASP Z3487 " --> pdb=" O ASP Z3483 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3505 through 3521 Processing helix chain 'Z' and resid 3525 through 3535 Processing helix chain 'Z' and resid 3537 through 3561 removed outlier: 3.545A pdb=" N PHE Z3541 " --> pdb=" O GLN Z3537 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3568 through 3570 No H-bonds generated for 'chain 'Z' and resid 3568 through 3570' Processing helix chain 'Z' and resid 3596 through 3601 removed outlier: 3.726A pdb=" N LEU Z3600 " --> pdb=" O VAL Z3596 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS Z3601 " --> pdb=" O LYS Z3597 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 3596 through 3601' Processing helix chain 'Z' and resid 3625 through 3633 Processing helix chain 'Z' and resid 3634 through 3640 Processing helix chain 'Z' and resid 3640 through 3654 removed outlier: 3.623A pdb=" N LEU Z3645 " --> pdb=" O PHE Z3641 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3657 through 3678 removed outlier: 3.877A pdb=" N LEU Z3665 " --> pdb=" O THR Z3661 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE Z3666 " --> pdb=" O TYR Z3662 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP Z3669 " --> pdb=" O LEU Z3665 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3684 through 3707 removed outlier: 3.725A pdb=" N GLU Z3690 " --> pdb=" O PRO Z3686 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU Z3706 " --> pdb=" O LYS Z3702 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY Z3707 " --> pdb=" O VAL Z3703 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3717 through 3729 Processing helix chain 'Z' and resid 3729 through 3734 Processing helix chain 'Z' and resid 3737 through 3741 Processing helix chain 'R' and resid 58 through 63 removed outlier: 4.650A pdb=" N GLY R 63 " --> pdb=" O GLU R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 97 Processing helix chain 'R' and resid 117 through 129 removed outlier: 3.603A pdb=" N LEU R 125 " --> pdb=" O ARG R 121 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU R 126 " --> pdb=" O LYS R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 151 Processing helix chain 'R' and resid 186 through 198 Processing helix chain 'R' and resid 205 through 207 No H-bonds generated for 'chain 'R' and resid 205 through 207' Processing helix chain 'R' and resid 226 through 238 removed outlier: 3.642A pdb=" N TYR R 230 " --> pdb=" O ASP R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 246 removed outlier: 3.577A pdb=" N GLU R 244 " --> pdb=" O GLN R 240 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR R 245 " --> pdb=" O GLU R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 288 removed outlier: 3.562A pdb=" N PHE R 288 " --> pdb=" O THR R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 293 Processing helix chain 'R' and resid 296 through 300 Processing helix chain 'R' and resid 384 through 396 removed outlier: 3.518A pdb=" N SER R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 397 through 407 removed outlier: 4.314A pdb=" N ALA R 402 " --> pdb=" O VAL R 398 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N THR R 403 " --> pdb=" O ASP R 399 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN R 407 " --> pdb=" O THR R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 417 removed outlier: 3.501A pdb=" N SER R 416 " --> pdb=" O GLY R 413 " (cutoff:3.500A) Processing helix chain 'R' and resid 419 through 432 removed outlier: 3.780A pdb=" N LYS R 430 " --> pdb=" O THR R 426 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE R 431 " --> pdb=" O GLU R 427 " (cutoff:3.500A) Processing helix chain 'R' and resid 444 through 449 Processing helix chain 'R' and resid 450 through 460 Processing helix chain 'R' and resid 472 through 478 removed outlier: 3.652A pdb=" N GLU R 476 " --> pdb=" O LYS R 472 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU R 477 " --> pdb=" O LYS R 473 " (cutoff:3.500A) Processing helix chain 'R' and resid 479 through 487 removed outlier: 3.653A pdb=" N ASN R 485 " --> pdb=" O GLU R 481 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP R 486 " --> pdb=" O ARG R 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.854A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.504A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.546A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 196 removed outlier: 3.666A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.650A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.669A pdb=" N ALA A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.269A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.584A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 305' Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 349 through 355 removed outlier: 3.726A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'P' and resid 504 through 531 removed outlier: 3.789A pdb=" N ASP P 531 " --> pdb=" O ARG P 527 " (cutoff:3.500A) Processing helix chain 'P' and resid 559 through 562 Processing helix chain 'P' and resid 563 through 568 Processing helix chain 'P' and resid 580 through 586 Processing helix chain 'P' and resid 611 through 616 Processing helix chain 'P' and resid 672 through 682 Processing helix chain 'P' and resid 697 through 709 removed outlier: 3.785A pdb=" N TRP P 709 " --> pdb=" O LEU P 705 " (cutoff:3.500A) Processing helix chain 'P' and resid 713 through 717 removed outlier: 3.585A pdb=" N GLU P 717 " --> pdb=" O PRO P 714 " (cutoff:3.500A) Processing helix chain 'P' and resid 721 through 723 No H-bonds generated for 'chain 'P' and resid 721 through 723' Processing helix chain 'P' and resid 724 through 730 Processing helix chain 'P' and resid 733 through 771 Processing helix chain 'E' and resid 241 through 248 removed outlier: 3.515A pdb=" N ILE E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 297 removed outlier: 3.553A pdb=" N LEU E 290 " --> pdb=" O PRO E 286 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR E 296 " --> pdb=" O TYR E 292 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU E 297 " --> pdb=" O MET E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 303 removed outlier: 3.846A pdb=" N LEU E 302 " --> pdb=" O PRO E 298 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 303 " --> pdb=" O LEU E 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 298 through 303' Processing helix chain 'E' and resid 311 through 337 Processing helix chain 'E' and resid 359 through 397 Processing helix chain 'E' and resid 398 through 402 removed outlier: 4.108A pdb=" N CYS E 401 " --> pdb=" O GLY E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 561 Processing helix chain 'E' and resid 612 through 617 Processing helix chain 'E' and resid 639 through 643 removed outlier: 3.634A pdb=" N LEU E 642 " --> pdb=" O LEU E 639 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN E 643 " --> pdb=" O ARG E 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 639 through 643' Processing helix chain 'E' and resid 651 through 666 Processing helix chain 'E' and resid 668 through 677 Processing helix chain 'E' and resid 692 through 705 removed outlier: 4.076A pdb=" N GLU E 705 " --> pdb=" O VAL E 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 717 through 734 Processing helix chain 'E' and resid 752 through 755 Processing helix chain 'E' and resid 756 through 773 Processing helix chain 'E' and resid 795 through 811 Processing helix chain 'S' and resid 41 through 50 removed outlier: 4.591A pdb=" N GLU S 45 " --> pdb=" O GLY S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 103 Processing helix chain 'S' and resid 110 through 114 removed outlier: 3.645A pdb=" N LYS S 113 " --> pdb=" O PRO S 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 124 through 134 removed outlier: 3.543A pdb=" N GLU S 133 " --> pdb=" O ALA S 129 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN S 134 " --> pdb=" O PHE S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 179 Processing helix chain 'S' and resid 182 through 189 removed outlier: 4.101A pdb=" N ASP S 188 " --> pdb=" O PHE S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 197 through 216 Processing helix chain 'S' and resid 220 through 227 removed outlier: 3.502A pdb=" N LEU S 223 " --> pdb=" O ASN S 220 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER S 224 " --> pdb=" O PRO S 221 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN S 227 " --> pdb=" O SER S 224 " (cutoff:3.500A) Processing helix chain 'S' and resid 229 through 245 removed outlier: 3.784A pdb=" N GLU S 235 " --> pdb=" O GLU S 231 " (cutoff:3.500A) Processing helix chain 'S' and resid 249 through 267 Processing helix chain 'S' and resid 267 through 283 Processing helix chain 'S' and resid 296 through 309 removed outlier: 3.553A pdb=" N SER S 301 " --> pdb=" O SER S 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 324 through 331 Processing helix chain 'S' and resid 332 through 334 No H-bonds generated for 'chain 'S' and resid 332 through 334' Processing sheet with id=AA1, first strand: chain 'Z' and resid 977 through 980 Processing sheet with id=AA2, first strand: chain 'Z' and resid 3331 through 3332 removed outlier: 7.225A pdb=" N MET Z3392 " --> pdb=" O PHE Z3374 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N PHE Z3374 " --> pdb=" O MET Z3392 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG Z3394 " --> pdb=" O ALA Z3372 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Z' and resid 3331 through 3332 removed outlier: 4.068A pdb=" N ARG Z3389 " --> pdb=" O VAL Z3405 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Z' and resid 3464 through 3466 Processing sheet with id=AA5, first strand: chain 'R' and resid 27 through 30 Processing sheet with id=AA6, first strand: chain 'R' and resid 55 through 56 Processing sheet with id=AA7, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA8, first strand: chain 'R' and resid 174 through 175 Processing sheet with id=AA9, first strand: chain 'R' and resid 174 through 175 removed outlier: 6.510A pdb=" N LEU R 156 " --> pdb=" O VAL R 409 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR R 411 " --> pdb=" O LEU R 156 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL R 158 " --> pdb=" O THR R 411 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL R 408 " --> pdb=" O LEU R 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 209 through 211 removed outlier: 6.742A pdb=" N ILE R 217 " --> pdb=" O LYS R 210 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 277 through 279 Processing sheet with id=AB3, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.494A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AB5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.519A pdb=" N THR A 160 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.104A pdb=" N ILE A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'P' and resid 489 through 490 removed outlier: 6.296A pdb=" N TRP E 650 " --> pdb=" O VAL E 743 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 535 through 537 Processing sheet with id=AC1, first strand: chain 'P' and resid 545 through 549 removed outlier: 6.528A pdb=" N VAL P 546 " --> pdb=" O SER P 575 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER P 575 " --> pdb=" O VAL P 546 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP P 548 " --> pdb=" O ASP P 573 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 594 through 596 removed outlier: 3.830A pdb=" N GLU E 267 " --> pdb=" O LEU E 605 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU E 600 " --> pdb=" O ILE P 636 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE P 636 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLU E 602 " --> pdb=" O TYR P 634 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N TYR P 634 " --> pdb=" O GLU E 602 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N GLN E 604 " --> pdb=" O ARG P 632 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ARG P 632 " --> pdb=" O GLN E 604 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 618 through 620 removed outlier: 5.928A pdb=" N GLU P 618 " --> pdb=" O ILE E 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'S' and resid 91 through 96 removed outlier: 4.106A pdb=" N LYS S 107 " --> pdb=" O GLU S 82 " (cutoff:3.500A) 2198 hydrogen bonds defined for protein. 6384 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: 13.33 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13917 1.34 - 1.46: 9673 1.46 - 1.58: 20341 1.58 - 1.70: 5 1.70 - 1.81: 302 Bond restraints: 44238 Sorted by residual: bond pdb=" CB PRO Z 41 " pdb=" CG PRO Z 41 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.67e+00 bond pdb=" C VAL Z 325 " pdb=" N PRO Z 326 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.66e+00 bond pdb=" C ILE Z1655 " pdb=" N PRO Z1656 " ideal model delta sigma weight residual 1.332 1.346 -0.013 8.90e-03 1.26e+04 2.27e+00 bond pdb=" C GLU Z3654 " pdb=" N PRO Z3655 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.47e-01 bond pdb=" CA ASN Z3525 " pdb=" CB ASN Z3525 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 9.10e-01 ... (remaining 44233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 58899 1.62 - 3.24: 776 3.24 - 4.86: 174 4.86 - 6.48: 38 6.48 - 8.09: 12 Bond angle restraints: 59899 Sorted by residual: angle pdb=" CA PRO Z 41 " pdb=" N PRO Z 41 " pdb=" CD PRO Z 41 " ideal model delta sigma weight residual 112.00 105.85 6.15 1.40e+00 5.10e-01 1.93e+01 angle pdb=" N ILE Z1770 " pdb=" CA ILE Z1770 " pdb=" C ILE Z1770 " ideal model delta sigma weight residual 106.42 112.72 -6.30 1.51e+00 4.39e-01 1.74e+01 angle pdb=" C LYS Z2573 " pdb=" N ASN Z2574 " pdb=" CA ASN Z2574 " ideal model delta sigma weight residual 125.66 132.05 -6.39 1.85e+00 2.92e-01 1.19e+01 angle pdb=" C ASN Z1769 " pdb=" N ILE Z1770 " pdb=" CA ILE Z1770 " ideal model delta sigma weight residual 122.96 119.97 2.99 9.50e-01 1.11e+00 9.93e+00 angle pdb=" CA ARG Z1738 " pdb=" CB ARG Z1738 " pdb=" CG ARG Z1738 " ideal model delta sigma weight residual 114.10 120.25 -6.15 2.00e+00 2.50e-01 9.47e+00 ... (remaining 59894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 24234 17.99 - 35.99: 2270 35.99 - 53.98: 337 53.98 - 71.97: 58 71.97 - 89.97: 32 Dihedral angle restraints: 26931 sinusoidal: 11179 harmonic: 15752 Sorted by residual: dihedral pdb=" CA SER Z3463 " pdb=" C SER Z3463 " pdb=" N PHE Z3464 " pdb=" CA PHE Z3464 " ideal model delta harmonic sigma weight residual 180.00 154.06 25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ARG Z1070 " pdb=" C ARG Z1070 " pdb=" N ASP Z1071 " pdb=" CA ASP Z1071 " ideal model delta harmonic sigma weight residual 180.00 156.96 23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA MET Z2850 " pdb=" C MET Z2850 " pdb=" N GLU Z2851 " pdb=" CA GLU Z2851 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 26928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 4823 0.038 - 0.076: 1473 0.076 - 0.114: 374 0.114 - 0.152: 50 0.152 - 0.189: 4 Chirality restraints: 6724 Sorted by residual: chirality pdb=" CB THR A 66 " pdb=" CA THR A 66 " pdb=" OG1 THR A 66 " pdb=" CG2 THR A 66 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA THR Z1594 " pdb=" N THR Z1594 " pdb=" C THR Z1594 " pdb=" CB THR Z1594 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA VAL P 560 " pdb=" N VAL P 560 " pdb=" C VAL P 560 " pdb=" CB VAL P 560 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 6721 not shown) Planarity restraints: 7622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER Z 40 " 0.071 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO Z 41 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO Z 41 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO Z 41 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP Z2133 " -0.014 2.00e-02 2.50e+03 1.46e-02 5.32e+00 pdb=" CG TRP Z2133 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP Z2133 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP Z2133 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP Z2133 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP Z2133 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP Z2133 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP Z2133 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP Z2133 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP Z2133 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 356 " 0.016 2.00e-02 2.50e+03 1.40e-02 4.88e+00 pdb=" CG TRP A 356 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 356 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 356 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 356 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 356 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 356 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 356 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 356 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 356 " 0.002 2.00e-02 2.50e+03 ... (remaining 7619 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 948 2.70 - 3.25: 45152 3.25 - 3.80: 68366 3.80 - 4.35: 91371 4.35 - 4.90: 148596 Nonbonded interactions: 354433 Sorted by model distance: nonbonded pdb=" O1B ATP R 501 " pdb="MG MG R 503 " model vdw 2.156 2.170 nonbonded pdb=" OH TYR Z3552 " pdb=" O ARG Z3623 " model vdw 2.236 3.040 nonbonded pdb=" O PHE Z 726 " pdb=" OG1 THR Z 732 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASP Z2246 " pdb=" OG SER Z2252 " model vdw 2.244 3.040 nonbonded pdb=" N GLY P 643 " pdb=" O ILE P 647 " model vdw 2.245 3.120 ... (remaining 354428 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 41.400 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.002 0.108 44238 Z= 0.102 Angle : 0.507 8.094 59899 Z= 0.249 Chirality : 0.039 0.189 6724 Planarity : 0.003 0.104 7622 Dihedral : 14.003 89.968 16659 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.02 % Allowed : 0.27 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: -0.12 (0.12), residues: 5252 helix: 0.48 (0.10), residues: 3004 sheet: 0.70 (0.38), residues: 202 loop : -0.90 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 588 TYR 0.016 0.001 TYR R 9 PHE 0.023 0.001 PHE Z1370 TRP 0.039 0.001 TRP Z2133 HIS 0.006 0.001 HIS R 248 Details of bonding type rmsd covalent geometry : bond 0.00242 (44238) covalent geometry : angle 0.50692 (59899) hydrogen bonds : bond 0.25871 ( 2188) hydrogen bonds : angle 6.98436 ( 6384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 553 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 218 MET cc_start: 0.2108 (mmp) cc_final: 0.1570 (mmp) REVERT: Z 482 TYR cc_start: 0.7922 (t80) cc_final: 0.7438 (t80) REVERT: Z 593 PHE cc_start: 0.7883 (m-10) cc_final: 0.7542 (m-10) REVERT: Z 685 TYR cc_start: 0.6650 (m-10) cc_final: 0.6284 (m-10) REVERT: Z 778 ASN cc_start: 0.7736 (m110) cc_final: 0.7528 (p0) REVERT: Z 912 TYR cc_start: 0.7988 (t80) cc_final: 0.7763 (t80) REVERT: Z 918 GLU cc_start: 0.8007 (tp30) cc_final: 0.7666 (tp30) REVERT: Z 1506 LEU cc_start: 0.6886 (tt) cc_final: 0.6104 (pp) REVERT: Z 2162 MET cc_start: 0.6493 (ttm) cc_final: 0.6245 (ttp) REVERT: Z 2652 THR cc_start: 0.7926 (p) cc_final: 0.7587 (t) REVERT: Z 2685 TYR cc_start: 0.8799 (m-80) cc_final: 0.8396 (m-80) REVERT: Z 2879 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7625 (ttp-110) REVERT: Z 3028 MET cc_start: 0.8490 (mtm) cc_final: 0.8026 (mtp) REVERT: Z 3075 ILE cc_start: 0.8628 (mm) cc_final: 0.8239 (mt) REVERT: Z 3248 LEU cc_start: 0.8792 (tp) cc_final: 0.8348 (mp) REVERT: Z 3465 THR cc_start: 0.8393 (p) cc_final: 0.8160 (p) REVERT: Z 3483 ASP cc_start: 0.7805 (m-30) cc_final: 0.7599 (m-30) REVERT: Z 3506 MET cc_start: 0.9080 (tpt) cc_final: 0.8729 (tpt) REVERT: Z 3594 GLU cc_start: 0.8036 (pp20) cc_final: 0.7586 (pm20) REVERT: Z 3683 ILE cc_start: 0.6594 (tp) cc_final: 0.6358 (tp) REVERT: Z 3691 MET cc_start: 0.8382 (ptp) cc_final: 0.8179 (ptm) REVERT: R 159 ASP cc_start: 0.7091 (m-30) cc_final: 0.6798 (m-30) REVERT: A 53 TYR cc_start: 0.6307 (m-80) cc_final: 0.6027 (m-80) REVERT: A 73 HIS cc_start: 0.6570 (m-70) cc_final: 0.6327 (m-70) REVERT: A 267 LEU cc_start: 0.7688 (pp) cc_final: 0.7441 (pp) REVERT: A 283 MET cc_start: 0.8517 (mmp) cc_final: 0.8309 (mmt) REVERT: P 504 ASP cc_start: 0.7708 (t0) cc_final: 0.7485 (t70) REVERT: P 517 ARG cc_start: 0.6553 (ptp90) cc_final: 0.6181 (ptp90) REVERT: P 522 GLU cc_start: 0.7367 (pt0) cc_final: 0.6999 (mt-10) REVERT: E 617 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7858 (tttp) REVERT: E 734 GLN cc_start: 0.6530 (mp-120) cc_final: 0.5659 (mp10) REVERT: S 42 MET cc_start: 0.8066 (mmt) cc_final: 0.7853 (mmt) REVERT: S 69 MET cc_start: 0.2526 (mpp) cc_final: 0.1248 (tpt) REVERT: S 255 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7483 (mm-30) REVERT: S 298 GLN cc_start: 0.7946 (pm20) cc_final: 0.7652 (mp10) outliers start: 1 outliers final: 0 residues processed: 554 average time/residue: 0.2767 time to fit residues: 248.0230 Evaluate side-chains 341 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 0.9980 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 0.5980 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 605 ASN Z 639 HIS Z 704 GLN Z 787 HIS Z 896 GLN Z 943 HIS ** Z1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z1407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z1717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1808 ASN ** Z1992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z2174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z2882 GLN ** Z3433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z3459 ASN R 60 GLN R 248 HIS A 228 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 678 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.176819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138507 restraints weight = 63394.037| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.12 r_work: 0.3246 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 44238 Z= 0.166 Angle : 0.605 9.895 59899 Z= 0.311 Chirality : 0.042 0.179 6724 Planarity : 0.004 0.057 7622 Dihedral : 5.053 64.036 5780 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.74 % Allowed : 7.61 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.31 (0.12), residues: 5252 helix: 0.92 (0.09), residues: 3115 sheet: 0.42 (0.37), residues: 210 loop : -0.93 (0.15), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 712 TYR 0.034 0.001 TYR Z 392 PHE 0.037 0.002 PHE Z2172 TRP 0.024 0.002 TRP Z2904 HIS 0.007 0.001 HIS E 678 Details of bonding type rmsd covalent geometry : bond 0.00371 (44238) covalent geometry : angle 0.60469 (59899) hydrogen bonds : bond 0.05822 ( 2188) hydrogen bonds : angle 4.63161 ( 6384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 374 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 88 MET cc_start: 0.1988 (mmm) cc_final: 0.1559 (ttm) REVERT: Z 218 MET cc_start: 0.2350 (mmp) cc_final: 0.1873 (mmp) REVERT: Z 392 TYR cc_start: 0.7235 (m-10) cc_final: 0.6578 (m-10) REVERT: Z 465 MET cc_start: 0.7480 (mmm) cc_final: 0.7049 (mmm) REVERT: Z 489 TYR cc_start: 0.5815 (t80) cc_final: 0.5562 (t80) REVERT: Z 593 PHE cc_start: 0.8033 (m-10) cc_final: 0.7672 (m-10) REVERT: Z 645 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7976 (mm) REVERT: Z 712 ARG cc_start: 0.8163 (mmm-85) cc_final: 0.7804 (mmm-85) REVERT: Z 778 ASN cc_start: 0.7712 (m110) cc_final: 0.7463 (m110) REVERT: Z 918 GLU cc_start: 0.8283 (tp30) cc_final: 0.7999 (tp30) REVERT: Z 1547 MET cc_start: 0.6872 (tpp) cc_final: 0.6577 (tpp) REVERT: Z 1789 PHE cc_start: 0.7053 (t80) cc_final: 0.6850 (t80) REVERT: Z 2316 TYR cc_start: 0.7493 (t80) cc_final: 0.6874 (t80) REVERT: Z 2652 THR cc_start: 0.8178 (p) cc_final: 0.7954 (t) REVERT: Z 3034 ARG cc_start: 0.7804 (mmm-85) cc_final: 0.7074 (mmt-90) REVERT: Z 3177 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7150 (t0) REVERT: Z 3244 ASP cc_start: 0.8308 (t0) cc_final: 0.7931 (t0) REVERT: Z 3248 LEU cc_start: 0.8994 (tp) cc_final: 0.8651 (mp) REVERT: Z 3419 MET cc_start: 0.8853 (mmp) cc_final: 0.8530 (mmp) REVERT: Z 3683 ILE cc_start: 0.6255 (tp) cc_final: 0.6054 (tp) REVERT: A 73 HIS cc_start: 0.6830 (m-70) cc_final: 0.6534 (m-70) REVERT: A 283 MET cc_start: 0.8830 (mmp) cc_final: 0.8434 (mmp) REVERT: P 504 ASP cc_start: 0.8210 (t0) cc_final: 0.7900 (t70) REVERT: S 69 MET cc_start: 0.2296 (mpp) cc_final: 0.1592 (mpp) REVERT: S 255 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7900 (mm-30) outliers start: 36 outliers final: 14 residues processed: 388 average time/residue: 0.2914 time to fit residues: 190.2071 Evaluate side-chains 337 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 321 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 645 LEU Chi-restraints excluded: chain Z residue 1066 THR Chi-restraints excluded: chain Z residue 1128 THR Chi-restraints excluded: chain Z residue 1262 LYS Chi-restraints excluded: chain Z residue 1408 LEU Chi-restraints excluded: chain Z residue 2631 ASN Chi-restraints excluded: chain Z residue 2923 LEU Chi-restraints excluded: chain Z residue 3177 ASP Chi-restraints excluded: chain Z residue 3410 VAL Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain P residue 539 THR Chi-restraints excluded: chain P residue 626 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 399 optimal weight: 0.9990 chunk 282 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 314 optimal weight: 0.9990 chunk 413 optimal weight: 10.0000 chunk 315 optimal weight: 0.9980 chunk 466 optimal weight: 1.9990 chunk 292 optimal weight: 0.8980 chunk 242 optimal weight: 0.0870 chunk 157 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1124 ASN ** Z1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z1407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1717 GLN ** Z1992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z2174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z3433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z3459 ASN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.175283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125117 restraints weight = 62726.366| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.02 r_work: 0.3190 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44238 Z= 0.135 Angle : 0.546 9.726 59899 Z= 0.278 Chirality : 0.041 0.182 6724 Planarity : 0.004 0.049 7622 Dihedral : 4.925 59.100 5780 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.01 % Allowed : 10.07 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.47 (0.12), residues: 5252 helix: 1.10 (0.09), residues: 3131 sheet: 0.51 (0.36), residues: 221 loop : -1.00 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 482 TYR 0.020 0.001 TYR Z 392 PHE 0.029 0.001 PHE Z3464 TRP 0.035 0.001 TRP Z2904 HIS 0.005 0.001 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00305 (44238) covalent geometry : angle 0.54556 (59899) hydrogen bonds : bond 0.04685 ( 2188) hydrogen bonds : angle 4.25368 ( 6384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 339 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 218 MET cc_start: 0.3107 (mmp) cc_final: 0.2637 (mmt) REVERT: Z 392 TYR cc_start: 0.7228 (m-10) cc_final: 0.6740 (m-10) REVERT: Z 465 MET cc_start: 0.7680 (mmm) cc_final: 0.7431 (mmp) REVERT: Z 593 PHE cc_start: 0.8010 (m-10) cc_final: 0.7630 (m-10) REVERT: Z 632 ILE cc_start: 0.8087 (mm) cc_final: 0.7846 (tt) REVERT: Z 645 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7749 (mm) REVERT: Z 712 ARG cc_start: 0.8175 (mmm-85) cc_final: 0.7936 (mmm-85) REVERT: Z 771 MET cc_start: 0.8283 (tmm) cc_final: 0.8069 (tmm) REVERT: Z 778 ASN cc_start: 0.7996 (m110) cc_final: 0.7709 (m-40) REVERT: Z 918 GLU cc_start: 0.8602 (tp30) cc_final: 0.8270 (tp30) REVERT: Z 1407 GLN cc_start: 0.6740 (tp40) cc_final: 0.6319 (tt0) REVERT: Z 1487 MET cc_start: 0.3304 (mmt) cc_final: 0.3043 (mtm) REVERT: Z 1506 LEU cc_start: 0.6548 (tt) cc_final: 0.5976 (pp) REVERT: Z 1547 MET cc_start: 0.6948 (tpp) cc_final: 0.6506 (tpp) REVERT: Z 2316 TYR cc_start: 0.7479 (t80) cc_final: 0.7187 (t80) REVERT: Z 2652 THR cc_start: 0.8345 (p) cc_final: 0.7990 (t) REVERT: Z 3177 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7348 (t0) REVERT: Z 3244 ASP cc_start: 0.8628 (t0) cc_final: 0.8283 (m-30) REVERT: Z 3248 LEU cc_start: 0.9095 (tp) cc_final: 0.8694 (mp) REVERT: Z 3419 MET cc_start: 0.9012 (mmp) cc_final: 0.8742 (mmp) REVERT: Z 3521 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7403 (p90) REVERT: Z 3525 ASN cc_start: 0.8402 (p0) cc_final: 0.7953 (p0) REVERT: Z 3643 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8195 (t) REVERT: Z 3683 ILE cc_start: 0.6680 (tp) cc_final: 0.6479 (tp) REVERT: A 73 HIS cc_start: 0.6946 (m-70) cc_final: 0.6598 (m-70) REVERT: A 187 ASP cc_start: 0.6618 (m-30) cc_final: 0.6417 (m-30) REVERT: A 283 MET cc_start: 0.8887 (mmp) cc_final: 0.8476 (mmp) REVERT: P 504 ASP cc_start: 0.8241 (t0) cc_final: 0.8002 (t70) REVERT: P 517 ARG cc_start: 0.7365 (mtm110) cc_final: 0.6994 (mtm110) REVERT: P 593 ARG cc_start: 0.8379 (tpp80) cc_final: 0.8120 (mtt90) REVERT: P 744 MET cc_start: 0.8359 (tmm) cc_final: 0.8091 (ttp) REVERT: E 285 LEU cc_start: 0.8692 (tt) cc_final: 0.8314 (mp) REVERT: E 562 ASP cc_start: 0.7705 (t0) cc_final: 0.7474 (t0) REVERT: S 42 MET cc_start: 0.8125 (mmt) cc_final: 0.7885 (mmt) REVERT: S 69 MET cc_start: 0.2555 (mpp) cc_final: 0.1966 (mpp) outliers start: 49 outliers final: 17 residues processed: 370 average time/residue: 0.2674 time to fit residues: 167.2172 Evaluate side-chains 338 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 317 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 376 LEU Chi-restraints excluded: chain Z residue 645 LEU Chi-restraints excluded: chain Z residue 1066 THR Chi-restraints excluded: chain Z residue 2629 SER Chi-restraints excluded: chain Z residue 2631 ASN Chi-restraints excluded: chain Z residue 2923 LEU Chi-restraints excluded: chain Z residue 3177 ASP Chi-restraints excluded: chain Z residue 3360 LEU Chi-restraints excluded: chain Z residue 3410 VAL Chi-restraints excluded: chain Z residue 3521 PHE Chi-restraints excluded: chain Z residue 3643 VAL Chi-restraints excluded: chain R residue 382 LEU Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 408 VAL Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain P residue 539 THR Chi-restraints excluded: chain P residue 588 ILE Chi-restraints excluded: chain P residue 626 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 324 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 380 optimal weight: 0.7980 chunk 156 optimal weight: 9.9990 chunk 416 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 230 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 357 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z1124 ASN ** Z1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1407 GLN ** Z1992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z2174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z2957 HIS Z3209 GLN ** Z3433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z3459 ASN A 228 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 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 = 0.4229 r_free = 0.4229 target = 0.175331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125237 restraints weight = 63080.187| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.83 r_work: 0.3151 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 44238 Z= 0.150 Angle : 0.546 10.210 59899 Z= 0.278 Chirality : 0.042 0.204 6724 Planarity : 0.004 0.051 7622 Dihedral : 4.873 65.902 5780 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.46 % Allowed : 11.74 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.55 (0.12), residues: 5252 helix: 1.19 (0.09), residues: 3137 sheet: 0.60 (0.37), residues: 208 loop : -1.00 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z3034 TYR 0.030 0.001 TYR Z 489 PHE 0.034 0.001 PHE Z3464 TRP 0.039 0.001 TRP Z2904 HIS 0.006 0.001 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00353 (44238) covalent geometry : angle 0.54606 (59899) hydrogen bonds : bond 0.04205 ( 2188) hydrogen bonds : angle 4.08477 ( 6384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 330 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 88 MET cc_start: 0.1944 (mmm) cc_final: 0.1329 (ttt) REVERT: Z 218 MET cc_start: 0.3306 (mmp) cc_final: 0.2552 (mmt) REVERT: Z 392 TYR cc_start: 0.7366 (m-10) cc_final: 0.7138 (m-10) REVERT: Z 465 MET cc_start: 0.7804 (mmm) cc_final: 0.7370 (mmp) REVERT: Z 593 PHE cc_start: 0.8007 (m-10) cc_final: 0.7578 (m-10) REVERT: Z 632 ILE cc_start: 0.8216 (mm) cc_final: 0.8012 (tt) REVERT: Z 645 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7850 (mm) REVERT: Z 771 MET cc_start: 0.8169 (tmm) cc_final: 0.7960 (tmm) REVERT: Z 918 GLU cc_start: 0.8568 (tp30) cc_final: 0.8237 (tp30) REVERT: Z 1407 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6453 (tt0) REVERT: Z 1547 MET cc_start: 0.6952 (tpp) cc_final: 0.6483 (tpp) REVERT: Z 2316 TYR cc_start: 0.7481 (t80) cc_final: 0.7083 (t80) REVERT: Z 2342 HIS cc_start: 0.7532 (m90) cc_final: 0.6914 (m90) REVERT: Z 2500 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8437 (pp) REVERT: Z 2652 THR cc_start: 0.8336 (p) cc_final: 0.7957 (t) REVERT: Z 3177 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7222 (t0) REVERT: Z 3244 ASP cc_start: 0.8508 (t0) cc_final: 0.8175 (m-30) REVERT: Z 3248 LEU cc_start: 0.9085 (tp) cc_final: 0.8687 (mp) REVERT: Z 3417 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8522 (mt-10) REVERT: Z 3521 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7193 (p90) REVERT: Z 3643 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8510 (t) REVERT: Z 3655 PRO cc_start: 0.8759 (Cg_endo) cc_final: 0.8444 (Cg_exo) REVERT: R 69 TYR cc_start: 0.8511 (t80) cc_final: 0.8016 (t80) REVERT: A 73 HIS cc_start: 0.6871 (m-70) cc_final: 0.6614 (m-70) REVERT: A 283 MET cc_start: 0.8957 (mmp) cc_final: 0.8488 (mmp) REVERT: P 504 ASP cc_start: 0.8172 (t0) cc_final: 0.7943 (t70) REVERT: P 594 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8662 (mm) REVERT: P 744 MET cc_start: 0.8372 (tmm) cc_final: 0.8146 (ttp) REVERT: E 285 LEU cc_start: 0.8686 (tt) cc_final: 0.8321 (mp) REVERT: E 562 ASP cc_start: 0.7863 (t0) cc_final: 0.7662 (t0) REVERT: E 622 PHE cc_start: 0.6894 (p90) cc_final: 0.6658 (p90) REVERT: E 726 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8101 (mm-30) REVERT: S 50 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8142 (pp) REVERT: S 69 MET cc_start: 0.2515 (mpp) cc_final: 0.1828 (mpp) REVERT: S 188 ASP cc_start: 0.8499 (p0) cc_final: 0.8140 (p0) REVERT: S 255 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8263 (mm-30) outliers start: 71 outliers final: 30 residues processed: 381 average time/residue: 0.2593 time to fit residues: 169.5183 Evaluate side-chains 348 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 376 LEU Chi-restraints excluded: chain Z residue 645 LEU Chi-restraints excluded: chain Z residue 908 LEU Chi-restraints excluded: chain Z residue 932 LEU Chi-restraints excluded: chain Z residue 1066 THR Chi-restraints excluded: chain Z residue 1262 LYS Chi-restraints excluded: chain Z residue 1407 GLN Chi-restraints excluded: chain Z residue 2007 ILE Chi-restraints excluded: chain Z residue 2500 LEU Chi-restraints excluded: chain Z residue 2629 SER Chi-restraints excluded: chain Z residue 2631 ASN Chi-restraints excluded: chain Z residue 2923 LEU Chi-restraints excluded: chain Z residue 2946 VAL Chi-restraints excluded: chain Z residue 3028 MET Chi-restraints excluded: chain Z residue 3177 ASP Chi-restraints excluded: chain Z residue 3307 TYR Chi-restraints excluded: chain Z residue 3360 LEU Chi-restraints excluded: chain Z residue 3410 VAL Chi-restraints excluded: chain Z residue 3417 GLU Chi-restraints excluded: chain Z residue 3447 ILE Chi-restraints excluded: chain Z residue 3521 PHE Chi-restraints excluded: chain Z residue 3643 VAL Chi-restraints excluded: chain Z residue 3645 LEU Chi-restraints excluded: chain Z residue 3738 VAL Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 408 VAL Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain P residue 539 THR Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 594 ILE Chi-restraints excluded: chain P residue 626 ASN Chi-restraints excluded: chain E residue 802 LEU Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 312 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 50 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 chunk 511 optimal weight: 7.9990 chunk 216 optimal weight: 0.9980 chunk 310 optimal weight: 0.4980 chunk 152 optimal weight: 8.9990 chunk 379 optimal weight: 0.0670 chunk 467 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 229 optimal weight: 1.9990 chunk 344 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z1124 ASN ** Z1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1674 ASN Z1892 ASN ** Z1992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z2174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z2237 GLN Z3433 ASN ** Z3459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 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 = 0.4239 r_free = 0.4239 target = 0.176264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126187 restraints weight = 63213.316| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.93 r_work: 0.3198 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44238 Z= 0.119 Angle : 0.525 9.926 59899 Z= 0.265 Chirality : 0.041 0.202 6724 Planarity : 0.004 0.058 7622 Dihedral : 4.734 70.022 5780 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.40 % Allowed : 12.85 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.68 (0.12), residues: 5252 helix: 1.31 (0.10), residues: 3137 sheet: 0.58 (0.36), residues: 213 loop : -0.99 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 712 TYR 0.030 0.001 TYR Z 489 PHE 0.026 0.001 PHE Z3464 TRP 0.038 0.001 TRP Z2904 HIS 0.004 0.001 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00269 (44238) covalent geometry : angle 0.52467 (59899) hydrogen bonds : bond 0.03847 ( 2188) hydrogen bonds : angle 3.97083 ( 6384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 324 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 218 MET cc_start: 0.3248 (mmp) cc_final: 0.2506 (mmt) REVERT: Z 593 PHE cc_start: 0.7982 (m-10) cc_final: 0.7548 (m-10) REVERT: Z 712 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.8000 (mmm-85) REVERT: Z 771 MET cc_start: 0.8154 (tmm) cc_final: 0.7934 (tmm) REVERT: Z 778 ASN cc_start: 0.8094 (m-40) cc_final: 0.7707 (p0) REVERT: Z 918 GLU cc_start: 0.8642 (tp30) cc_final: 0.8311 (tp30) REVERT: Z 1280 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5090 (pp) REVERT: Z 1547 MET cc_start: 0.6932 (tpp) cc_final: 0.6436 (tpp) REVERT: Z 1626 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7316 (t0) REVERT: Z 1716 LEU cc_start: 0.7723 (pp) cc_final: 0.7191 (tt) REVERT: Z 2342 HIS cc_start: 0.7432 (m90) cc_final: 0.7044 (m90) REVERT: Z 2581 ARG cc_start: 0.8593 (tpt90) cc_final: 0.7828 (mmm160) REVERT: Z 2652 THR cc_start: 0.8295 (p) cc_final: 0.7909 (t) REVERT: Z 3177 ASP cc_start: 0.7658 (t70) cc_final: 0.7191 (t0) REVERT: Z 3244 ASP cc_start: 0.8461 (t0) cc_final: 0.8173 (m-30) REVERT: Z 3248 LEU cc_start: 0.9217 (tp) cc_final: 0.8821 (mp) REVERT: Z 3307 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.6106 (t80) REVERT: Z 3417 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8525 (mt-10) REVERT: Z 3506 MET cc_start: 0.9266 (tpt) cc_final: 0.9020 (tpt) REVERT: Z 3521 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7076 (p90) REVERT: Z 3655 PRO cc_start: 0.8676 (Cg_endo) cc_final: 0.8426 (Cg_exo) REVERT: A 283 MET cc_start: 0.8939 (mmp) cc_final: 0.8523 (mmp) REVERT: P 504 ASP cc_start: 0.8179 (t0) cc_final: 0.7943 (t70) REVERT: P 594 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8529 (mm) REVERT: P 744 MET cc_start: 0.8369 (tmm) cc_final: 0.8157 (ttp) REVERT: E 285 LEU cc_start: 0.8670 (tt) cc_final: 0.8308 (mp) REVERT: E 622 PHE cc_start: 0.6823 (p90) cc_final: 0.6608 (p90) REVERT: E 734 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6503 (mp10) REVERT: S 50 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8033 (pp) REVERT: S 69 MET cc_start: 0.2677 (mpp) cc_final: 0.2003 (mpp) REVERT: S 188 ASP cc_start: 0.8420 (p0) cc_final: 0.8064 (p0) REVERT: S 255 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8266 (mm-30) outliers start: 68 outliers final: 27 residues processed: 376 average time/residue: 0.2667 time to fit residues: 170.9612 Evaluate side-chains 349 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 314 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 376 LEU Chi-restraints excluded: chain Z residue 908 LEU Chi-restraints excluded: chain Z residue 1066 THR Chi-restraints excluded: chain Z residue 1262 LYS Chi-restraints excluded: chain Z residue 1280 LEU Chi-restraints excluded: chain Z residue 1594 THR Chi-restraints excluded: chain Z residue 1626 ASN Chi-restraints excluded: chain Z residue 1948 VAL Chi-restraints excluded: chain Z residue 2299 MET Chi-restraints excluded: chain Z residue 2500 LEU Chi-restraints excluded: chain Z residue 2629 SER Chi-restraints excluded: chain Z residue 2631 ASN Chi-restraints excluded: chain Z residue 2923 LEU Chi-restraints excluded: chain Z residue 3028 MET Chi-restraints excluded: chain Z residue 3307 TYR Chi-restraints excluded: chain Z residue 3360 LEU Chi-restraints excluded: chain Z residue 3410 VAL Chi-restraints excluded: chain Z residue 3417 GLU Chi-restraints excluded: chain Z residue 3441 ILE Chi-restraints excluded: chain Z residue 3521 PHE Chi-restraints excluded: chain Z residue 3645 LEU Chi-restraints excluded: chain R residue 383 ILE Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 408 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain P residue 539 THR Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 594 ILE Chi-restraints excluded: chain P residue 626 ASN Chi-restraints excluded: chain E residue 734 GLN Chi-restraints excluded: chain E residue 802 LEU Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 118 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 435 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 522 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 413 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 402 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 488 optimal weight: 0.0980 chunk 424 optimal weight: 10.0000 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z1124 ASN ** Z1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1328 HIS Z1769 ASN ** Z1992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z2174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z3459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 ASN ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 731 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.174260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124240 restraints weight = 63092.381| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.73 r_work: 0.3112 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 44238 Z= 0.169 Angle : 0.561 11.236 59899 Z= 0.282 Chirality : 0.042 0.217 6724 Planarity : 0.004 0.048 7622 Dihedral : 4.824 70.328 5780 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.40 % Allowed : 13.70 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.61 (0.12), residues: 5252 helix: 1.28 (0.09), residues: 3127 sheet: 0.20 (0.36), residues: 220 loop : -1.01 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z1412 TYR 0.034 0.001 TYR Z 489 PHE 0.037 0.002 PHE Z3464 TRP 0.019 0.002 TRP A 356 HIS 0.017 0.001 HIS Z1328 Details of bonding type rmsd covalent geometry : bond 0.00408 (44238) covalent geometry : angle 0.56128 (59899) hydrogen bonds : bond 0.04084 ( 2188) hydrogen bonds : angle 4.01317 ( 6384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 314 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 88 MET cc_start: 0.2289 (mmt) cc_final: 0.1662 (ttm) REVERT: Z 218 MET cc_start: 0.3463 (mmp) cc_final: 0.2903 (mmt) REVERT: Z 392 TYR cc_start: 0.7429 (m-10) cc_final: 0.7145 (m-10) REVERT: Z 593 PHE cc_start: 0.7972 (m-10) cc_final: 0.7600 (m-10) REVERT: Z 688 PHE cc_start: 0.7800 (t80) cc_final: 0.7518 (t80) REVERT: Z 712 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.7969 (mmm-85) REVERT: Z 778 ASN cc_start: 0.7999 (m-40) cc_final: 0.7640 (p0) REVERT: Z 918 GLU cc_start: 0.8624 (tp30) cc_final: 0.8272 (tp30) REVERT: Z 1139 MET cc_start: 0.8632 (mtm) cc_final: 0.8341 (mtm) REVERT: Z 1280 LEU cc_start: 0.5752 (OUTLIER) cc_final: 0.5195 (pp) REVERT: Z 1349 MET cc_start: 0.7244 (ptp) cc_final: 0.6799 (mtt) REVERT: Z 1547 MET cc_start: 0.6927 (tpp) cc_final: 0.6427 (tpp) REVERT: Z 1626 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7263 (t0) REVERT: Z 1716 LEU cc_start: 0.7600 (pp) cc_final: 0.7069 (tt) REVERT: Z 2342 HIS cc_start: 0.7435 (m90) cc_final: 0.6987 (m90) REVERT: Z 2652 THR cc_start: 0.8336 (p) cc_final: 0.7937 (t) REVERT: Z 3177 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7242 (t0) REVERT: Z 3244 ASP cc_start: 0.8470 (t0) cc_final: 0.8190 (m-30) REVERT: Z 3248 LEU cc_start: 0.9150 (tp) cc_final: 0.8702 (mp) REVERT: Z 3307 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.6649 (t80) REVERT: Z 3417 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8541 (mt-10) REVERT: Z 3506 MET cc_start: 0.9320 (tpt) cc_final: 0.9097 (tpt) REVERT: R 404 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8737 (mp) REVERT: A 208 ILE cc_start: 0.7730 (mp) cc_final: 0.7471 (tt) REVERT: A 283 MET cc_start: 0.8995 (mmp) cc_final: 0.8735 (mmt) REVERT: P 504 ASP cc_start: 0.8184 (t0) cc_final: 0.7933 (t70) REVERT: P 543 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7620 (p90) REVERT: P 594 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8631 (mm) REVERT: E 285 LEU cc_start: 0.8691 (tt) cc_final: 0.8295 (mp) REVERT: E 734 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6607 (mp10) REVERT: S 50 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8291 (pp) REVERT: S 69 MET cc_start: 0.2550 (mpp) cc_final: 0.1861 (mpp) REVERT: S 188 ASP cc_start: 0.8501 (p0) cc_final: 0.8095 (p0) REVERT: S 255 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8262 (mm-30) outliers start: 68 outliers final: 44 residues processed: 368 average time/residue: 0.2514 time to fit residues: 156.4217 Evaluate side-chains 356 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 376 LEU Chi-restraints excluded: chain Z residue 908 LEU Chi-restraints excluded: chain Z residue 932 LEU Chi-restraints excluded: chain Z residue 952 LEU Chi-restraints excluded: chain Z residue 1066 THR Chi-restraints excluded: chain Z residue 1131 ILE Chi-restraints excluded: chain Z residue 1160 VAL Chi-restraints excluded: chain Z residue 1189 PHE Chi-restraints excluded: chain Z residue 1205 THR Chi-restraints excluded: chain Z residue 1262 LYS Chi-restraints excluded: chain Z residue 1280 LEU Chi-restraints excluded: chain Z residue 1594 THR Chi-restraints excluded: chain Z residue 1626 ASN Chi-restraints excluded: chain Z residue 1948 VAL Chi-restraints excluded: chain Z residue 2012 ASN Chi-restraints excluded: chain Z residue 2162 MET Chi-restraints excluded: chain Z residue 2299 MET Chi-restraints excluded: chain Z residue 2500 LEU Chi-restraints excluded: chain Z residue 2629 SER Chi-restraints excluded: chain Z residue 2686 THR Chi-restraints excluded: chain Z residue 2923 LEU Chi-restraints excluded: chain Z residue 2946 VAL Chi-restraints excluded: chain Z residue 3028 MET Chi-restraints excluded: chain Z residue 3177 ASP Chi-restraints excluded: chain Z residue 3307 TYR Chi-restraints excluded: chain Z residue 3360 LEU Chi-restraints excluded: chain Z residue 3410 VAL Chi-restraints excluded: chain Z residue 3417 GLU Chi-restraints excluded: chain Z residue 3441 ILE Chi-restraints excluded: chain Z residue 3521 PHE Chi-restraints excluded: chain Z residue 3645 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 382 LEU Chi-restraints excluded: chain R residue 383 ILE Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 404 LEU Chi-restraints excluded: chain R residue 408 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain P residue 539 THR Chi-restraints excluded: chain P residue 543 PHE Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 594 ILE Chi-restraints excluded: chain P residue 626 ASN Chi-restraints excluded: chain E residue 563 LEU Chi-restraints excluded: chain E residue 644 ASN Chi-restraints excluded: chain E residue 734 GLN Chi-restraints excluded: chain E residue 802 LEU Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain S residue 312 THR Chi-restraints excluded: chain S residue 329 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 7 optimal weight: 8.9990 chunk 271 optimal weight: 0.8980 chunk 365 optimal weight: 0.5980 chunk 247 optimal weight: 9.9990 chunk 327 optimal weight: 0.6980 chunk 449 optimal weight: 0.0270 chunk 249 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 267 optimal weight: 0.6980 chunk 409 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z1124 ASN ** Z1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1328 HIS ** Z1992 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z2174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z2289 HIS ** Z3459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.175605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.131923 restraints weight = 62726.554| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.00 r_work: 0.3199 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 44238 Z= 0.118 Angle : 0.525 10.112 59899 Z= 0.264 Chirality : 0.040 0.231 6724 Planarity : 0.004 0.051 7622 Dihedral : 4.696 73.133 5780 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.36 % Allowed : 13.99 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.73 (0.12), residues: 5252 helix: 1.38 (0.10), residues: 3129 sheet: 0.45 (0.37), residues: 211 loop : -1.00 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 344 TYR 0.033 0.001 TYR Z 489 PHE 0.028 0.001 PHE Z2264 TRP 0.019 0.001 TRP A 356 HIS 0.014 0.001 HIS Z1328 Details of bonding type rmsd covalent geometry : bond 0.00268 (44238) covalent geometry : angle 0.52546 (59899) hydrogen bonds : bond 0.03663 ( 2188) hydrogen bonds : angle 3.89698 ( 6384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 321 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 218 MET cc_start: 0.3424 (mmp) cc_final: 0.2858 (mmt) REVERT: Z 392 TYR cc_start: 0.7444 (m-10) cc_final: 0.7109 (m-10) REVERT: Z 586 LEU cc_start: 0.8775 (tt) cc_final: 0.8529 (pp) REVERT: Z 593 PHE cc_start: 0.7981 (m-10) cc_final: 0.7615 (m-10) REVERT: Z 688 PHE cc_start: 0.7852 (t80) cc_final: 0.7560 (t80) REVERT: Z 716 ASP cc_start: 0.7517 (t0) cc_final: 0.6234 (p0) REVERT: Z 778 ASN cc_start: 0.8060 (m-40) cc_final: 0.7694 (p0) REVERT: Z 793 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8641 (mt) REVERT: Z 918 GLU cc_start: 0.8600 (tp30) cc_final: 0.8295 (tp30) REVERT: Z 1139 MET cc_start: 0.8576 (mtm) cc_final: 0.8142 (mtt) REVERT: Z 1280 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5197 (pp) REVERT: Z 1547 MET cc_start: 0.6893 (tpp) cc_final: 0.6373 (tpp) REVERT: Z 1716 LEU cc_start: 0.7572 (pp) cc_final: 0.6983 (tt) REVERT: Z 2342 HIS cc_start: 0.7190 (m90) cc_final: 0.6552 (m90) REVERT: Z 2581 ARG cc_start: 0.8624 (tpt90) cc_final: 0.7863 (mmm160) REVERT: Z 2652 THR cc_start: 0.8434 (p) cc_final: 0.8047 (t) REVERT: Z 3244 ASP cc_start: 0.8339 (t0) cc_final: 0.8126 (m-30) REVERT: Z 3248 LEU cc_start: 0.9231 (tp) cc_final: 0.8833 (mp) REVERT: Z 3307 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.6399 (t80) REVERT: Z 3417 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8517 (mt-10) REVERT: Z 3506 MET cc_start: 0.9279 (tpt) cc_final: 0.9051 (tpt) REVERT: Z 3521 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7147 (p90) REVERT: Z 3655 PRO cc_start: 0.8752 (Cg_endo) cc_final: 0.8547 (Cg_exo) REVERT: R 404 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8718 (mp) REVERT: R 482 ARG cc_start: 0.7410 (ptp-170) cc_final: 0.6994 (ptm160) REVERT: A 283 MET cc_start: 0.8939 (mmp) cc_final: 0.8540 (mmp) REVERT: P 504 ASP cc_start: 0.8258 (t0) cc_final: 0.8026 (t70) REVERT: P 594 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8494 (mm) REVERT: E 285 LEU cc_start: 0.8662 (tt) cc_final: 0.8317 (mp) REVERT: S 50 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8171 (pp) REVERT: S 69 MET cc_start: 0.2804 (mpp) cc_final: 0.2183 (mpp) REVERT: S 188 ASP cc_start: 0.8369 (p0) cc_final: 0.7988 (p0) outliers start: 66 outliers final: 39 residues processed: 373 average time/residue: 0.2299 time to fit residues: 146.3978 Evaluate side-chains 356 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 309 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 376 LEU Chi-restraints excluded: chain Z residue 793 LEU Chi-restraints excluded: chain Z residue 908 LEU Chi-restraints excluded: chain Z residue 952 LEU Chi-restraints excluded: chain Z residue 1066 THR Chi-restraints excluded: chain Z residue 1128 THR Chi-restraints excluded: chain Z residue 1131 ILE Chi-restraints excluded: chain Z residue 1189 PHE Chi-restraints excluded: chain Z residue 1205 THR Chi-restraints excluded: chain Z residue 1262 LYS Chi-restraints excluded: chain Z residue 1280 LEU Chi-restraints excluded: chain Z residue 1594 THR Chi-restraints excluded: chain Z residue 1948 VAL Chi-restraints excluded: chain Z residue 2162 MET Chi-restraints excluded: chain Z residue 2299 MET Chi-restraints excluded: chain Z residue 2500 LEU Chi-restraints excluded: chain Z residue 2629 SER Chi-restraints excluded: chain Z residue 2631 ASN Chi-restraints excluded: chain Z residue 2686 THR Chi-restraints excluded: chain Z residue 2923 LEU Chi-restraints excluded: chain Z residue 2946 VAL Chi-restraints excluded: chain Z residue 3028 MET Chi-restraints excluded: chain Z residue 3307 TYR Chi-restraints excluded: chain Z residue 3360 LEU Chi-restraints excluded: chain Z residue 3410 VAL Chi-restraints excluded: chain Z residue 3417 GLU Chi-restraints excluded: chain Z residue 3441 ILE Chi-restraints excluded: chain Z residue 3521 PHE Chi-restraints excluded: chain Z residue 3645 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 383 ILE Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 404 LEU Chi-restraints excluded: chain R residue 408 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain P residue 539 THR Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 594 ILE Chi-restraints excluded: chain E residue 563 LEU Chi-restraints excluded: chain E residue 802 LEU Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain S residue 312 THR Chi-restraints excluded: chain S residue 329 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 126 optimal weight: 0.3980 chunk 479 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 367 optimal weight: 0.5980 chunk 338 optimal weight: 0.9980 chunk 87 optimal weight: 0.0570 chunk 102 optimal weight: 2.9990 chunk 445 optimal weight: 0.2980 chunk 210 optimal weight: 10.0000 chunk 412 optimal weight: 5.9990 chunk 466 optimal weight: 0.0980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1328 HIS Z1808 ASN Z1992 HIS ** Z2174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z3459 ASN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.176747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127225 restraints weight = 63553.640| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.05 r_work: 0.3157 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 44238 Z= 0.104 Angle : 0.529 13.847 59899 Z= 0.264 Chirality : 0.040 0.248 6724 Planarity : 0.003 0.051 7622 Dihedral : 4.605 75.641 5780 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.09 % Allowed : 14.38 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.80 (0.12), residues: 5252 helix: 1.44 (0.10), residues: 3130 sheet: 0.43 (0.36), residues: 211 loop : -0.97 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z1412 TYR 0.031 0.001 TYR Z 489 PHE 0.033 0.001 PHE Z2172 TRP 0.019 0.001 TRP A 356 HIS 0.016 0.001 HIS Z1328 Details of bonding type rmsd covalent geometry : bond 0.00226 (44238) covalent geometry : angle 0.52886 (59899) hydrogen bonds : bond 0.03452 ( 2188) hydrogen bonds : angle 3.83035 ( 6384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 323 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 218 MET cc_start: 0.3403 (mmp) cc_final: 0.2840 (mmt) REVERT: Z 392 TYR cc_start: 0.7381 (m-10) cc_final: 0.7176 (m-10) REVERT: Z 593 PHE cc_start: 0.7924 (m-10) cc_final: 0.7583 (m-10) REVERT: Z 688 PHE cc_start: 0.7822 (t80) cc_final: 0.7509 (t80) REVERT: Z 712 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7704 (mmm-85) REVERT: Z 716 ASP cc_start: 0.7537 (t0) cc_final: 0.6186 (p0) REVERT: Z 793 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8391 (mt) REVERT: Z 918 GLU cc_start: 0.8604 (tp30) cc_final: 0.8263 (tp30) REVERT: Z 1063 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7676 (pp) REVERT: Z 1139 MET cc_start: 0.8416 (mtm) cc_final: 0.7933 (mtt) REVERT: Z 1280 LEU cc_start: 0.5618 (OUTLIER) cc_final: 0.5103 (pp) REVERT: Z 1408 LEU cc_start: 0.7585 (mt) cc_final: 0.7218 (mt) REVERT: Z 1473 LEU cc_start: 0.4771 (OUTLIER) cc_final: 0.4432 (pp) REVERT: Z 1547 MET cc_start: 0.6957 (tpp) cc_final: 0.6409 (tpp) REVERT: Z 1647 PHE cc_start: 0.6291 (m-10) cc_final: 0.5765 (m-80) REVERT: Z 1673 PHE cc_start: 0.7227 (t80) cc_final: 0.6884 (t80) REVERT: Z 1716 LEU cc_start: 0.7611 (pp) cc_final: 0.6995 (tt) REVERT: Z 2342 HIS cc_start: 0.7299 (m90) cc_final: 0.6833 (m90) REVERT: Z 2581 ARG cc_start: 0.8641 (tpt90) cc_final: 0.7903 (mmm160) REVERT: Z 2652 THR cc_start: 0.8310 (p) cc_final: 0.7910 (t) REVERT: Z 3177 ASP cc_start: 0.7687 (t70) cc_final: 0.7172 (t0) REVERT: Z 3307 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.6399 (t80) REVERT: Z 3417 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8497 (mt-10) REVERT: Z 3485 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8911 (mt) REVERT: Z 3521 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7017 (p90) REVERT: R 404 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8677 (mp) REVERT: R 482 ARG cc_start: 0.7136 (ptp-170) cc_final: 0.6759 (ttp-170) REVERT: A 73 HIS cc_start: 0.6925 (m-70) cc_final: 0.6621 (m-70) REVERT: A 283 MET cc_start: 0.8944 (mmp) cc_final: 0.8551 (mmp) REVERT: P 504 ASP cc_start: 0.8234 (t0) cc_final: 0.7994 (t70) REVERT: P 594 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8488 (mm) REVERT: E 285 LEU cc_start: 0.8616 (tt) cc_final: 0.8251 (mp) REVERT: E 369 MET cc_start: 0.9218 (tpp) cc_final: 0.8977 (tpt) REVERT: E 726 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8226 (mm-30) REVERT: E 734 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6574 (mm110) REVERT: S 50 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8051 (pp) REVERT: S 69 MET cc_start: 0.2648 (mpp) cc_final: 0.1936 (mpp) REVERT: S 188 ASP cc_start: 0.8364 (p0) cc_final: 0.7943 (p0) REVERT: S 327 MET cc_start: 0.8533 (mmm) cc_final: 0.8108 (mmp) outliers start: 53 outliers final: 34 residues processed: 365 average time/residue: 0.2341 time to fit residues: 145.2859 Evaluate side-chains 358 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 312 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 376 LEU Chi-restraints excluded: chain Z residue 793 LEU Chi-restraints excluded: chain Z residue 908 LEU Chi-restraints excluded: chain Z residue 952 LEU Chi-restraints excluded: chain Z residue 1063 LEU Chi-restraints excluded: chain Z residue 1066 THR Chi-restraints excluded: chain Z residue 1131 ILE Chi-restraints excluded: chain Z residue 1189 PHE Chi-restraints excluded: chain Z residue 1205 THR Chi-restraints excluded: chain Z residue 1262 LYS Chi-restraints excluded: chain Z residue 1280 LEU Chi-restraints excluded: chain Z residue 1328 HIS Chi-restraints excluded: chain Z residue 1473 LEU Chi-restraints excluded: chain Z residue 1594 THR Chi-restraints excluded: chain Z residue 1948 VAL Chi-restraints excluded: chain Z residue 2162 MET Chi-restraints excluded: chain Z residue 2299 MET Chi-restraints excluded: chain Z residue 2500 LEU Chi-restraints excluded: chain Z residue 2629 SER Chi-restraints excluded: chain Z residue 2686 THR Chi-restraints excluded: chain Z residue 2923 LEU Chi-restraints excluded: chain Z residue 2946 VAL Chi-restraints excluded: chain Z residue 3028 MET Chi-restraints excluded: chain Z residue 3307 TYR Chi-restraints excluded: chain Z residue 3410 VAL Chi-restraints excluded: chain Z residue 3417 GLU Chi-restraints excluded: chain Z residue 3441 ILE Chi-restraints excluded: chain Z residue 3447 ILE Chi-restraints excluded: chain Z residue 3485 ILE Chi-restraints excluded: chain Z residue 3521 PHE Chi-restraints excluded: chain Z residue 3645 LEU Chi-restraints excluded: chain R residue 382 LEU Chi-restraints excluded: chain R residue 383 ILE Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 404 LEU Chi-restraints excluded: chain R residue 408 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain P residue 539 THR Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 594 ILE Chi-restraints excluded: chain E residue 734 GLN Chi-restraints excluded: chain E residue 802 LEU Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 199 optimal weight: 5.9990 chunk 333 optimal weight: 1.9990 chunk 459 optimal weight: 4.9990 chunk 373 optimal weight: 0.4980 chunk 317 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 385 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 455 optimal weight: 0.9980 chunk 175 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 935 GLN ** Z1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1328 HIS ** Z2174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z3459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.174814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.135473 restraints weight = 62787.003| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.13 r_work: 0.3229 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 44238 Z= 0.150 Angle : 0.561 20.673 59899 Z= 0.279 Chirality : 0.041 0.204 6724 Planarity : 0.004 0.076 7622 Dihedral : 4.693 73.204 5780 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.28 % Allowed : 14.57 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.73 (0.12), residues: 5252 helix: 1.38 (0.10), residues: 3128 sheet: 0.36 (0.36), residues: 211 loop : -0.99 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z1412 TYR 0.033 0.001 TYR Z 489 PHE 0.031 0.001 PHE Z3464 TRP 0.019 0.001 TRP A 356 HIS 0.028 0.001 HIS Z1328 Details of bonding type rmsd covalent geometry : bond 0.00359 (44238) covalent geometry : angle 0.56125 (59899) hydrogen bonds : bond 0.03780 ( 2188) hydrogen bonds : angle 3.88456 ( 6384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 314 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 218 MET cc_start: 0.3219 (mmp) cc_final: 0.2848 (mmt) REVERT: Z 392 TYR cc_start: 0.7527 (m-10) cc_final: 0.7283 (m-10) REVERT: Z 593 PHE cc_start: 0.7642 (m-10) cc_final: 0.7183 (m-10) REVERT: Z 793 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8630 (mt) REVERT: Z 845 MET cc_start: 0.8731 (mmm) cc_final: 0.8149 (mtm) REVERT: Z 918 GLU cc_start: 0.8304 (tp30) cc_final: 0.7994 (tp30) REVERT: Z 1139 MET cc_start: 0.8346 (mtm) cc_final: 0.8138 (mtm) REVERT: Z 1280 LEU cc_start: 0.5406 (OUTLIER) cc_final: 0.4940 (pp) REVERT: Z 1408 LEU cc_start: 0.8007 (mt) cc_final: 0.7765 (mt) REVERT: Z 1473 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.4891 (pp) REVERT: Z 1547 MET cc_start: 0.6880 (tpp) cc_final: 0.6382 (tpp) REVERT: Z 1647 PHE cc_start: 0.6004 (m-10) cc_final: 0.5621 (m-80) REVERT: Z 1673 PHE cc_start: 0.7421 (t80) cc_final: 0.7051 (t80) REVERT: Z 1716 LEU cc_start: 0.7419 (pp) cc_final: 0.6865 (tt) REVERT: Z 2342 HIS cc_start: 0.7223 (m90) cc_final: 0.6825 (m90) REVERT: Z 2360 ILE cc_start: 0.8475 (mm) cc_final: 0.8218 (mm) REVERT: Z 2581 ARG cc_start: 0.8288 (tpt90) cc_final: 0.7521 (mmm160) REVERT: Z 2652 THR cc_start: 0.8171 (p) cc_final: 0.7801 (t) REVERT: Z 3177 ASP cc_start: 0.7425 (t70) cc_final: 0.6922 (t0) REVERT: Z 3307 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.6338 (t80) REVERT: Z 3417 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: Z 3485 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8937 (mt) REVERT: Z 3521 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.6993 (p90) REVERT: R 404 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8694 (mp) REVERT: R 482 ARG cc_start: 0.6813 (ptp-170) cc_final: 0.6480 (ttp-170) REVERT: A 283 MET cc_start: 0.8840 (mmp) cc_final: 0.8411 (mmt) REVERT: P 504 ASP cc_start: 0.8175 (t0) cc_final: 0.7939 (t70) REVERT: P 543 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7557 (p90) REVERT: P 594 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8509 (mm) REVERT: E 285 LEU cc_start: 0.8595 (tt) cc_final: 0.8221 (mp) REVERT: S 50 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8239 (pp) REVERT: S 69 MET cc_start: 0.2462 (mpp) cc_final: 0.1632 (mpp) REVERT: S 188 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7746 (p0) REVERT: S 310 ASP cc_start: 0.7585 (t0) cc_final: 0.7336 (t0) REVERT: S 327 MET cc_start: 0.8513 (mmm) cc_final: 0.8058 (mmp) outliers start: 62 outliers final: 43 residues processed: 359 average time/residue: 0.2369 time to fit residues: 144.0305 Evaluate side-chains 363 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 308 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 376 LEU Chi-restraints excluded: chain Z residue 586 LEU Chi-restraints excluded: chain Z residue 793 LEU Chi-restraints excluded: chain Z residue 908 LEU Chi-restraints excluded: chain Z residue 952 LEU Chi-restraints excluded: chain Z residue 1066 THR Chi-restraints excluded: chain Z residue 1128 THR Chi-restraints excluded: chain Z residue 1131 ILE Chi-restraints excluded: chain Z residue 1160 VAL Chi-restraints excluded: chain Z residue 1189 PHE Chi-restraints excluded: chain Z residue 1205 THR Chi-restraints excluded: chain Z residue 1262 LYS Chi-restraints excluded: chain Z residue 1280 LEU Chi-restraints excluded: chain Z residue 1328 HIS Chi-restraints excluded: chain Z residue 1473 LEU Chi-restraints excluded: chain Z residue 1500 LEU Chi-restraints excluded: chain Z residue 1948 VAL Chi-restraints excluded: chain Z residue 2162 MET Chi-restraints excluded: chain Z residue 2299 MET Chi-restraints excluded: chain Z residue 2500 LEU Chi-restraints excluded: chain Z residue 2629 SER Chi-restraints excluded: chain Z residue 2631 ASN Chi-restraints excluded: chain Z residue 2686 THR Chi-restraints excluded: chain Z residue 2923 LEU Chi-restraints excluded: chain Z residue 2946 VAL Chi-restraints excluded: chain Z residue 3028 MET Chi-restraints excluded: chain Z residue 3307 TYR Chi-restraints excluded: chain Z residue 3360 LEU Chi-restraints excluded: chain Z residue 3410 VAL Chi-restraints excluded: chain Z residue 3417 GLU Chi-restraints excluded: chain Z residue 3441 ILE Chi-restraints excluded: chain Z residue 3447 ILE Chi-restraints excluded: chain Z residue 3485 ILE Chi-restraints excluded: chain Z residue 3521 PHE Chi-restraints excluded: chain Z residue 3645 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 382 LEU Chi-restraints excluded: chain R residue 383 ILE Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 404 LEU Chi-restraints excluded: chain R residue 408 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain P residue 539 THR Chi-restraints excluded: chain P residue 543 PHE Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 594 ILE Chi-restraints excluded: chain P residue 626 ASN Chi-restraints excluded: chain E residue 563 LEU Chi-restraints excluded: chain E residue 802 LEU Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain S residue 188 ASP Chi-restraints excluded: chain S residue 312 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 341 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 168 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 252 optimal weight: 0.3980 chunk 150 optimal weight: 5.9990 chunk 468 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 487 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z1124 ASN ** Z1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1328 HIS Z2025 HIS ** Z2174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z3459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.173266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.135619 restraints weight = 62861.391| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.04 r_work: 0.3207 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 44238 Z= 0.213 Angle : 0.608 19.089 59899 Z= 0.306 Chirality : 0.044 0.190 6724 Planarity : 0.004 0.067 7622 Dihedral : 4.882 72.119 5780 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.26 % Allowed : 14.65 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.54 (0.12), residues: 5252 helix: 1.24 (0.09), residues: 3127 sheet: 0.05 (0.36), residues: 220 loop : -1.05 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z1412 TYR 0.036 0.002 TYR Z 489 PHE 0.041 0.002 PHE Z3464 TRP 0.021 0.002 TRP A 356 HIS 0.039 0.001 HIS Z1328 Details of bonding type rmsd covalent geometry : bond 0.00518 (44238) covalent geometry : angle 0.60816 (59899) hydrogen bonds : bond 0.04192 ( 2188) hydrogen bonds : angle 4.00864 ( 6384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10504 Ramachandran restraints generated. 5252 Oldfield, 0 Emsley, 5252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 314 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 218 MET cc_start: 0.3259 (mmp) cc_final: 0.2908 (mmt) REVERT: Z 645 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8342 (mm) REVERT: Z 688 PHE cc_start: 0.7303 (t80) cc_final: 0.7038 (t80) REVERT: Z 793 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8713 (mt) REVERT: Z 845 MET cc_start: 0.8759 (mmm) cc_final: 0.8211 (mtm) REVERT: Z 918 GLU cc_start: 0.8317 (tp30) cc_final: 0.8040 (tp30) REVERT: Z 1041 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: Z 1063 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7609 (pp) REVERT: Z 1100 MET cc_start: 0.8443 (mmm) cc_final: 0.8236 (tpp) REVERT: Z 1280 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5363 (pp) REVERT: Z 1408 LEU cc_start: 0.8041 (mt) cc_final: 0.7794 (mt) REVERT: Z 1473 LEU cc_start: 0.5284 (OUTLIER) cc_final: 0.4927 (pp) REVERT: Z 1547 MET cc_start: 0.6758 (tpp) cc_final: 0.6302 (tpp) REVERT: Z 1647 PHE cc_start: 0.5982 (m-10) cc_final: 0.5647 (m-80) REVERT: Z 1673 PHE cc_start: 0.7538 (t80) cc_final: 0.7196 (t80) REVERT: Z 1716 LEU cc_start: 0.7392 (pp) cc_final: 0.6665 (tt) REVERT: Z 2341 ASP cc_start: 0.7594 (m-30) cc_final: 0.7294 (t0) REVERT: Z 2342 HIS cc_start: 0.7188 (m90) cc_final: 0.6764 (m90) REVERT: Z 2652 THR cc_start: 0.8362 (p) cc_final: 0.7990 (t) REVERT: Z 3177 ASP cc_start: 0.7494 (t70) cc_final: 0.6974 (t0) REVERT: Z 3248 LEU cc_start: 0.9088 (tp) cc_final: 0.8675 (mp) REVERT: Z 3307 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.6779 (t80) REVERT: Z 3417 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: Z 3485 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9185 (mt) REVERT: R 404 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8714 (mp) REVERT: R 482 ARG cc_start: 0.6938 (ptp-170) cc_final: 0.6563 (ptm160) REVERT: A 283 MET cc_start: 0.8902 (mmp) cc_final: 0.8585 (mmt) REVERT: P 543 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7648 (p90) REVERT: P 594 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8639 (mm) REVERT: E 369 MET cc_start: 0.9101 (tpp) cc_final: 0.8823 (tpt) REVERT: S 50 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8314 (pp) REVERT: S 69 MET cc_start: 0.2528 (mpp) cc_final: 0.1668 (mpp) REVERT: S 188 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7739 (p0) REVERT: S 310 ASP cc_start: 0.7422 (t0) cc_final: 0.7218 (t0) outliers start: 61 outliers final: 42 residues processed: 362 average time/residue: 0.2096 time to fit residues: 130.1398 Evaluate side-chains 356 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 376 LEU Chi-restraints excluded: chain Z residue 645 LEU Chi-restraints excluded: chain Z residue 793 LEU Chi-restraints excluded: chain Z residue 908 LEU Chi-restraints excluded: chain Z residue 952 LEU Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1041 GLU Chi-restraints excluded: chain Z residue 1063 LEU Chi-restraints excluded: chain Z residue 1066 THR Chi-restraints excluded: chain Z residue 1128 THR Chi-restraints excluded: chain Z residue 1131 ILE Chi-restraints excluded: chain Z residue 1160 VAL Chi-restraints excluded: chain Z residue 1189 PHE Chi-restraints excluded: chain Z residue 1205 THR Chi-restraints excluded: chain Z residue 1262 LYS Chi-restraints excluded: chain Z residue 1280 LEU Chi-restraints excluded: chain Z residue 1349 MET Chi-restraints excluded: chain Z residue 1473 LEU Chi-restraints excluded: chain Z residue 1500 LEU Chi-restraints excluded: chain Z residue 1948 VAL Chi-restraints excluded: chain Z residue 2162 MET Chi-restraints excluded: chain Z residue 2299 MET Chi-restraints excluded: chain Z residue 2500 LEU Chi-restraints excluded: chain Z residue 2629 SER Chi-restraints excluded: chain Z residue 2686 THR Chi-restraints excluded: chain Z residue 2923 LEU Chi-restraints excluded: chain Z residue 2946 VAL Chi-restraints excluded: chain Z residue 3028 MET Chi-restraints excluded: chain Z residue 3307 TYR Chi-restraints excluded: chain Z residue 3360 LEU Chi-restraints excluded: chain Z residue 3400 VAL Chi-restraints excluded: chain Z residue 3410 VAL Chi-restraints excluded: chain Z residue 3417 GLU Chi-restraints excluded: chain Z residue 3447 ILE Chi-restraints excluded: chain Z residue 3485 ILE Chi-restraints excluded: chain Z residue 3521 PHE Chi-restraints excluded: chain Z residue 3645 LEU Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 382 LEU Chi-restraints excluded: chain R residue 383 ILE Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 404 LEU Chi-restraints excluded: chain R residue 408 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain P residue 539 THR Chi-restraints excluded: chain P residue 543 PHE Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 594 ILE Chi-restraints excluded: chain E residue 563 LEU Chi-restraints excluded: chain E residue 802 LEU Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain S residue 188 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 426 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 509 optimal weight: 0.6980 chunk 205 optimal weight: 10.0000 chunk 82 optimal weight: 0.0570 chunk 343 optimal weight: 0.9990 chunk 317 optimal weight: 0.9990 chunk 527 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 399 optimal weight: 0.0070 chunk 237 optimal weight: 0.9980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z1124 ASN ** Z1234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1328 HIS ** Z2174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z3459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.175277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136797 restraints weight = 63148.368| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.11 r_work: 0.3250 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44238 Z= 0.115 Angle : 0.545 18.701 59899 Z= 0.272 Chirality : 0.040 0.208 6724 Planarity : 0.004 0.065 7622 Dihedral : 4.713 74.283 5780 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.26 % Allowed : 14.71 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 aren not related in a simple way. whole: 0.72 (0.12), residues: 5252 helix: 1.39 (0.10), residues: 3122 sheet: 0.30 (0.36), residues: 211 loop : -1.02 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z1412 TYR 0.031 0.001 TYR Z2316 PHE 0.031 0.001 PHE Z2172 TRP 0.020 0.001 TRP A 356 HIS 0.020 0.001 HIS Z1328 Details of bonding type rmsd covalent geometry : bond 0.00260 (44238) covalent geometry : angle 0.54453 (59899) hydrogen bonds : bond 0.03579 ( 2188) hydrogen bonds : angle 3.87287 ( 6384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13473.91 seconds wall clock time: 230 minutes 53.38 seconds (13853.38 seconds total)