Starting phenix.real_space_refine on Sun Aug 9 00:34:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k60_36914/08_2026/8k60_36914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k60_36914/08_2026/8k60_36914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k60_36914/08_2026/8k60_36914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k60_36914/08_2026/8k60_36914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k60_36914/08_2026/8k60_36914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k60_36914/08_2026/8k60_36914.map" } resolution = 3.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 113 5.49 5 Mg 1 5.21 5 S 98 5.16 5 C 19478 2.51 5 N 5666 2.21 5 O 6301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 209 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31659 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1785 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 219} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 9812 Classifications: {'peptide': 1259} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 594 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2465 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 301} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1148 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "H" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1180 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "I" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1904 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Chain: "J" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1896 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain: "K" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12666 SG CYS D 60 68.579 117.305 60.887 1.00 51.48 S ATOM 12684 SG CYS D 62 69.288 120.672 59.930 1.00 52.09 S ATOM 12793 SG CYS D 75 67.071 118.641 57.198 1.00 57.28 S ATOM 12819 SG CYS D 78 71.063 117.677 58.227 1.00 53.48 S ATOM 19748 SG CYS D 962 72.221 52.024 57.014 1.00 45.14 S ATOM 19796 SG CYS D 969 68.977 50.616 59.275 1.00 40.88 S ATOM 19815 SG CYS D 972 71.840 48.685 58.353 1.00 39.87 S Time building chain proxies: 6.26, per 1000 atoms: 0.20 Number of scatterers: 31659 At special positions: 0 Unit cell: (173.8, 171.6, 152.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 98 16.00 P 113 15.00 Mg 1 11.99 O 6301 8.00 N 5666 7.00 C 19478 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: 2.77 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " Number of angles added : 6 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6964 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 45 sheets defined 47.8% alpha, 12.7% beta 27 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.984A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.733A pdb=" N GLU A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.069A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.578A pdb=" N LEU B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 203 through 221 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.914A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 73 through 81 removed outlier: 3.580A pdb=" N ILE C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.556A pdb=" N LYS C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.713A pdb=" N GLU C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.600A pdb=" N ARG C 247 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 288 removed outlier: 3.601A pdb=" N LEU C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 309 Processing helix chain 'C' and resid 320 through 336 removed outlier: 3.531A pdb=" N ILE C 325 " --> pdb=" O THR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 391 removed outlier: 3.549A pdb=" N VAL C 386 " --> pdb=" O MET C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 removed outlier: 4.277A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 removed outlier: 3.885A pdb=" N PHE C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 439 removed outlier: 3.515A pdb=" N LYS C 438 " --> pdb=" O GLY C 434 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.891A pdb=" N ARG C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.637A pdb=" N ARG C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.711A pdb=" N GLU C 553 " --> pdb=" O ARG C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 579 Processing helix chain 'C' and resid 582 through 586 Processing helix chain 'C' and resid 587 through 598 removed outlier: 3.532A pdb=" N MET C 593 " --> pdb=" O ASN C 589 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 624 removed outlier: 4.621A pdb=" N ARG C 619 " --> pdb=" O GLY C 615 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 801 through 812 removed outlier: 3.551A pdb=" N GLY C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 removed outlier: 4.548A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 928 Processing helix chain 'C' and resid 937 through 947 removed outlier: 4.082A pdb=" N ARG C 942 " --> pdb=" O GLU C 938 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 943 " --> pdb=" O TRP C 939 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL C 945 " --> pdb=" O GLN C 941 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE C 946 " --> pdb=" O ARG C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 976 removed outlier: 3.732A pdb=" N HIS C 976 " --> pdb=" O GLY C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1026 removed outlier: 3.599A pdb=" N LYS C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1065 removed outlier: 3.536A pdb=" N TRP C1059 " --> pdb=" O GLU C1055 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C1060 " --> pdb=" O MET C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1075 removed outlier: 3.591A pdb=" N LEU C1070 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1094 removed outlier: 4.077A pdb=" N VAL C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C1086 " --> pdb=" O THR C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1115 removed outlier: 3.663A pdb=" N LYS C1107 " --> pdb=" O PRO C1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.633A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 188 removed outlier: 3.943A pdb=" N ILE D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 227 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 283 Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.000A pdb=" N THR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.835A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 360 removed outlier: 4.203A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.700A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.688A pdb=" N LYS D 407 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.734A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 492 removed outlier: 4.217A pdb=" N TYR D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP D 485 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 580 through 589 Processing helix chain 'D' and resid 606 through 616 Processing helix chain 'D' and resid 636 through 640 removed outlier: 3.561A pdb=" N GLU D 640 " --> pdb=" O ARG D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 672 removed outlier: 3.561A pdb=" N GLU D 670 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU D 672 " --> pdb=" O PHE D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 723 removed outlier: 3.627A pdb=" N ASP D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 721 " --> pdb=" O PHE D 717 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 757 removed outlier: 3.704A pdb=" N LYS D 750 " --> pdb=" O GLY D 746 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL D 751 " --> pdb=" O GLN D 747 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 removed outlier: 3.521A pdb=" N ASN D 778 " --> pdb=" O THR D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 800 removed outlier: 3.836A pdb=" N VAL D 798 " --> pdb=" O VAL D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 814 removed outlier: 3.592A pdb=" N ILE D 812 " --> pdb=" O GLN D 808 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 813 " --> pdb=" O MET D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 877 removed outlier: 3.911A pdb=" N HIS D 849 " --> pdb=" O PHE D 845 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 874 " --> pdb=" O ARG D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 915 Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 958 through 962 removed outlier: 3.557A pdb=" N CYS D 962 " --> pdb=" O ILE D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 974 removed outlier: 3.518A pdb=" N TYR D 973 " --> pdb=" O CYS D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 999 removed outlier: 3.509A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1005 removed outlier: 4.475A pdb=" N THR D1005 " --> pdb=" O GLY D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1107 removed outlier: 3.604A pdb=" N VAL D1104 " --> pdb=" O ASN D1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1129 removed outlier: 3.834A pdb=" N VAL D1124 " --> pdb=" O GLU D1120 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D1125 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN D1128 " --> pdb=" O VAL D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 3.899A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1180 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1208 Processing helix chain 'D' and resid 1213 through 1223 Processing helix chain 'D' and resid 1232 through 1237 removed outlier: 3.655A pdb=" N ILE D1237 " --> pdb=" O GLU D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1243 through 1246 removed outlier: 3.882A pdb=" N GLY D1246 " --> pdb=" O ALA D1243 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1243 through 1246' Processing helix chain 'D' and resid 1247 through 1252 Processing helix chain 'D' and resid 1258 through 1265 removed outlier: 3.565A pdb=" N MET D1265 " --> pdb=" O ALA D1261 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 24 removed outlier: 3.697A pdb=" N ALA E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 45 removed outlier: 3.621A pdb=" N VAL E 30 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'F' and resid 198 through 208 removed outlier: 4.308A pdb=" N ALA F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA F 208 " --> pdb=" O GLN F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 223 removed outlier: 3.643A pdb=" N GLY F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 252 Processing helix chain 'F' and resid 257 through 282 Processing helix chain 'F' and resid 282 through 292 removed outlier: 3.745A pdb=" N VAL F 286 " --> pdb=" O ASN F 282 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL F 287 " --> pdb=" O LEU F 283 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG F 292 " --> pdb=" O SER F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 317 removed outlier: 3.516A pdb=" N GLY F 310 " --> pdb=" O GLU F 306 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU F 316 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS F 317 " --> pdb=" O ARG F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 346 removed outlier: 3.798A pdb=" N TYR F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP F 333 " --> pdb=" O TYR F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 374 Processing helix chain 'F' and resid 378 through 387 removed outlier: 3.608A pdb=" N GLU F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 429 through 450 removed outlier: 3.553A pdb=" N THR F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU F 450 " --> pdb=" O VAL F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 463 removed outlier: 3.509A pdb=" N VAL F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 479 removed outlier: 3.776A pdb=" N GLY F 476 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS F 477 " --> pdb=" O ASP F 473 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL F 478 " --> pdb=" O GLU F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 499 Processing helix chain 'F' and resid 503 through 510 removed outlier: 4.432A pdb=" N ASP F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR F 509 " --> pdb=" O VAL F 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 58 Processing helix chain 'I' and resid 65 through 75 Processing helix chain 'I' and resid 81 through 97 removed outlier: 3.542A pdb=" N VAL I 96 " --> pdb=" O ARG I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 137 Processing helix chain 'I' and resid 139 through 152 Processing helix chain 'I' and resid 164 through 192 Processing helix chain 'I' and resid 194 through 209 removed outlier: 3.664A pdb=" N ALA I 198 " --> pdb=" O CYS I 194 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU I 201 " --> pdb=" O GLU I 197 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA I 204 " --> pdb=" O SER I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 226 removed outlier: 3.660A pdb=" N ARG I 216 " --> pdb=" O ARG I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 247 Processing helix chain 'I' and resid 252 through 264 Processing helix chain 'I' and resid 266 through 270 removed outlier: 3.528A pdb=" N LEU I 269 " --> pdb=" O ASP I 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 58 Processing helix chain 'J' and resid 66 through 75 Processing helix chain 'J' and resid 81 through 97 Processing helix chain 'J' and resid 119 through 137 Processing helix chain 'J' and resid 139 through 153 removed outlier: 3.560A pdb=" N LEU J 153 " --> pdb=" O ARG J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 193 removed outlier: 3.542A pdb=" N MET J 188 " --> pdb=" O THR J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 209 removed outlier: 4.033A pdb=" N SER J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA J 204 " --> pdb=" O SER J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 226 removed outlier: 3.835A pdb=" N ARG J 216 " --> pdb=" O ARG J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 246 removed outlier: 3.570A pdb=" N LEU J 233 " --> pdb=" O GLN J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 265 Processing helix chain 'J' and resid 266 through 270 Processing helix chain 'K' and resid 250 through 255 Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 271 through 278 Processing helix chain 'K' and resid 279 through 286 Processing helix chain 'K' and resid 290 through 304 removed outlier: 4.013A pdb=" N MET K 304 " --> pdb=" O LYS K 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 15 removed outlier: 6.382A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.782A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.730A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 13 removed outlier: 3.713A pdb=" N LEU B 192 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR B 187 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG B 182 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE B 189 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA B 180 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS B 191 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL B 178 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 99 removed outlier: 7.941A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.563A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.714A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.506A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 100 removed outlier: 6.579A pdb=" N THR C 124 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N HIS C 98 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE C 122 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE C 100 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY C 143 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C 123 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N PHE C 141 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA C 125 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR C 139 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE C 127 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SER C 137 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASN C 129 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE C 135 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 362 through 364 removed outlier: 6.218A pdb=" N SER C 165 " --> pdb=" O ASN C 442 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C 484 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.712A pdb=" N LYS C 185 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN C 220 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB8, first strand: chain 'C' and resid 491 through 492 removed outlier: 5.546A pdb=" N ASP C 513 " --> pdb=" O LYS C 504 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL C 506 " --> pdb=" O THR C 511 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR C 511 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 629 removed outlier: 6.740A pdb=" N VAL C 628 " --> pdb=" O LEU C 688 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 634 through 639 removed outlier: 6.551A pdb=" N THR C 645 " --> pdb=" O GLN C 637 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL C 639 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N TYR C 643 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC4, first strand: chain 'C' and resid 992 through 993 removed outlier: 7.200A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE C 884 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 723 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE C 722 " --> pdb=" O ILE C 902 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ILE C 901 " --> pdb=" O ASN C 704 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU C 706 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU C 903 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA C 708 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 734 through 746 removed outlier: 3.542A pdb=" N GLN C 853 " --> pdb=" O ALA C 745 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 835 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA C 860 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL C 833 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N LYS C 862 " --> pdb=" O GLY C 831 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N GLY C 831 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 831 " --> pdb=" O VAL C 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 754 through 755 removed outlier: 3.516A pdb=" N GLU C 754 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 787 through 789 removed outlier: 7.045A pdb=" N LEU C 823 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 3.640A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 7.558A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 431 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1052 through 1053 Processing sheet with id=AD2, first strand: chain 'C' and resid 1121 through 1123 Processing sheet with id=AD3, first strand: chain 'D' and resid 94 through 102 removed outlier: 7.033A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.848A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.410A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 328 through 329 removed outlier: 6.312A pdb=" N PHE D 335 " --> pdb=" O ILE F 404 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 443 through 444 removed outlier: 5.644A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 566 through 567 removed outlier: 3.829A pdb=" N ARG D 572 " --> pdb=" O LYS D 567 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 821 Processing sheet with id=AE1, first strand: chain 'D' and resid 892 through 894 Processing sheet with id=AE2, first strand: chain 'D' and resid 1038 through 1039 Processing sheet with id=AE3, first strand: chain 'D' and resid 1070 through 1073 removed outlier: 4.038A pdb=" N THR D1070 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D1061 " --> pdb=" O THR D1070 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY D1046 " --> pdb=" O VAL D1088 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP D1086 " --> pdb=" O VAL D1048 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id=AE5, first strand: chain 'D' and resid 1254 through 1256 Processing sheet with id=AE6, first strand: chain 'I' and resid 25 through 28 removed outlier: 4.676A pdb=" N ALA I 35 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 102 through 105 Processing sheet with id=AE8, first strand: chain 'J' and resid 25 through 28 removed outlier: 4.700A pdb=" N ALA J 35 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 64 through 65 1371 hydrogen bonds defined for protein. 3906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 7.25 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8450 1.33 - 1.45: 6226 1.45 - 1.58: 17328 1.58 - 1.70: 222 1.70 - 1.82: 176 Bond restraints: 32402 Sorted by residual: bond pdb=" C1' DC H 26 " pdb=" N1 DC H 26 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.91e+01 bond pdb=" C1' DT H 48 " pdb=" N1 DT H 48 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.43e+01 bond pdb=" C3' DA H 21 " pdb=" O3' DA H 21 " ideal model delta sigma weight residual 1.435 1.498 -0.063 1.30e-02 5.92e+03 2.32e+01 bond pdb=" C3' DC H 45 " pdb=" O3' DC H 45 " ideal model delta sigma weight residual 1.435 1.493 -0.058 1.30e-02 5.92e+03 2.00e+01 bond pdb=" O3' DT H 37 " pdb=" P DA H 38 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.20e-02 6.94e+03 1.94e+01 ... (remaining 32397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 42563 2.52 - 5.04: 1570 5.04 - 7.56: 166 7.56 - 10.08: 35 10.08 - 12.60: 3 Bond angle restraints: 44337 Sorted by residual: angle pdb=" O4' DT G 17 " pdb=" C4' DT G 17 " pdb=" C3' DT G 17 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.35e+01 angle pdb=" O4' DT H 48 " pdb=" C4' DT H 48 " pdb=" C3' DT H 48 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.34e+01 angle pdb=" N GLU A 24 " pdb=" CA GLU A 24 " pdb=" C GLU A 24 " ideal model delta sigma weight residual 109.81 122.41 -12.60 2.21e+00 2.05e-01 3.25e+01 angle pdb=" O4' DC H 14 " pdb=" C4' DC H 14 " pdb=" C3' DC H 14 " ideal model delta sigma weight residual 106.00 103.07 2.93 6.00e-01 2.78e+00 2.38e+01 angle pdb=" C3' DT H 23 " pdb=" O3' DT H 23 " pdb=" P DA H 24 " ideal model delta sigma weight residual 119.70 125.45 -5.75 1.20e+00 6.94e-01 2.30e+01 ... (remaining 44332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 18590 35.94 - 71.88: 921 71.88 - 107.82: 48 107.82 - 143.75: 3 143.75 - 179.69: 6 Dihedral angle restraints: 19568 sinusoidal: 8750 harmonic: 10818 Sorted by residual: dihedral pdb=" CA ASP D 748 " pdb=" C ASP D 748 " pdb=" N GLU D 749 " pdb=" CA GLU D 749 " ideal model delta harmonic sigma weight residual -180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA PRO D 577 " pdb=" C PRO D 577 " pdb=" N THR D 578 " pdb=" CA THR D 578 " ideal model delta harmonic sigma weight residual 180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLU D 682 " pdb=" C GLU D 682 " pdb=" N VAL D 683 " pdb=" CA VAL D 683 " ideal model delta harmonic sigma weight residual -180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 19565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3756 0.071 - 0.142: 1041 0.142 - 0.213: 211 0.213 - 0.284: 35 0.284 - 0.355: 7 Chirality restraints: 5050 Sorted by residual: chirality pdb=" CB VAL C 792 " pdb=" CA VAL C 792 " pdb=" CG1 VAL C 792 " pdb=" CG2 VAL C 792 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA GLU A 24 " pdb=" N GLU A 24 " pdb=" C GLU A 24 " pdb=" CB GLU A 24 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE A 193 " pdb=" CA ILE A 193 " pdb=" CG1 ILE A 193 " pdb=" CG2 ILE A 193 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 5047 not shown) Planarity restraints: 5436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 110 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.10e+01 pdb=" N PRO D 111 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO D 111 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 111 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 579 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C MET C 579 " 0.065 2.00e-02 2.50e+03 pdb=" O MET C 579 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE C 580 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 225 " 0.058 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO F 226 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO F 226 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 226 " 0.048 5.00e-02 4.00e+02 ... (remaining 5433 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4150 2.76 - 3.29: 30547 3.29 - 3.83: 51985 3.83 - 4.36: 60148 4.36 - 4.90: 102452 Nonbonded interactions: 249282 Sorted by model distance: nonbonded pdb=" OG SER D1202 " pdb=" OE1 GLU D1233 " model vdw 2.223 3.040 nonbonded pdb=" N2 DG G 16 " pdb=" O2 DC H 41 " model vdw 2.257 3.120 nonbonded pdb=" OG1 THR F 389 " pdb=" OE1 GLU F 391 " model vdw 2.257 3.040 nonbonded pdb=" O LEU F 285 " pdb=" OG SER F 288 " model vdw 2.268 3.040 nonbonded pdb=" OG SER D1153 " pdb=" O LEU D1158 " model vdw 2.277 3.040 ... (remaining 249277 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 152 or (resid 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 227)) selection = (chain 'B' and resid 2 through 227) } ncs_group { reference = (chain 'I' and resid 23 through 271) selection = chain 'J' } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.420 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.123 32409 Z= 0.449 Angle : 1.120 14.799 44343 Z= 0.676 Chirality : 0.069 0.355 5050 Planarity : 0.009 0.114 5436 Dihedral : 18.954 179.693 12604 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.02 % Allowed : 13.32 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 3764 helix: 0.66 (0.12), residues: 1542 sheet: -1.10 (0.26), residues: 361 loop : -0.68 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 113 TYR 0.031 0.003 TYR D 106 PHE 0.035 0.004 PHE C 709 TRP 0.017 0.003 TRP D 773 HIS 0.018 0.003 HIS D1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00926 / 0.45 (32402) covalent geometry : angle 1.11320 / 0.68 (44337) hydrogen bonds : bond 0.26644 / 18.00 ( 1432) hydrogen bonds : angle 7.22214 / 5.00 ( 4028) metal coordination : bond 0.10787 / 5.17 ( 7) metal coordination : angle 10.51659 / 5.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 571 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.7136 (pt0) cc_final: 0.6913 (pt0) REVERT: B 13 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8370 (m) REVERT: C 281 GLN cc_start: 0.7439 (tp40) cc_final: 0.6963 (mt0) REVERT: C 359 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8943 (m-10) REVERT: C 366 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.6864 (p0) REVERT: C 642 ASP cc_start: 0.7652 (t70) cc_final: 0.7262 (t0) REVERT: C 725 GLN cc_start: 0.8318 (tt0) cc_final: 0.7913 (tt0) REVERT: C 781 GLU cc_start: 0.8214 (tm-30) cc_final: 0.8002 (tm-30) REVERT: C 1056 MET cc_start: 0.8711 (mtt) cc_final: 0.8332 (mtp) REVERT: C 1104 GLU cc_start: 0.7750 (tp30) cc_final: 0.7529 (tp30) REVERT: D 8 ASP cc_start: 0.7923 (t0) cc_final: 0.7631 (t0) REVERT: D 581 MET cc_start: 0.8692 (mtm) cc_final: 0.8472 (mtt) REVERT: D 971 MET cc_start: 0.7303 (mmt) cc_final: 0.6884 (mmt) REVERT: D 1210 GLN cc_start: 0.8017 (mt0) cc_final: 0.7741 (pt0) REVERT: E 41 ASN cc_start: 0.8724 (t0) cc_final: 0.8508 (t0) REVERT: F 241 GLU cc_start: 0.6732 (mp0) cc_final: 0.6482 (mp0) REVERT: F 296 ARG cc_start: 0.5840 (mmm-85) cc_final: 0.5632 (tpp80) REVERT: F 404 ILE cc_start: 0.8591 (pt) cc_final: 0.8355 (pt) REVERT: F 508 ASP cc_start: 0.7237 (p0) cc_final: 0.6779 (p0) REVERT: I 62 ARG cc_start: 0.6970 (mtm180) cc_final: 0.6726 (mtp180) REVERT: I 209 HIS cc_start: 0.8382 (m-70) cc_final: 0.7799 (m90) REVERT: I 241 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7225 (ttp-110) REVERT: I 261 ARG cc_start: 0.6567 (mtp180) cc_final: 0.6303 (ttm170) REVERT: J 236 TYR cc_start: 0.4499 (t80) cc_final: 0.4235 (t80) outliers start: 32 outliers final: 14 residues processed: 599 average time/residue: 0.2300 time to fit residues: 205.9498 Evaluate side-chains 378 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 361 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1126 ASP Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 443 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN A 226 ASN B 5 GLN B 226 ASN C 157 ASN C 235 GLN C 258 GLN C 358 HIS C 509 GLN C 600 GLN C 686 GLN C 729 GLN C 852 ASN C 861 GLN D 232 GLN D 307 ASN D 396 ASN D 440 GLN D 494 HIS D 669 ASN D 799 ASN D 935 ASN ** D1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 ASN F 282 ASN F 368 GLN F 371 GLN I 170 GLN J 192 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.145610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106863 restraints weight = 55162.472| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.36 r_work: 0.3188 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32409 Z= 0.182 Angle : 0.689 10.928 44343 Z= 0.374 Chirality : 0.046 0.351 5050 Planarity : 0.006 0.145 5436 Dihedral : 17.790 179.878 5403 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.46 % Allowed : 18.34 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 3764 helix: 1.19 (0.12), residues: 1592 sheet: -0.66 (0.27), residues: 347 loop : -0.55 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1111 TYR 0.024 0.002 TYR E 32 PHE 0.017 0.002 PHE D 226 TRP 0.014 0.002 TRP D 718 HIS 0.006 0.001 HIS C 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (32402) covalent geometry : angle 0.68728 / 0.37 (44337) hydrogen bonds : bond 0.07232 / 4.81 ( 1432) hydrogen bonds : angle 5.06443 / 3.51 ( 4028) metal coordination : bond 0.00670 / 0.31 ( 7) metal coordination : angle 3.72136 / 1.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 406 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.7977 (pt0) cc_final: 0.7732 (pt0) REVERT: A 213 LYS cc_start: 0.8585 (tptp) cc_final: 0.8306 (ttpt) REVERT: B 82 GLN cc_start: 0.8730 (tp40) cc_final: 0.8254 (tt0) REVERT: C 642 ASP cc_start: 0.8182 (t70) cc_final: 0.7767 (t0) REVERT: C 1118 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8457 (mt) REVERT: D 126 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: D 389 ARG cc_start: 0.7717 (mtp85) cc_final: 0.7434 (mtt90) REVERT: D 691 ILE cc_start: 0.8839 (pt) cc_final: 0.8620 (mt) REVERT: D 919 MET cc_start: 0.7027 (ptm) cc_final: 0.6633 (ptp) REVERT: D 971 MET cc_start: 0.8236 (mmt) cc_final: 0.7911 (mmt) REVERT: E 41 ASN cc_start: 0.8764 (t0) cc_final: 0.8468 (t0) REVERT: I 62 ARG cc_start: 0.7176 (mtm180) cc_final: 0.6880 (mtp180) REVERT: I 209 HIS cc_start: 0.8128 (m-70) cc_final: 0.7794 (m90) REVERT: I 241 ARG cc_start: 0.7766 (ttp80) cc_final: 0.7236 (ttp-110) REVERT: K 300 LYS cc_start: 0.7883 (mmtt) cc_final: 0.7372 (tptp) REVERT: K 304 MET cc_start: 0.5319 (tmm) cc_final: 0.5003 (tmm) outliers start: 77 outliers final: 43 residues processed: 468 average time/residue: 0.1998 time to fit residues: 147.2714 Evaluate side-chains 395 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 350 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1113 MET Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1168 LYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 214 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 247 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 361 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN C 258 GLN C 428 GLN C 637 GLN C 729 GLN ** D1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.142575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.103737 restraints weight = 55257.999| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.34 r_work: 0.3143 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 32409 Z= 0.237 Angle : 0.687 9.157 44343 Z= 0.368 Chirality : 0.047 0.334 5050 Planarity : 0.006 0.057 5436 Dihedral : 17.823 179.210 5396 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.16 % Allowed : 19.91 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 3764 helix: 1.23 (0.13), residues: 1597 sheet: -0.58 (0.26), residues: 375 loop : -0.61 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 209 TYR 0.023 0.002 TYR J 224 PHE 0.018 0.002 PHE C 127 TRP 0.016 0.002 TRP J 36 HIS 0.015 0.002 HIS E 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (32402) covalent geometry : angle 0.68638 / 0.37 (44337) hydrogen bonds : bond 0.06517 / 4.34 ( 1432) hydrogen bonds : angle 4.78886 / 3.29 ( 4028) metal coordination : bond 0.00943 / 0.44 ( 7) metal coordination : angle 2.71183 / 1.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 370 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8074 (pt0) cc_final: 0.7798 (pt0) REVERT: C 109 GLU cc_start: 0.7921 (tp30) cc_final: 0.6846 (tp30) REVERT: C 113 ARG cc_start: 0.7598 (mtt-85) cc_final: 0.7280 (mtt-85) REVERT: C 199 TRP cc_start: 0.6157 (OUTLIER) cc_final: 0.4608 (p-90) REVERT: C 382 MET cc_start: 0.8131 (ttp) cc_final: 0.7679 (ttt) REVERT: C 390 MET cc_start: 0.6242 (mmp) cc_final: 0.5963 (mmp) REVERT: C 653 TYR cc_start: 0.7312 (m-10) cc_final: 0.6866 (m-10) REVERT: C 795 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.6273 (mptt) REVERT: C 969 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: D 135 MET cc_start: 0.8351 (ttm) cc_final: 0.8009 (ttt) REVERT: D 389 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7513 (mtt90) REVERT: D 919 MET cc_start: 0.7155 (ptm) cc_final: 0.6755 (ptp) REVERT: D 971 MET cc_start: 0.8363 (mmt) cc_final: 0.8045 (mmt) REVERT: E 41 ASN cc_start: 0.8770 (t0) cc_final: 0.8473 (t0) REVERT: I 209 HIS cc_start: 0.7964 (m-70) cc_final: 0.7648 (m90) REVERT: I 241 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7390 (ttp-110) REVERT: J 83 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7650 (pp) REVERT: J 147 LEU cc_start: 0.7763 (tt) cc_final: 0.7446 (tt) REVERT: J 148 ARG cc_start: 0.7272 (mtt90) cc_final: 0.7059 (mtm180) REVERT: J 215 LEU cc_start: 0.4897 (OUTLIER) cc_final: 0.4505 (mt) REVERT: K 300 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7643 (mmtt) REVERT: K 304 MET cc_start: 0.4979 (tmm) cc_final: 0.4684 (tmm) outliers start: 130 outliers final: 83 residues processed: 478 average time/residue: 0.1957 time to fit residues: 149.0890 Evaluate side-chains 429 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 341 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1113 MET Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 821 ASN Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1082 VAL Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1168 LYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain J residue 36 TRP Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 371 optimal weight: 5.9990 chunk 363 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 chunk 330 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 299 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN A 200 GLN C 258 GLN D 416 ASN ** D1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.143767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.105748 restraints weight = 54859.973| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.28 r_work: 0.3184 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32409 Z= 0.154 Angle : 0.594 7.331 44343 Z= 0.321 Chirality : 0.044 0.344 5050 Planarity : 0.005 0.053 5436 Dihedral : 17.638 178.549 5396 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.75 % Allowed : 21.83 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.13), residues: 3764 helix: 1.40 (0.13), residues: 1597 sheet: -0.32 (0.27), residues: 352 loop : -0.56 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 264 TYR 0.016 0.001 TYR D 106 PHE 0.016 0.001 PHE C 811 TRP 0.016 0.001 TRP J 36 HIS 0.009 0.001 HIS E 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (32402) covalent geometry : angle 0.59389 / 0.32 (44337) hydrogen bonds : bond 0.05460 / 3.60 ( 1432) hydrogen bonds : angle 4.51214 / 3.11 ( 4028) metal coordination : bond 0.00587 / 0.28 ( 7) metal coordination : angle 2.21129 / 1.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 369 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.7993 (pt0) cc_final: 0.7682 (pt0) REVERT: A 213 LYS cc_start: 0.8646 (tptp) cc_final: 0.8344 (ttpt) REVERT: C 85 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: C 199 TRP cc_start: 0.6127 (OUTLIER) cc_final: 0.4449 (p-90) REVERT: C 390 MET cc_start: 0.6330 (mmp) cc_final: 0.6094 (mmp) REVERT: C 527 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8557 (mt) REVERT: C 721 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9080 (mt) REVERT: C 744 ASP cc_start: 0.8133 (p0) cc_final: 0.7798 (p0) REVERT: C 969 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: D 135 MET cc_start: 0.8237 (ttm) cc_final: 0.7914 (ttt) REVERT: D 248 PHE cc_start: 0.6209 (OUTLIER) cc_final: 0.4737 (p90) REVERT: D 389 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7450 (mtt90) REVERT: D 401 SER cc_start: 0.8605 (t) cc_final: 0.8116 (p) REVERT: D 919 MET cc_start: 0.7043 (ptm) cc_final: 0.6708 (ptp) REVERT: D 971 MET cc_start: 0.8334 (mmt) cc_final: 0.8018 (mmt) REVERT: D 1254 ARG cc_start: 0.8277 (mmt180) cc_final: 0.8045 (mpt-90) REVERT: E 41 ASN cc_start: 0.8711 (t0) cc_final: 0.8383 (t0) REVERT: F 344 ASP cc_start: 0.8261 (m-30) cc_final: 0.7849 (t0) REVERT: I 209 HIS cc_start: 0.7871 (m-70) cc_final: 0.7563 (m90) REVERT: I 241 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7449 (ttp-110) REVERT: J 83 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7570 (pp) REVERT: J 147 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7636 (tt) REVERT: K 300 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7633 (mmmt) REVERT: K 304 MET cc_start: 0.5147 (tmm) cc_final: 0.4875 (tmm) outliers start: 117 outliers final: 75 residues processed: 462 average time/residue: 0.2040 time to fit residues: 150.4382 Evaluate side-chains 429 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 346 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1070 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1168 LYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain F residue 483 ARG Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 291 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 314 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 231 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 304 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 827 HIS ** D1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.143600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105405 restraints weight = 55157.712| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.30 r_work: 0.3177 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32409 Z= 0.152 Angle : 0.575 7.248 44343 Z= 0.311 Chirality : 0.043 0.345 5050 Planarity : 0.004 0.052 5436 Dihedral : 17.554 178.963 5394 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.07 % Allowed : 22.54 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.13), residues: 3764 helix: 1.52 (0.13), residues: 1597 sheet: -0.27 (0.26), residues: 368 loop : -0.53 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 57 TYR 0.014 0.001 TYR D 106 PHE 0.012 0.001 PHE C 141 TRP 0.021 0.001 TRP J 177 HIS 0.005 0.001 HIS D 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (32402) covalent geometry : angle 0.57498 / 0.31 (44337) hydrogen bonds : bond 0.05192 / 3.42 ( 1432) hydrogen bonds : angle 4.37889 / 3.02 ( 4028) metal coordination : bond 0.00628 / 0.30 ( 7) metal coordination : angle 2.06263 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 362 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8000 (pt0) cc_final: 0.7706 (pt0) REVERT: C 85 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: C 199 TRP cc_start: 0.6095 (OUTLIER) cc_final: 0.4420 (p-90) REVERT: C 390 MET cc_start: 0.6345 (mmp) cc_final: 0.6092 (mmp) REVERT: C 527 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8559 (mt) REVERT: C 653 TYR cc_start: 0.7352 (m-10) cc_final: 0.7128 (m-10) REVERT: C 721 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9073 (mt) REVERT: C 744 ASP cc_start: 0.8087 (p0) cc_final: 0.7696 (p0) REVERT: C 969 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: C 1118 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8320 (mt) REVERT: D 135 MET cc_start: 0.8301 (ttm) cc_final: 0.7978 (ttt) REVERT: D 248 PHE cc_start: 0.6224 (OUTLIER) cc_final: 0.4902 (p90) REVERT: D 389 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7419 (mtt90) REVERT: D 401 SER cc_start: 0.8609 (t) cc_final: 0.8132 (p) REVERT: D 447 MET cc_start: 0.8879 (tpp) cc_final: 0.8329 (ttp) REVERT: D 919 MET cc_start: 0.7063 (ptm) cc_final: 0.6702 (ptp) REVERT: D 971 MET cc_start: 0.8379 (mmt) cc_final: 0.8031 (mmt) REVERT: D 1162 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: D 1170 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7586 (pt0) REVERT: D 1175 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7176 (ttp-170) REVERT: D 1254 ARG cc_start: 0.8333 (mmt180) cc_final: 0.8112 (mpt-90) REVERT: E 18 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: E 41 ASN cc_start: 0.8734 (t0) cc_final: 0.8406 (t0) REVERT: F 344 ASP cc_start: 0.8276 (m-30) cc_final: 0.7859 (t0) REVERT: I 148 ARG cc_start: 0.6571 (mtm-85) cc_final: 0.5977 (mtt180) REVERT: I 209 HIS cc_start: 0.7851 (m-70) cc_final: 0.7555 (m90) REVERT: I 241 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7474 (ttp-110) REVERT: I 258 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6127 (mm) REVERT: J 83 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7553 (pp) REVERT: J 147 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7682 (tt) REVERT: J 148 ARG cc_start: 0.7395 (mtt90) cc_final: 0.7071 (mtm180) outliers start: 127 outliers final: 90 residues processed: 464 average time/residue: 0.2079 time to fit residues: 153.4538 Evaluate side-chains 446 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 343 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1118 LEU Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 821 ASN Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1162 GLU Chi-restraints excluded: chain D residue 1168 LYS Chi-restraints excluded: chain D residue 1175 ARG Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 151 optimal weight: 0.5980 chunk 281 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 353 optimal weight: 0.3980 chunk 185 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 66 optimal weight: 0.0980 chunk 310 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 301 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN D 752 GLN D1010 HIS ** D1100 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 = 0.3978 r_free = 0.3978 target = 0.145787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.107913 restraints weight = 54769.131| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.29 r_work: 0.3222 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32409 Z= 0.113 Angle : 0.537 7.930 44343 Z= 0.291 Chirality : 0.041 0.352 5050 Planarity : 0.004 0.048 5436 Dihedral : 17.427 176.490 5394 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.78 % Allowed : 22.95 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.13), residues: 3764 helix: 1.66 (0.13), residues: 1597 sheet: -0.08 (0.27), residues: 357 loop : -0.49 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 57 TYR 0.012 0.001 TYR D 681 PHE 0.014 0.001 PHE B 30 TRP 0.021 0.001 TRP C 939 HIS 0.009 0.001 HIS E 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (32402) covalent geometry : angle 0.53635 / 0.29 (44337) hydrogen bonds : bond 0.04621 / 3.01 ( 1432) hydrogen bonds : angle 4.18250 / 2.90 ( 4028) metal coordination : bond 0.00343 / 0.17 ( 7) metal coordination : angle 1.86495 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 375 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.7962 (pt0) cc_final: 0.7594 (pt0) REVERT: C 76 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8268 (tt0) REVERT: C 199 TRP cc_start: 0.6004 (OUTLIER) cc_final: 0.4341 (p-90) REVERT: C 340 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: C 744 ASP cc_start: 0.7969 (p0) cc_final: 0.7705 (p0) REVERT: C 889 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8767 (m-30) REVERT: C 969 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: D 7 PHE cc_start: 0.7352 (m-80) cc_final: 0.7101 (m-80) REVERT: D 119 ASP cc_start: 0.6959 (m-30) cc_final: 0.6331 (p0) REVERT: D 135 MET cc_start: 0.8245 (ttm) cc_final: 0.7963 (ttt) REVERT: D 248 PHE cc_start: 0.6124 (OUTLIER) cc_final: 0.4975 (p90) REVERT: D 276 ARG cc_start: 0.7734 (mpt180) cc_final: 0.7489 (tpm170) REVERT: D 337 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8579 (t) REVERT: D 389 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7420 (mtt90) REVERT: D 401 SER cc_start: 0.8426 (t) cc_final: 0.7885 (p) REVERT: D 447 MET cc_start: 0.8792 (tpp) cc_final: 0.8112 (ttp) REVERT: D 539 ASP cc_start: 0.8159 (m-30) cc_final: 0.7899 (m-30) REVERT: D 650 GLU cc_start: 0.3161 (OUTLIER) cc_final: 0.1637 (mt-10) REVERT: D 806 MET cc_start: 0.7740 (tpt) cc_final: 0.7324 (tpt) REVERT: D 919 MET cc_start: 0.6861 (ptm) cc_final: 0.6476 (ptp) REVERT: D 971 MET cc_start: 0.8339 (mmt) cc_final: 0.7982 (mmt) REVERT: D 1162 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: D 1170 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7609 (pt0) REVERT: D 1175 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7156 (ttp-170) REVERT: D 1254 ARG cc_start: 0.8312 (mmt180) cc_final: 0.8106 (mpt-90) REVERT: E 18 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: E 41 ASN cc_start: 0.8617 (t0) cc_final: 0.8291 (t0) REVERT: F 344 ASP cc_start: 0.8268 (m-30) cc_final: 0.7876 (t0) REVERT: F 507 ARG cc_start: 0.7867 (mmm160) cc_final: 0.7522 (tpt170) REVERT: I 148 ARG cc_start: 0.6734 (mtm-85) cc_final: 0.6108 (mtt180) REVERT: I 209 HIS cc_start: 0.7812 (m-70) cc_final: 0.7518 (m90) REVERT: I 241 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7495 (ttp-110) REVERT: I 258 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6075 (mm) REVERT: J 83 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7537 (pp) REVERT: J 147 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7698 (tt) REVERT: J 148 ARG cc_start: 0.7325 (mtt90) cc_final: 0.7009 (mtm180) REVERT: J 197 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6217 (pm20) REVERT: J 242 LEU cc_start: 0.4996 (tp) cc_final: 0.4709 (tt) outliers start: 118 outliers final: 63 residues processed: 472 average time/residue: 0.1861 time to fit residues: 141.2747 Evaluate side-chains 427 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 350 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1162 GLU Chi-restraints excluded: chain D residue 1175 ARG Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 382 LEU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain F residue 483 ARG Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 65 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 362 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 282 optimal weight: 2.9990 chunk 72 optimal weight: 0.0060 chunk 56 optimal weight: 10.0000 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN D 579 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.142096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103917 restraints weight = 55167.487| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.29 r_work: 0.3151 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 32409 Z= 0.211 Angle : 0.631 7.721 44343 Z= 0.336 Chirality : 0.044 0.333 5050 Planarity : 0.005 0.051 5436 Dihedral : 17.486 178.923 5393 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.39 % Allowed : 22.89 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.13), residues: 3764 helix: 1.57 (0.13), residues: 1604 sheet: -0.24 (0.27), residues: 362 loop : -0.57 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 57 TYR 0.016 0.002 TYR J 224 PHE 0.013 0.002 PHE D 452 TRP 0.013 0.002 TRP J 177 HIS 0.010 0.001 HIS E 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (32402) covalent geometry : angle 0.63020 / 0.34 (44337) hydrogen bonds : bond 0.05230 / 3.47 ( 1432) hydrogen bonds : angle 4.33572 / 2.99 ( 4028) metal coordination : bond 0.00926 / 0.43 ( 7) metal coordination : angle 2.12076 / 1.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 357 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8037 (pt0) cc_final: 0.7713 (pt0) REVERT: A 159 ILE cc_start: 0.7693 (mm) cc_final: 0.7353 (mt) REVERT: B 203 ARG cc_start: 0.7357 (ptt-90) cc_final: 0.7085 (ptt-90) REVERT: C 76 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8374 (tt0) REVERT: C 199 TRP cc_start: 0.6119 (OUTLIER) cc_final: 0.4429 (p-90) REVERT: C 340 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7396 (tp30) REVERT: C 527 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8580 (mt) REVERT: C 653 TYR cc_start: 0.7757 (m-10) cc_final: 0.7470 (m-10) REVERT: C 721 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9092 (mt) REVERT: C 744 ASP cc_start: 0.8056 (p0) cc_final: 0.7757 (p0) REVERT: C 969 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: D 119 ASP cc_start: 0.7244 (m-30) cc_final: 0.6544 (p0) REVERT: D 135 MET cc_start: 0.8354 (ttm) cc_final: 0.8083 (ttp) REVERT: D 248 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.5120 (p90) REVERT: D 252 PHE cc_start: 0.8888 (p90) cc_final: 0.8674 (p90) REVERT: D 276 ARG cc_start: 0.7762 (mpt180) cc_final: 0.7447 (tpm170) REVERT: D 401 SER cc_start: 0.8725 (t) cc_final: 0.8349 (p) REVERT: D 447 MET cc_start: 0.9062 (tpp) cc_final: 0.8811 (ttt) REVERT: D 583 LEU cc_start: 0.8704 (tt) cc_final: 0.8496 (tp) REVERT: D 919 MET cc_start: 0.7066 (ptm) cc_final: 0.6731 (ptp) REVERT: D 971 MET cc_start: 0.8332 (mmt) cc_final: 0.7944 (mmt) REVERT: D 1162 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: D 1170 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7640 (pt0) REVERT: D 1175 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7175 (ttp-170) REVERT: D 1253 ILE cc_start: 0.9134 (pt) cc_final: 0.8773 (pt) REVERT: D 1254 ARG cc_start: 0.8393 (mmt180) cc_final: 0.8171 (mpt-90) REVERT: E 18 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: E 41 ASN cc_start: 0.8754 (t0) cc_final: 0.8429 (t0) REVERT: F 217 ASP cc_start: 0.8353 (t0) cc_final: 0.8135 (t0) REVERT: F 344 ASP cc_start: 0.8298 (m-30) cc_final: 0.7851 (t0) REVERT: F 420 ASP cc_start: 0.8205 (t0) cc_final: 0.7721 (t0) REVERT: F 507 ARG cc_start: 0.7972 (mmm160) cc_final: 0.7520 (tpt170) REVERT: I 148 ARG cc_start: 0.6659 (mtm-85) cc_final: 0.6019 (mtt180) REVERT: I 209 HIS cc_start: 0.7891 (m-70) cc_final: 0.7609 (m90) REVERT: I 241 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7478 (ttp-110) REVERT: I 258 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6393 (mm) REVERT: J 83 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7617 (pp) REVERT: J 147 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7699 (tt) REVERT: J 177 TRP cc_start: 0.7562 (t-100) cc_final: 0.7237 (t-100) outliers start: 137 outliers final: 98 residues processed: 464 average time/residue: 0.1915 time to fit residues: 144.3796 Evaluate side-chains 454 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 344 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 821 ASN Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1070 THR Chi-restraints excluded: chain D residue 1082 VAL Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1162 GLU Chi-restraints excluded: chain D residue 1168 LYS Chi-restraints excluded: chain D residue 1175 ARG Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 141 optimal weight: 0.1980 chunk 192 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 271 optimal weight: 0.3980 chunk 42 optimal weight: 0.3980 chunk 291 optimal weight: 5.9990 chunk 308 optimal weight: 6.9990 chunk 266 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.145018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106458 restraints weight = 54770.558| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.35 r_work: 0.3195 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 32409 Z= 0.113 Angle : 0.544 7.732 44343 Z= 0.294 Chirality : 0.041 0.350 5050 Planarity : 0.004 0.056 5436 Dihedral : 17.393 176.340 5393 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.23 % Allowed : 24.23 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.13), residues: 3764 helix: 1.73 (0.13), residues: 1600 sheet: 0.20 (0.29), residues: 327 loop : -0.50 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 57 TYR 0.017 0.001 TYR J 224 PHE 0.020 0.001 PHE C 709 TRP 0.017 0.001 TRP J 177 HIS 0.006 0.001 HIS D1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (32402) covalent geometry : angle 0.54366 / 0.29 (44337) hydrogen bonds : bond 0.04516 / 2.92 ( 1432) hydrogen bonds : angle 4.14478 / 2.87 ( 4028) metal coordination : bond 0.00324 / 0.16 ( 7) metal coordination : angle 1.67961 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 356 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8010 (pt0) cc_final: 0.7647 (pt0) REVERT: C 76 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8339 (tt0) REVERT: C 199 TRP cc_start: 0.5977 (OUTLIER) cc_final: 0.4262 (p-90) REVERT: C 340 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7352 (tp30) REVERT: C 415 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7548 (mm-30) REVERT: C 527 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8556 (mt) REVERT: C 653 TYR cc_start: 0.7435 (m-10) cc_final: 0.7172 (m-10) REVERT: C 744 ASP cc_start: 0.8014 (p0) cc_final: 0.7709 (p0) REVERT: C 846 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7183 (pt0) REVERT: C 969 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: D 7 PHE cc_start: 0.7403 (m-80) cc_final: 0.7153 (m-80) REVERT: D 119 ASP cc_start: 0.7081 (m-30) cc_final: 0.6408 (p0) REVERT: D 135 MET cc_start: 0.8366 (ttm) cc_final: 0.8056 (ttt) REVERT: D 248 PHE cc_start: 0.6191 (OUTLIER) cc_final: 0.5069 (p90) REVERT: D 276 ARG cc_start: 0.7735 (mpt180) cc_final: 0.7466 (tpm170) REVERT: D 337 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8581 (t) REVERT: D 389 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7509 (mtt90) REVERT: D 401 SER cc_start: 0.8559 (t) cc_final: 0.8199 (p) REVERT: D 447 MET cc_start: 0.8932 (tpp) cc_final: 0.8576 (ttp) REVERT: D 629 PHE cc_start: 0.8693 (m-10) cc_final: 0.8412 (m-80) REVERT: D 919 MET cc_start: 0.6883 (ptm) cc_final: 0.6569 (ptp) REVERT: D 971 MET cc_start: 0.8277 (mmt) cc_final: 0.7892 (mmt) REVERT: D 1162 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: D 1170 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7628 (pt0) REVERT: D 1175 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7130 (ttp-170) REVERT: E 18 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: E 41 ASN cc_start: 0.8658 (t0) cc_final: 0.8322 (t0) REVERT: F 344 ASP cc_start: 0.8277 (m-30) cc_final: 0.7875 (t0) REVERT: F 420 ASP cc_start: 0.8249 (t0) cc_final: 0.7769 (t0) REVERT: F 507 ARG cc_start: 0.7903 (mmm160) cc_final: 0.7451 (tpt170) REVERT: I 148 ARG cc_start: 0.6555 (mtm-85) cc_final: 0.5927 (mtt180) REVERT: I 209 HIS cc_start: 0.7785 (m-70) cc_final: 0.7507 (m90) REVERT: I 241 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7379 (ttp-110) REVERT: I 258 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6075 (mm) REVERT: J 83 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7579 (pp) REVERT: J 147 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7743 (tt) REVERT: J 148 ARG cc_start: 0.7148 (mtt90) cc_final: 0.6878 (mtm180) REVERT: J 177 TRP cc_start: 0.7512 (t-100) cc_final: 0.7123 (t-100) outliers start: 101 outliers final: 71 residues processed: 437 average time/residue: 0.1990 time to fit residues: 140.5288 Evaluate side-chains 428 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 345 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1070 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1123 LYS Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1162 GLU Chi-restraints excluded: chain D residue 1175 ARG Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 328 optimal weight: 40.0000 chunk 153 optimal weight: 0.0010 chunk 107 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 chunk 322 optimal weight: 30.0000 chunk 342 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 380 optimal weight: 30.0000 chunk 175 optimal weight: 20.0000 chunk 260 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 overall best weight: 5.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.102343 restraints weight = 55029.822| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.25 r_work: 0.3119 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 32409 Z= 0.301 Angle : 0.719 9.036 44343 Z= 0.380 Chirality : 0.048 0.335 5050 Planarity : 0.006 0.055 5436 Dihedral : 17.542 176.414 5393 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.26 % Allowed : 23.82 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.13), residues: 3764 helix: 1.39 (0.13), residues: 1607 sheet: -0.48 (0.26), residues: 388 loop : -0.68 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 57 TYR 0.021 0.002 TYR C 266 PHE 0.029 0.002 PHE D 639 TRP 0.018 0.002 TRP C 231 HIS 0.010 0.002 HIS E 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.30 (32402) covalent geometry : angle 0.71827 / 0.38 (44337) hydrogen bonds : bond 0.05727 / 3.83 ( 1432) hydrogen bonds : angle 4.48596 / 3.08 ( 4028) metal coordination : bond 0.01294 / 0.60 ( 7) metal coordination : angle 2.39293 / 1.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 345 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8056 (pt0) cc_final: 0.7727 (pt0) REVERT: A 159 ILE cc_start: 0.7756 (mm) cc_final: 0.7341 (mt) REVERT: C 199 TRP cc_start: 0.6266 (OUTLIER) cc_final: 0.4406 (p-90) REVERT: C 340 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: C 527 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8603 (mt) REVERT: C 721 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9135 (mt) REVERT: C 744 ASP cc_start: 0.8001 (p0) cc_final: 0.7750 (p0) REVERT: C 830 ILE cc_start: 0.8320 (mt) cc_final: 0.8101 (tp) REVERT: C 846 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7243 (pt0) REVERT: C 889 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8892 (m-30) REVERT: C 969 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: D 135 MET cc_start: 0.8391 (ttm) cc_final: 0.8118 (ttp) REVERT: D 215 GLU cc_start: 0.6791 (pt0) cc_final: 0.6484 (tp30) REVERT: D 248 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.5303 (p90) REVERT: D 252 PHE cc_start: 0.8878 (p90) cc_final: 0.8663 (p90) REVERT: D 276 ARG cc_start: 0.7778 (mpt180) cc_final: 0.7468 (tpm170) REVERT: D 389 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7565 (mtt90) REVERT: D 401 SER cc_start: 0.8818 (t) cc_final: 0.8517 (p) REVERT: D 893 LYS cc_start: 0.7856 (tttt) cc_final: 0.7617 (tmtt) REVERT: D 919 MET cc_start: 0.7156 (ptm) cc_final: 0.6909 (ptp) REVERT: D 971 MET cc_start: 0.8271 (mmt) cc_final: 0.7902 (mmt) REVERT: D 1162 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: D 1170 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7612 (pt0) REVERT: D 1175 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7372 (ttp-170) REVERT: D 1253 ILE cc_start: 0.9255 (pt) cc_final: 0.9045 (pt) REVERT: E 18 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: E 41 ASN cc_start: 0.8791 (t0) cc_final: 0.8476 (t0) REVERT: F 344 ASP cc_start: 0.8258 (m-30) cc_final: 0.7814 (t0) REVERT: F 420 ASP cc_start: 0.8141 (t0) cc_final: 0.7674 (t0) REVERT: I 148 ARG cc_start: 0.6447 (mtm-85) cc_final: 0.5779 (mtt180) REVERT: I 209 HIS cc_start: 0.7914 (m-70) cc_final: 0.7628 (m90) REVERT: I 241 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7315 (ttp-110) REVERT: I 258 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6330 (mm) REVERT: J 83 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7578 (pp) REVERT: J 147 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7775 (tt) REVERT: J 177 TRP cc_start: 0.7581 (t-100) cc_final: 0.7196 (t-100) REVERT: J 213 GLU cc_start: 0.5047 (pm20) cc_final: 0.4716 (pp20) REVERT: K 300 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7312 (tptp) outliers start: 133 outliers final: 106 residues processed: 450 average time/residue: 0.1992 time to fit residues: 144.6140 Evaluate side-chains 448 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 329 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 769 ASP Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 889 ASP Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 MET Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 821 ASN Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1029 LEU Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1070 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1162 GLU Chi-restraints excluded: chain D residue 1175 ARG Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 74 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 15 optimal weight: 0.0000 chunk 167 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 300 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 372 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 ASN D1100 ASN ** J 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.144115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.105680 restraints weight = 54633.288| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.31 r_work: 0.3184 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32409 Z= 0.120 Angle : 0.572 9.005 44343 Z= 0.308 Chirality : 0.041 0.353 5050 Planarity : 0.004 0.051 5436 Dihedral : 17.423 177.392 5393 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.78 % Allowed : 25.06 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.13), residues: 3764 helix: 1.61 (0.13), residues: 1608 sheet: -0.09 (0.27), residues: 360 loop : -0.51 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 57 TYR 0.021 0.001 TYR C 266 PHE 0.016 0.001 PHE A 189 TRP 0.025 0.002 TRP D 718 HIS 0.006 0.001 HIS D1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (32402) covalent geometry : angle 0.57182 / 0.31 (44337) hydrogen bonds : bond 0.04607 / 2.99 ( 1432) hydrogen bonds : angle 4.18995 / 2.89 ( 4028) metal coordination : bond 0.00363 / 0.17 ( 7) metal coordination : angle 1.15662 / 0.47 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 352 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8035 (pt0) cc_final: 0.7699 (pt0) REVERT: B 82 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8601 (tt0) REVERT: C 76 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8278 (tt0) REVERT: C 199 TRP cc_start: 0.6007 (OUTLIER) cc_final: 0.4329 (p-90) REVERT: C 340 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7364 (tp30) REVERT: C 415 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7431 (mm-30) REVERT: C 653 TYR cc_start: 0.7833 (m-10) cc_final: 0.7385 (m-10) REVERT: C 699 MET cc_start: 0.8582 (tpp) cc_final: 0.8317 (tpp) REVERT: C 721 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.9047 (mt) REVERT: C 744 ASP cc_start: 0.7999 (p0) cc_final: 0.7760 (p0) REVERT: C 830 ILE cc_start: 0.8129 (mt) cc_final: 0.7786 (tp) REVERT: C 969 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: D 119 ASP cc_start: 0.7106 (m-30) cc_final: 0.6367 (p0) REVERT: D 135 MET cc_start: 0.8355 (ttm) cc_final: 0.8057 (ttt) REVERT: D 248 PHE cc_start: 0.6304 (OUTLIER) cc_final: 0.5164 (p90) REVERT: D 252 PHE cc_start: 0.8915 (p90) cc_final: 0.8690 (p90) REVERT: D 276 ARG cc_start: 0.7723 (mpt180) cc_final: 0.7462 (tpm170) REVERT: D 389 ARG cc_start: 0.7788 (mtp85) cc_final: 0.7487 (mtt90) REVERT: D 401 SER cc_start: 0.8707 (t) cc_final: 0.8366 (p) REVERT: D 1162 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: D 1170 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7640 (pt0) REVERT: D 1175 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7340 (ttp-170) REVERT: D 1254 ARG cc_start: 0.8270 (mpt-90) cc_final: 0.8065 (mmt-90) REVERT: E 18 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: E 41 ASN cc_start: 0.8701 (t0) cc_final: 0.8402 (t0) REVERT: F 344 ASP cc_start: 0.8285 (m-30) cc_final: 0.7858 (t0) REVERT: F 420 ASP cc_start: 0.8167 (t0) cc_final: 0.7807 (t0) REVERT: I 209 HIS cc_start: 0.7775 (m-70) cc_final: 0.7502 (m90) REVERT: I 241 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7464 (ttp-110) REVERT: I 258 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6184 (mm) REVERT: J 83 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7517 (pp) REVERT: J 147 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7755 (tt) REVERT: J 177 TRP cc_start: 0.7515 (t-100) cc_final: 0.7111 (t-100) REVERT: J 213 GLU cc_start: 0.5060 (pm20) cc_final: 0.4639 (pp20) REVERT: K 300 LYS cc_start: 0.7887 (mmtt) cc_final: 0.7324 (tptp) outliers start: 87 outliers final: 70 residues processed: 418 average time/residue: 0.1932 time to fit residues: 130.4546 Evaluate side-chains 420 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 339 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 926 ILE Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1038 VAL Chi-restraints excluded: chain D residue 1070 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1090 VAL Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1158 LEU Chi-restraints excluded: chain D residue 1162 GLU Chi-restraints excluded: chain D residue 1175 ARG Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain F residue 298 MET Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 444 HIS Chi-restraints excluded: chain F residue 479 TYR Chi-restraints excluded: chain F residue 494 MET Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 195 HIS Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 295 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 382 optimal weight: 0.8980 chunk 375 optimal weight: 5.9990 chunk 376 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 256 optimal weight: 0.0870 chunk 271 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 236 optimal weight: 0.3980 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D1100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.144066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.106262 restraints weight = 54882.557| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.29 r_work: 0.3191 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.195 32409 Z= 0.157 Angle : 0.695 59.185 44343 Z= 0.399 Chirality : 0.042 0.355 5050 Planarity : 0.004 0.049 5436 Dihedral : 17.423 177.388 5393 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.91 % Allowed : 25.22 % Favored : 71.86 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.13), residues: 3764 helix: 1.61 (0.13), residues: 1608 sheet: -0.08 (0.27), residues: 360 loop : -0.51 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 57 TYR 0.017 0.001 TYR C 266 PHE 0.022 0.001 PHE C 115 TRP 0.022 0.001 TRP D 718 HIS 0.006 0.001 HIS D1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (32402) covalent geometry : angle 0.69482 / 0.40 (44337) hydrogen bonds : bond 0.04610 / 2.99 ( 1432) hydrogen bonds : angle 4.19033 / 2.89 ( 4028) metal coordination : bond 0.00385 / 0.18 ( 7) metal coordination : angle 1.16207 / 0.47 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7280.92 seconds wall clock time: 125 minutes 11.87 seconds (7511.87 seconds total)