Starting phenix.real_space_refine on Tue Aug 26 07:33:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hko_0238/08_2025/6hko_0238.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hko_0238/08_2025/6hko_0238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6hko_0238/08_2025/6hko_0238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hko_0238/08_2025/6hko_0238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hko_0238/08_2025/6hko_0238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hko_0238/08_2025/6hko_0238.map" } resolution = 3.42 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= 0.011 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 6 6.06 5 P 76 5.49 5 Mg 1 5.21 5 S 167 5.16 5 C 21594 2.51 5 N 5999 2.21 5 O 6675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34518 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 11513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1458, 11513 Classifications: {'peptide': 1458} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1398} Chain breaks: 8 Chain: "B" Number of atoms: 9270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9270 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 59, 'TRANS': 1106} Chain breaks: 3 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2415 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1751 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 1 Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1052 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 486 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 766 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "S" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 581 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "T" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 732 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "N" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1110 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain breaks: 2 Chain: "M" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1011 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Chain: "A" 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} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 68.006 53.414 55.211 1.00 74.00 S ATOM 480 SG CYS A 65 71.975 51.423 54.643 1.00 71.20 S ATOM 535 SG CYS A 72 70.921 53.328 57.636 1.00 65.70 S ATOM 781 SG CYS A 102 73.075 103.735 44.141 1.00 86.04 S ATOM 806 SG CYS A 105 75.877 102.219 41.235 1.00 84.96 S ATOM 1597 SG CYS A 233 76.987 104.755 43.724 1.00 90.06 S ATOM 1619 SG CYS A 236 74.511 105.590 40.608 1.00 96.18 S ATOM 20113 SG CYS B1104 83.786 60.894 47.386 1.00 63.28 S ATOM 20139 SG CYS B1107 81.464 64.042 47.458 1.00 63.94 S ATOM 20286 SG CYS B1128 80.119 60.764 47.638 1.00 70.38 S ATOM 20314 SG CYS B1131 82.000 64.245 43.988 1.00 76.84 S ATOM 28740 SG CYS I 10 46.436 130.417 100.974 1.00 95.45 S ATOM 28762 SG CYS I 13 45.071 126.221 100.349 1.00 97.79 S ATOM 28882 SG CYS I 30 45.923 128.780 97.235 1.00102.41 S ATOM 28903 SG CYS I 33 42.671 128.809 100.275 1.00103.05 S ATOM 29217 SG CYS J 7 86.136 42.499 126.430 1.00 45.91 S ATOM 29240 SG CYS J 10 89.493 41.626 127.229 1.00 48.67 S ATOM 29520 SG CYS J 45 89.869 45.223 127.881 1.00 47.13 S ATOM 29526 SG CYS J 46 87.354 42.819 129.878 1.00 47.10 S ATOM 30541 SG CYS L 31 45.745 43.948 108.738 1.00 64.80 S ATOM 30561 SG CYS L 34 43.843 42.481 112.041 1.00 68.55 S ATOM 30665 SG CYS L 48 42.569 41.377 108.561 1.00 76.47 S ATOM 30688 SG CYS L 51 42.262 45.259 110.203 1.00 75.72 S Time building chain proxies: 8.03, per 1000 atoms: 0.23 Number of scatterers: 34518 At special positions: 0 Unit cell: (166.4, 161.2, 169.52, 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 6 29.99 S 167 16.00 P 76 15.00 Mg 1 11.99 O 6675 8.00 N 5999 7.00 C 21594 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: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 236 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1131 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 10 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 33 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " Number of angles added : 33 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7812 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 52 sheets defined 34.3% alpha, 18.1% beta 22 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'A' and resid 22 through 26 Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.871A pdb=" N GLY A 55 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.525A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 removed outlier: 4.042A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.861A pdb=" N LYS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.935A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 228 removed outlier: 3.553A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.671A pdb=" N VAL A 266 " --> pdb=" O ASN A 263 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 267 " --> pdb=" O ASN A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 267' Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.789A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.622A pdb=" N LEU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.726A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 removed outlier: 3.776A pdb=" N GLN A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 439 removed outlier: 3.567A pdb=" N VAL A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.958A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 removed outlier: 3.650A pdb=" N ALA A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 648 removed outlier: 4.067A pdb=" N GLU A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 removed outlier: 3.724A pdb=" N GLY A 677 " --> pdb=" O HIS A 673 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.712A pdb=" N GLN A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 728 through 739 removed outlier: 3.564A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 738 " --> pdb=" O THR A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 802 through 817 removed outlier: 3.581A pdb=" N ALA A 807 " --> pdb=" O PRO A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 847 Processing helix chain 'A' and resid 848 through 851 removed outlier: 3.617A pdb=" N VAL A 851 " --> pdb=" O LYS A 848 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 848 through 851' Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.556A pdb=" N GLN A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 884 " --> pdb=" O GLN A 880 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 removed outlier: 3.610A pdb=" N ILE A 891 " --> pdb=" O ASN A 887 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1011 removed outlier: 3.821A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1001 " --> pdb=" O PHE A 997 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1028 removed outlier: 3.686A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 3.859A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1085 Processing helix chain 'A' and resid 1091 through 1108 removed outlier: 3.989A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A1102 " --> pdb=" O SER A1098 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1151 removed outlier: 3.505A pdb=" N GLU A1145 " --> pdb=" O GLN A1141 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1177 removed outlier: 3.805A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A1171 " --> pdb=" O ARG A1167 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1198 removed outlier: 3.929A pdb=" N VAL A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1218 through 1226 removed outlier: 3.513A pdb=" N LEU A1222 " --> pdb=" O GLY A1218 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A1223 " --> pdb=" O ILE A1219 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1253 removed outlier: 3.544A pdb=" N THR A1253 " --> pdb=" O GLU A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1259 removed outlier: 3.629A pdb=" N ILE A1258 " --> pdb=" O PHE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 3.506A pdb=" N SER A1303 " --> pdb=" O ASN A1299 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.561A pdb=" N ILE A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1336 removed outlier: 3.551A pdb=" N LEU A1324 " --> pdb=" O GLN A1320 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A1328 " --> pdb=" O LEU A1324 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A1335 " --> pdb=" O LYS A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1454 removed outlier: 3.834A pdb=" N ARG A1444 " --> pdb=" O ASN A1440 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1496 removed outlier: 3.538A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1527 through 1531 removed outlier: 3.712A pdb=" N ASP A1531 " --> pdb=" O ALA A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1547 through 1553 Processing helix chain 'A' and resid 1555 through 1568 removed outlier: 3.759A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A1568 " --> pdb=" O ASN A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1590 removed outlier: 3.747A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.581A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1627 Processing helix chain 'A' and resid 1638 through 1643 removed outlier: 3.811A pdb=" N VAL A1642 " --> pdb=" O SER A1638 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1638 through 1643' Processing helix chain 'A' and resid 1649 through 1652 removed outlier: 4.320A pdb=" N GLY A1652 " --> pdb=" O VAL A1649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1652' Processing helix chain 'B' and resid 17 through 27 removed outlier: 3.762A pdb=" N SER B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 41 removed outlier: 3.537A pdb=" N ALA B 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.854A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.932A pdb=" N ASN B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.590A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.576A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.607A pdb=" N ASN B 224 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.125A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 removed outlier: 3.669A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.577A pdb=" N LEU B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.853A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.635A pdb=" N GLU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 406 through 434 removed outlier: 3.509A pdb=" N LEU B 413 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.735A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 506 through 511 removed outlier: 3.618A pdb=" N ALA B 510 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 506 through 511' Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.672A pdb=" N TRP B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.892A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.926A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.726A pdb=" N LEU B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.538A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 removed outlier: 3.541A pdb=" N TYR B 717 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 718 " --> pdb=" O ARG B 714 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 833 through 838 removed outlier: 3.918A pdb=" N TRP B 836 " --> pdb=" O PRO B 833 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 837 " --> pdb=" O LYS B 834 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU B 838 " --> pdb=" O GLU B 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 833 through 838' Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 951 through 954 Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.857A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 removed outlier: 3.577A pdb=" N LYS B1002 " --> pdb=" O GLU B 998 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B1004 " --> pdb=" O LEU B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 removed outlier: 3.670A pdb=" N ASP B1042 " --> pdb=" O MET B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1077 Processing helix chain 'B' and resid 1078 through 1080 No H-bonds generated for 'chain 'B' and resid 1078 through 1080' Processing helix chain 'B' and resid 1085 through 1093 Processing helix chain 'B' and resid 1180 through 1191 removed outlier: 3.690A pdb=" N ALA B1191 " --> pdb=" O SER B1187 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 4.003A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.521A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.532A pdb=" N ASP C 166 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 167 " --> pdb=" O ALA C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 174 through 179 removed outlier: 4.230A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.515A pdb=" N PHE C 251 " --> pdb=" O GLN C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.538A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 removed outlier: 3.653A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 41 Processing helix chain 'D' and resid 44 through 49 removed outlier: 3.596A pdb=" N GLU D 48 " --> pdb=" O ILE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'E' and resid 4 through 27 removed outlier: 4.510A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.555A pdb=" N ALA E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.553A pdb=" N ILE E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 103 removed outlier: 4.112A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 123 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.688A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 56 through 72 removed outlier: 3.666A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.558A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.691A pdb=" N ALA F 126 " --> pdb=" O MET F 122 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 66 removed outlier: 3.733A pdb=" N VAL G 61 " --> pdb=" O PRO G 57 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.708A pdb=" N ASP H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 135 removed outlier: 4.479A pdb=" N ASN H 134 " --> pdb=" O ASN H 131 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 135 " --> pdb=" O LEU H 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 131 through 135' Processing helix chain 'I' and resid 58 through 67 removed outlier: 3.678A pdb=" N LYS I 63 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.619A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.316A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.618A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 128 Processing helix chain 'K' and resid 129 through 142 removed outlier: 3.931A pdb=" N PHE K 135 " --> pdb=" O VAL K 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 97 removed outlier: 4.235A pdb=" N GLU N 96 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 removed outlier: 3.702A pdb=" N ARG N 154 " --> pdb=" O TYR N 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 129 removed outlier: 4.119A pdb=" N GLY M 129 " --> pdb=" O ASN M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 142 removed outlier: 3.536A pdb=" N ILE M 141 " --> pdb=" O ALA M 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 78 removed outlier: 3.610A pdb=" N GLY A 77 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.758A pdb=" N CYS A 85 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.638A pdb=" N HIS A 378 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AA7, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 3.716A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.943A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB1, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.693A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB3, first strand: chain 'A' and resid 1238 through 1241 removed outlier: 3.526A pdb=" N MET A1238 " --> pdb=" O THR A1521 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.743A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.759A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA G 44 " --> pdb=" O HIS D 23 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A1655 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.546A pdb=" N GLN D 29 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR G 123 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR G 84 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TRP G 125 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU G 82 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 96 through 104 removed outlier: 4.556A pdb=" N VAL B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER B 144 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 108 through 110 Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC2, first strand: chain 'B' and resid 400 through 403 removed outlier: 4.066A pdb=" N MET B 205 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 215 through 218 removed outlier: 6.010A pdb=" N TYR B 252 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR B 232 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 250 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE B 234 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN B 248 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 236 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN B 246 " --> pdb=" O ILE B 236 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.810A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC6, first strand: chain 'B' and resid 571 through 572 removed outlier: 3.505A pdb=" N LYS B 591 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 725 through 726 removed outlier: 4.694A pdb=" N ARG B1035 " --> pdb=" O MET B 726 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS B 916 " --> pdb=" O LEU B1036 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N MET B 787 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TRP B 931 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE B 789 " --> pdb=" O TRP B 931 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 788 " --> pdb=" O ILE B 948 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.671A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 902 " --> pdb=" O ASN B 886 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.671A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 902 " --> pdb=" O ASN B 886 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 823 through 825 removed outlier: 3.691A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 938 through 939 removed outlier: 3.515A pdb=" N PHE B 938 " --> pdb=" O TYR B1014 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1010 through 1011 Processing sheet with id=AD4, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD5, first strand: chain 'B' and resid 1114 through 1115 Processing sheet with id=AD6, first strand: chain 'B' and resid 1158 through 1160 Processing sheet with id=AD7, first strand: chain 'C' and resid 41 through 46 removed outlier: 3.596A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 232 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N PHE C 300 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR C 224 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N VAL C 302 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N VAL C 222 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.521A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.336A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE2, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AE3, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE4, first strand: chain 'E' and resid 61 through 62 removed outlier: 6.355A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.990A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE E 199 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AE8, first strand: chain 'G' and resid 132 through 134 Processing sheet with id=AE9, first strand: chain 'G' and resid 136 through 140 removed outlier: 4.107A pdb=" N PHE G 138 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 167 through 168 Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 16 removed outlier: 7.105A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU H 126 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL H 107 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF4, first strand: chain 'I' and resid 28 through 29 Processing sheet with id=AF5, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF6, first strand: chain 'N' and resid 30 through 31 removed outlier: 3.685A pdb=" N VAL M 52 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA M 22 " --> pdb=" O LEU N 110 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 79 through 81 removed outlier: 3.552A pdb=" N MET N 90 " --> pdb=" O SER N 138 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER N 138 " --> pdb=" O MET N 90 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS N 135 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N GLU N 141 " --> pdb=" O PRO N 59 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU M 80 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN M 89 " --> pdb=" O LEU M 80 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU M 90 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL M 15 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS M 92 " --> pdb=" O VAL M 15 " (cutoff:3.500A) 1114 hydrogen bonds defined for protein. 3057 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 10.30 Time building geometry restraints manager: 3.83 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: 10198 1.33 - 1.45: 6302 1.45 - 1.58: 18418 1.58 - 1.70: 147 1.70 - 1.82: 267 Bond restraints: 35332 Sorted by residual: bond pdb=" O3B G2P T3000 " pdb=" PG G2P T3000 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" O2A G2P T3000 " pdb=" PA G2P T3000 " ideal model delta sigma weight residual 1.513 1.610 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" O2B G2P T3000 " pdb=" PB G2P T3000 " ideal model delta sigma weight residual 1.517 1.610 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C4 G2P T3000 " pdb=" C5 G2P T3000 " ideal model delta sigma weight residual 1.384 1.469 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C6 G2P T3000 " pdb=" N1 G2P T3000 " ideal model delta sigma weight residual 1.402 1.333 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 35327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 46831 2.44 - 4.88: 1049 4.88 - 7.32: 128 7.32 - 9.76: 40 9.76 - 12.21: 9 Bond angle restraints: 48057 Sorted by residual: angle pdb=" N ILE B 696 " pdb=" CA ILE B 696 " pdb=" C ILE B 696 " ideal model delta sigma weight residual 112.96 105.00 7.96 1.00e+00 1.00e+00 6.34e+01 angle pdb=" C SER I 40 " pdb=" N GLN I 41 " pdb=" CA GLN I 41 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C LYS E 103 " pdb=" N ASN E 104 " pdb=" CA ASN E 104 " ideal model delta sigma weight residual 122.46 129.48 -7.02 1.41e+00 5.03e-01 2.48e+01 angle pdb=" C LEU G 49 " pdb=" N ALA G 50 " pdb=" CA ALA G 50 " ideal model delta sigma weight residual 120.97 133.18 -12.21 2.84e+00 1.24e-01 1.85e+01 angle pdb=" N PHE B 954 " pdb=" CA PHE B 954 " pdb=" C PHE B 954 " ideal model delta sigma weight residual 109.81 118.67 -8.86 2.21e+00 2.05e-01 1.61e+01 ... (remaining 48052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 20065 17.47 - 34.93: 950 34.93 - 52.40: 290 52.40 - 69.87: 79 69.87 - 87.33: 18 Dihedral angle restraints: 21402 sinusoidal: 9317 harmonic: 12085 Sorted by residual: dihedral pdb=" CA ASP B 15 " pdb=" C ASP B 15 " pdb=" N PHE B 16 " pdb=" CA PHE B 16 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA LYS A 463 " pdb=" C LYS A 463 " pdb=" N GLU A 464 " pdb=" CA GLU A 464 " ideal model delta harmonic sigma weight residual -180.00 -152.97 -27.03 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASP C 273 " pdb=" C ASP C 273 " pdb=" N THR C 274 " pdb=" CA THR C 274 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 21399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4797 0.090 - 0.179: 543 0.179 - 0.269: 37 0.269 - 0.359: 2 0.359 - 0.449: 1 Chirality restraints: 5380 Sorted by residual: chirality pdb=" CB ILE A1219 " pdb=" CA ILE A1219 " pdb=" CG1 ILE A1219 " pdb=" CG2 ILE A1219 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CB ILE B 207 " pdb=" CA ILE B 207 " pdb=" CG1 ILE B 207 " pdb=" CG2 ILE B 207 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE A 581 " pdb=" CA ILE A 581 " pdb=" CG1 ILE A 581 " pdb=" CG2 ILE A 581 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 5377 not shown) Planarity restraints: 5944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 150 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO E 151 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1044 " 0.016 2.00e-02 2.50e+03 2.15e-02 8.10e+00 pdb=" CG PHE B1044 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE B1044 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE B1044 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B1044 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B1044 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B1044 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1033 " -0.025 2.00e-02 2.50e+03 1.95e-02 7.63e+00 pdb=" CG TYR B1033 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B1033 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B1033 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B1033 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B1033 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B1033 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B1033 " -0.004 2.00e-02 2.50e+03 ... (remaining 5941 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 50 2.39 - 3.02: 16814 3.02 - 3.64: 51322 3.64 - 4.27: 80335 4.27 - 4.90: 131532 Nonbonded interactions: 280053 Sorted by model distance: nonbonded pdb=" OD1 ASP A 627 " pdb="MG MG A1701 " model vdw 1.761 2.170 nonbonded pdb=" O3' C R 20 " pdb="MG MG A1701 " model vdw 1.801 2.170 nonbonded pdb=" OG1 THR A 621 " pdb=" O ALA A 626 " model vdw 2.243 3.040 nonbonded pdb=" O VAL A 483 " pdb=" OG1 THR A 613 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASP A 629 " pdb="MG MG A1701 " model vdw 2.267 2.170 ... (remaining 280048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 42.300 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 0.584 35356 Z= 0.331 Angle : 1.005 44.935 48090 Z= 0.487 Chirality : 0.057 0.449 5380 Planarity : 0.007 0.073 5944 Dihedral : 12.355 87.332 13590 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.14 % Allowed : 3.13 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.42 (0.10), residues: 4092 helix: -4.28 (0.06), residues: 1244 sheet: -2.29 (0.18), residues: 628 loop : -2.27 (0.11), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 920 TYR 0.048 0.003 TYR B1033 PHE 0.049 0.003 PHE B1044 TRP 0.044 0.003 TRP B 836 HIS 0.016 0.002 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00613 (35332) covalent geometry : angle 0.90368 (48057) hydrogen bonds : bond 0.29848 ( 1138) hydrogen bonds : angle 10.82045 ( 3163) metal coordination : bond 0.22738 ( 24) metal coordination : angle 16.81238 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1139 time to evaluate : 1.416 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 52 LEU cc_start: 0.9132 (mm) cc_final: 0.8823 (mt) REVERT: A 238 MET cc_start: 0.7480 (pmm) cc_final: 0.7177 (ptp) REVERT: A 381 SER cc_start: 0.9217 (p) cc_final: 0.8906 (t) REVERT: A 456 VAL cc_start: 0.9714 (p) cc_final: 0.9475 (t) REVERT: A 925 MET cc_start: 0.9234 (tpp) cc_final: 0.9030 (tpp) REVERT: A 1105 ARG cc_start: 0.6902 (ttt90) cc_final: 0.6605 (ttp-110) REVERT: A 1198 THR cc_start: 0.9030 (m) cc_final: 0.8817 (p) REVERT: A 1300 ASN cc_start: 0.7917 (t0) cc_final: 0.7711 (t0) REVERT: A 1588 MET cc_start: 0.8728 (tpt) cc_final: 0.8359 (tpt) REVERT: B 190 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8612 (pp) REVERT: B 255 ASP cc_start: 0.8337 (t70) cc_final: 0.7910 (t0) REVERT: B 288 ILE cc_start: 0.9518 (mm) cc_final: 0.9234 (mm) REVERT: B 304 ASP cc_start: 0.8332 (m-30) cc_final: 0.7962 (t0) REVERT: B 943 ILE cc_start: 0.8369 (pt) cc_final: 0.8067 (mt) REVERT: C 127 THR cc_start: 0.8862 (p) cc_final: 0.8650 (t) REVERT: D 27 LEU cc_start: 0.8117 (mp) cc_final: 0.7687 (mt) REVERT: D 84 SER cc_start: 0.7710 (p) cc_final: 0.7509 (m) REVERT: E 25 ASP cc_start: 0.8378 (m-30) cc_final: 0.8070 (m-30) REVERT: E 58 MET cc_start: 0.8516 (mtp) cc_final: 0.8274 (mtp) REVERT: E 119 SER cc_start: 0.8734 (m) cc_final: 0.8427 (t) REVERT: E 187 TYR cc_start: 0.8793 (t80) cc_final: 0.8331 (t80) REVERT: F 77 ASP cc_start: 0.8433 (p0) cc_final: 0.8203 (p0) REVERT: G 123 TYR cc_start: 0.8311 (m-10) cc_final: 0.7452 (m-80) REVERT: G 159 LYS cc_start: 0.6920 (tttm) cc_final: 0.6707 (tptp) REVERT: H 9 ILE cc_start: 0.9102 (mp) cc_final: 0.8888 (mm) REVERT: H 14 GLU cc_start: 0.8273 (pp20) cc_final: 0.7471 (pp20) REVERT: H 116 TYR cc_start: 0.8477 (m-10) cc_final: 0.8273 (m-80) REVERT: K 138 LYS cc_start: 0.9101 (mmtt) cc_final: 0.8651 (mmtt) REVERT: N 134 ASP cc_start: 0.5182 (m-30) cc_final: 0.4899 (t70) REVERT: N 135 LYS cc_start: 0.5984 (mttm) cc_final: 0.5398 (tppt) REVERT: M 16 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7558 (tp-100) REVERT: M 53 LEU cc_start: 0.7945 (tp) cc_final: 0.7196 (tp) REVERT: M 60 LEU cc_start: 0.7448 (mt) cc_final: 0.7187 (mt) REVERT: M 135 LYS cc_start: 0.8349 (tptt) cc_final: 0.8106 (mtpt) outliers start: 5 outliers final: 3 residues processed: 1141 average time/residue: 0.2540 time to fit residues: 451.4966 Evaluate side-chains 658 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 654 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 1111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.4980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 213 ASN A 559 ASN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN A 880 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS A1454 HIS A1647 ASN B 39 GLN B 45 HIS B 339 GLN B 368 GLN B 456 ASN B 669 GLN B 710 ASN B 896 GLN B 921 HIS ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1045 GLN B1171 ASN C 99 HIS C 172 GLN C 175 GLN C 216 HIS C 301 ASN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN D 81 ASN F 61 HIS F 100 GLN G 121 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS G 216 HIS I 41 GLN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN N 132 GLN M 75 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.092605 restraints weight = 61840.219| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.20 r_work: 0.2984 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35356 Z= 0.212 Angle : 0.715 26.706 48090 Z= 0.365 Chirality : 0.046 0.194 5380 Planarity : 0.006 0.059 5944 Dihedral : 13.359 78.426 5378 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.69 % Allowed : 11.09 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.11), residues: 4092 helix: -2.56 (0.11), residues: 1280 sheet: -1.98 (0.18), residues: 636 loop : -1.67 (0.12), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 305 TYR 0.030 0.002 TYR B1184 PHE 0.037 0.002 PHE B1044 TRP 0.027 0.002 TRP B 836 HIS 0.007 0.001 HIS B 952 Details of bonding type rmsd covalent geometry : bond 0.00492 (35332) covalent geometry : angle 0.68709 (48057) hydrogen bonds : bond 0.05489 ( 1138) hydrogen bonds : angle 6.21943 ( 3163) metal coordination : bond 0.00987 ( 24) metal coordination : angle 7.53613 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 703 time to evaluate : 1.234 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 439 ASP cc_start: 0.8614 (t0) cc_final: 0.8343 (t0) REVERT: A 464 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8060 (tm-30) REVERT: A 833 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9046 (pp) REVERT: A 1300 ASN cc_start: 0.8084 (t0) cc_final: 0.7568 (t0) REVERT: A 1459 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7274 (ttpt) REVERT: A 1474 LEU cc_start: 0.9057 (tt) cc_final: 0.8752 (tt) REVERT: A 1529 MET cc_start: 0.9214 (mmm) cc_final: 0.8759 (mmt) REVERT: B 67 ASP cc_start: 0.8991 (t70) cc_final: 0.8530 (t70) REVERT: B 70 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8003 (mp0) REVERT: B 190 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8717 (pp) REVERT: B 215 MET cc_start: 0.9167 (ptp) cc_final: 0.8606 (ptp) REVERT: B 255 ASP cc_start: 0.8750 (t70) cc_final: 0.8543 (t0) REVERT: B 304 ASP cc_start: 0.8885 (m-30) cc_final: 0.8662 (t0) REVERT: B 456 ASN cc_start: 0.8703 (t0) cc_final: 0.8211 (t0) REVERT: B 477 ASP cc_start: 0.7134 (t0) cc_final: 0.6923 (t0) REVERT: B 943 ILE cc_start: 0.8750 (pt) cc_final: 0.8361 (mt) REVERT: B 1110 ILE cc_start: 0.9114 (mm) cc_final: 0.8912 (mm) REVERT: B 1134 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7875 (mmm160) REVERT: E 25 ASP cc_start: 0.8919 (m-30) cc_final: 0.8654 (m-30) REVERT: E 29 PHE cc_start: 0.9044 (t80) cc_final: 0.8751 (t80) REVERT: E 32 GLN cc_start: 0.8429 (tp40) cc_final: 0.8072 (tm-30) REVERT: E 50 MET cc_start: 0.7855 (tpt) cc_final: 0.7594 (ptp) REVERT: E 58 MET cc_start: 0.8787 (mtp) cc_final: 0.8586 (mtp) REVERT: E 75 MET cc_start: 0.9149 (mtp) cc_final: 0.8901 (mtm) REVERT: E 119 SER cc_start: 0.8884 (m) cc_final: 0.8592 (t) REVERT: E 187 TYR cc_start: 0.9241 (t80) cc_final: 0.8807 (t80) REVERT: F 122 MET cc_start: 0.9260 (mtm) cc_final: 0.9026 (mtt) REVERT: G 45 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8510 (pt) REVERT: G 73 TYR cc_start: 0.8507 (t80) cc_final: 0.8297 (t80) REVERT: G 75 ASN cc_start: 0.8929 (t0) cc_final: 0.8715 (m110) REVERT: G 123 TYR cc_start: 0.8356 (m-10) cc_final: 0.7982 (m-80) REVERT: G 126 GLN cc_start: 0.8933 (pm20) cc_final: 0.8699 (pm20) REVERT: G 159 LYS cc_start: 0.7094 (tttm) cc_final: 0.6814 (tptp) REVERT: H 9 ILE cc_start: 0.9199 (mp) cc_final: 0.8937 (mm) REVERT: H 27 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8485 (mt-10) REVERT: H 103 LYS cc_start: 0.9300 (ttpt) cc_final: 0.9017 (ttmm) REVERT: I 29 GLU cc_start: 0.7778 (tt0) cc_final: 0.7550 (tp30) REVERT: I 61 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7390 (ttm-80) REVERT: J 68 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8635 (ttmt) REVERT: K 124 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9208 (tp) REVERT: K 137 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8277 (tm-30) REVERT: K 138 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8809 (mmtm) REVERT: N 57 LYS cc_start: 0.7928 (tmtt) cc_final: 0.7647 (tmtt) REVERT: N 79 THR cc_start: 0.8617 (t) cc_final: 0.8412 (m) REVERT: N 80 MET cc_start: 0.7884 (ppp) cc_final: 0.7489 (ppp) REVERT: N 134 ASP cc_start: 0.6098 (m-30) cc_final: 0.5333 (t70) REVERT: M 11 GLU cc_start: 0.8150 (tp30) cc_final: 0.7158 (pt0) REVERT: M 16 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7443 (tp-100) REVERT: M 48 LYS cc_start: 0.5026 (tptt) cc_final: 0.4643 (tptt) REVERT: M 51 PHE cc_start: 0.7326 (m-10) cc_final: 0.7043 (m-10) REVERT: M 56 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6955 (mt-10) REVERT: M 57 ASN cc_start: 0.7865 (p0) cc_final: 0.7653 (p0) REVERT: M 67 ASP cc_start: 0.8214 (t0) cc_final: 0.7930 (t0) REVERT: M 82 ASN cc_start: 0.6701 (t0) cc_final: 0.6381 (t0) REVERT: M 91 TYR cc_start: 0.7953 (m-80) cc_final: 0.7641 (m-80) outliers start: 99 outliers final: 51 residues processed: 770 average time/residue: 0.2107 time to fit residues: 262.6080 Evaluate side-chains 641 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 586 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 286 optimal weight: 0.7980 chunk 373 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 48 optimal weight: 0.0050 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 538 ASN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A 880 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN A1141 GLN A1293 HIS A1454 HIS A1581 HIS B 339 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1045 GLN C 172 GLN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN D 81 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS G 237 HIS K 64 GLN K 70 HIS N 51 GLN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.092545 restraints weight = 61582.623| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.20 r_work: 0.2984 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35356 Z= 0.163 Angle : 0.629 18.540 48090 Z= 0.322 Chirality : 0.044 0.211 5380 Planarity : 0.005 0.056 5944 Dihedral : 13.097 78.984 5377 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.13 % Allowed : 12.67 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.12), residues: 4092 helix: -1.39 (0.13), residues: 1279 sheet: -1.55 (0.19), residues: 636 loop : -1.36 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 219 TYR 0.023 0.001 TYR A 995 PHE 0.030 0.002 PHE B1044 TRP 0.024 0.001 TRP B 836 HIS 0.013 0.001 HIS A1293 Details of bonding type rmsd covalent geometry : bond 0.00379 (35332) covalent geometry : angle 0.61052 (48057) hydrogen bonds : bond 0.04288 ( 1138) hydrogen bonds : angle 5.55523 ( 3163) metal coordination : bond 0.00760 ( 24) metal coordination : angle 5.74065 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 635 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8689 (tp) REVERT: A 204 GLU cc_start: 0.8743 (pm20) cc_final: 0.8282 (pt0) REVERT: A 439 ASP cc_start: 0.8608 (t0) cc_final: 0.8319 (t0) REVERT: A 464 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7957 (tm-30) REVERT: A 635 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8600 (ttt) REVERT: A 747 ILE cc_start: 0.9085 (mp) cc_final: 0.8853 (mp) REVERT: A 749 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9227 (tt) REVERT: A 773 ASP cc_start: 0.8864 (t0) cc_final: 0.8648 (t0) REVERT: A 833 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9003 (pp) REVERT: A 937 ASN cc_start: 0.8982 (t0) cc_final: 0.8641 (t0) REVERT: A 1230 SER cc_start: 0.9258 (m) cc_final: 0.8814 (p) REVERT: A 1459 LYS cc_start: 0.7680 (ttmt) cc_final: 0.7222 (ttpt) REVERT: A 1474 LEU cc_start: 0.9085 (tt) cc_final: 0.8742 (tt) REVERT: B 67 ASP cc_start: 0.9005 (t70) cc_final: 0.8593 (t70) REVERT: B 70 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8005 (mp0) REVERT: B 190 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8778 (pp) REVERT: B 255 ASP cc_start: 0.8744 (t70) cc_final: 0.8535 (t0) REVERT: B 304 ASP cc_start: 0.8872 (m-30) cc_final: 0.8619 (t0) REVERT: B 430 MET cc_start: 0.8434 (tmm) cc_final: 0.8122 (tmm) REVERT: B 456 ASN cc_start: 0.8449 (t0) cc_final: 0.8047 (t0) REVERT: B 477 ASP cc_start: 0.7021 (t0) cc_final: 0.6743 (t0) REVERT: B 778 TYR cc_start: 0.9095 (t80) cc_final: 0.8785 (t80) REVERT: B 842 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7558 (mm-30) REVERT: B 943 ILE cc_start: 0.8762 (pt) cc_final: 0.8298 (mt) REVERT: C 127 THR cc_start: 0.9236 (p) cc_final: 0.9014 (t) REVERT: D 38 GLN cc_start: 0.8642 (tt0) cc_final: 0.8238 (tp40) REVERT: E 29 PHE cc_start: 0.9053 (t80) cc_final: 0.8789 (t80) REVERT: E 32 GLN cc_start: 0.8275 (tp40) cc_final: 0.8014 (tm-30) REVERT: E 66 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8539 (pm20) REVERT: E 75 MET cc_start: 0.9056 (mtp) cc_final: 0.8845 (mtm) REVERT: E 119 SER cc_start: 0.8877 (m) cc_final: 0.8587 (t) REVERT: E 196 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8794 (p) REVERT: E 215 MET cc_start: 0.8892 (mmp) cc_final: 0.8627 (mmp) REVERT: F 143 PHE cc_start: 0.9022 (p90) cc_final: 0.8762 (p90) REVERT: G 126 GLN cc_start: 0.8998 (pm20) cc_final: 0.8484 (pm20) REVERT: G 159 LYS cc_start: 0.7085 (tttm) cc_final: 0.6797 (tptp) REVERT: H 9 ILE cc_start: 0.9252 (mp) cc_final: 0.8964 (mm) REVERT: H 80 ARG cc_start: 0.8501 (tpp80) cc_final: 0.8296 (mmm-85) REVERT: H 103 LYS cc_start: 0.9326 (ttpt) cc_final: 0.8867 (ttmm) REVERT: H 115 TYR cc_start: 0.8996 (m-80) cc_final: 0.8401 (m-80) REVERT: I 15 ASP cc_start: 0.8659 (t70) cc_final: 0.8405 (t0) REVERT: I 29 GLU cc_start: 0.7850 (tt0) cc_final: 0.7379 (tp30) REVERT: I 40 SER cc_start: 0.8067 (p) cc_final: 0.7768 (p) REVERT: I 61 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7463 (ttm-80) REVERT: J 68 LYS cc_start: 0.8903 (ttpt) cc_final: 0.8662 (ttmt) REVERT: K 138 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8754 (mmtm) REVERT: N 80 MET cc_start: 0.7644 (ppp) cc_final: 0.7313 (ppp) REVERT: N 134 ASP cc_start: 0.6124 (m-30) cc_final: 0.5293 (t70) REVERT: M 11 GLU cc_start: 0.8082 (tp30) cc_final: 0.7259 (pt0) REVERT: M 16 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7116 (tp-100) REVERT: M 48 LYS cc_start: 0.4935 (tptt) cc_final: 0.4656 (tptt) REVERT: M 67 ASP cc_start: 0.8107 (t0) cc_final: 0.7563 (t0) outliers start: 115 outliers final: 55 residues processed: 709 average time/residue: 0.1925 time to fit residues: 223.8429 Evaluate side-chains 638 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 576 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 57 optimal weight: 0.0670 chunk 138 optimal weight: 0.5980 chunk 194 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 299 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1454 HIS A1648 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN D 81 ASN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.095342 restraints weight = 61251.356| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.20 r_work: 0.3033 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 35356 Z= 0.107 Angle : 0.570 15.388 48090 Z= 0.292 Chirality : 0.043 0.207 5380 Planarity : 0.004 0.057 5944 Dihedral : 12.925 80.030 5377 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.36 % Allowed : 14.81 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.13), residues: 4092 helix: -0.71 (0.14), residues: 1274 sheet: -1.38 (0.19), residues: 652 loop : -1.10 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 119 TYR 0.024 0.001 TYR G 73 PHE 0.025 0.001 PHE B1044 TRP 0.019 0.001 TRP B 836 HIS 0.004 0.001 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00236 (35332) covalent geometry : angle 0.55594 (48057) hydrogen bonds : bond 0.03523 ( 1138) hydrogen bonds : angle 5.13706 ( 3163) metal coordination : bond 0.00509 ( 24) metal coordination : angle 4.79417 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 652 time to evaluate : 1.509 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 130 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8785 (tp) REVERT: A 213 ASN cc_start: 0.8837 (t0) cc_final: 0.8593 (t0) REVERT: A 366 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8106 (ttm-80) REVERT: A 439 ASP cc_start: 0.8582 (t0) cc_final: 0.8329 (t0) REVERT: A 464 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7750 (tm-30) REVERT: A 747 ILE cc_start: 0.8996 (mp) cc_final: 0.8754 (mp) REVERT: A 749 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9233 (tt) REVERT: A 773 ASP cc_start: 0.8889 (t0) cc_final: 0.8633 (t0) REVERT: A 833 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.8982 (pp) REVERT: A 1230 SER cc_start: 0.9252 (m) cc_final: 0.9027 (p) REVERT: A 1459 LYS cc_start: 0.7538 (ttmt) cc_final: 0.7119 (ttpt) REVERT: A 1474 LEU cc_start: 0.8991 (tt) cc_final: 0.8681 (tt) REVERT: B 67 ASP cc_start: 0.8983 (t70) cc_final: 0.8569 (t0) REVERT: B 70 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8046 (mp0) REVERT: B 90 TYR cc_start: 0.6880 (p90) cc_final: 0.6151 (p90) REVERT: B 190 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8713 (pp) REVERT: B 304 ASP cc_start: 0.8827 (m-30) cc_final: 0.8573 (t0) REVERT: B 456 ASN cc_start: 0.8369 (t0) cc_final: 0.7928 (t0) REVERT: B 477 ASP cc_start: 0.6909 (t0) cc_final: 0.6592 (t0) REVERT: B 763 ASP cc_start: 0.8383 (m-30) cc_final: 0.7942 (p0) REVERT: B 778 TYR cc_start: 0.9009 (t80) cc_final: 0.8606 (t80) REVERT: B 842 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7538 (mm-30) REVERT: B 1039 MET cc_start: 0.9263 (mtm) cc_final: 0.8995 (mtm) REVERT: C 127 THR cc_start: 0.9217 (p) cc_final: 0.8986 (t) REVERT: C 315 PHE cc_start: 0.8371 (t80) cc_final: 0.8137 (t80) REVERT: D 38 GLN cc_start: 0.8594 (tt0) cc_final: 0.8217 (tp40) REVERT: D 40 LEU cc_start: 0.8716 (mm) cc_final: 0.8406 (mm) REVERT: E 29 PHE cc_start: 0.9051 (t80) cc_final: 0.8759 (t80) REVERT: E 32 GLN cc_start: 0.8279 (tp40) cc_final: 0.8049 (tm-30) REVERT: E 50 MET cc_start: 0.7853 (tpt) cc_final: 0.7621 (ptp) REVERT: E 66 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8505 (pm20) REVERT: E 119 SER cc_start: 0.8856 (m) cc_final: 0.8568 (t) REVERT: E 215 MET cc_start: 0.8920 (mmp) cc_final: 0.8674 (mmp) REVERT: F 143 PHE cc_start: 0.8856 (p90) cc_final: 0.8655 (p90) REVERT: G 59 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: G 126 GLN cc_start: 0.9019 (pm20) cc_final: 0.8709 (pm20) REVERT: G 159 LYS cc_start: 0.7065 (tttm) cc_final: 0.6814 (tptp) REVERT: H 8 ASP cc_start: 0.8194 (t0) cc_final: 0.7854 (t0) REVERT: H 9 ILE cc_start: 0.9214 (mp) cc_final: 0.8876 (mm) REVERT: H 14 GLU cc_start: 0.8393 (pp20) cc_final: 0.7332 (pp20) REVERT: H 27 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8143 (mt-10) REVERT: H 103 LYS cc_start: 0.9309 (ttpt) cc_final: 0.8851 (ttmm) REVERT: H 115 TYR cc_start: 0.9027 (m-80) cc_final: 0.8430 (m-80) REVERT: I 29 GLU cc_start: 0.7908 (tt0) cc_final: 0.7479 (tp30) REVERT: I 40 SER cc_start: 0.7988 (p) cc_final: 0.7237 (p) REVERT: I 41 GLN cc_start: 0.8631 (pm20) cc_final: 0.7808 (pm20) REVERT: I 60 LEU cc_start: 0.8666 (tp) cc_final: 0.8328 (tt) REVERT: J 68 LYS cc_start: 0.8901 (ttpt) cc_final: 0.8655 (ttmt) REVERT: K 137 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8272 (tm-30) REVERT: K 138 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8549 (mmtt) REVERT: N 27 ASP cc_start: 0.7448 (p0) cc_final: 0.7230 (p0) REVERT: N 29 PHE cc_start: 0.8330 (m-10) cc_final: 0.7969 (m-80) REVERT: N 134 ASP cc_start: 0.6261 (m-30) cc_final: 0.5316 (t70) REVERT: M 11 GLU cc_start: 0.8039 (tp30) cc_final: 0.7249 (pt0) REVERT: M 16 GLN cc_start: 0.7838 (tp-100) cc_final: 0.6735 (tp-100) REVERT: M 37 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7775 (m) REVERT: M 67 ASP cc_start: 0.8252 (t0) cc_final: 0.7664 (t0) outliers start: 87 outliers final: 48 residues processed: 703 average time/residue: 0.2203 time to fit residues: 255.0286 Evaluate side-chains 635 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 579 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 303 optimal weight: 9.9990 chunk 298 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 134 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 374 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 350 optimal weight: 0.0770 overall best weight: 2.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 378 HIS ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1454 HIS A1648 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 301 ASN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS H 139 ASN M 75 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.093037 restraints weight = 61507.879| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.20 r_work: 0.2993 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35356 Z= 0.147 Angle : 0.583 17.614 48090 Z= 0.298 Chirality : 0.044 0.196 5380 Planarity : 0.004 0.054 5944 Dihedral : 12.867 80.511 5375 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.13 % Allowed : 15.33 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.13), residues: 4092 helix: -0.34 (0.15), residues: 1275 sheet: -1.24 (0.20), residues: 647 loop : -0.99 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 265 TYR 0.027 0.001 TYR A 995 PHE 0.027 0.001 PHE B1044 TRP 0.020 0.001 TRP B 836 HIS 0.004 0.001 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00348 (35332) covalent geometry : angle 0.56889 (48057) hydrogen bonds : bond 0.03580 ( 1138) hydrogen bonds : angle 4.98758 ( 3163) metal coordination : bond 0.00691 ( 24) metal coordination : angle 4.84101 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 574 time to evaluate : 1.276 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 213 ASN cc_start: 0.8919 (t0) cc_final: 0.8673 (t0) REVERT: A 353 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8559 (m-30) REVERT: A 366 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8108 (ttm-80) REVERT: A 439 ASP cc_start: 0.8621 (t0) cc_final: 0.8371 (t0) REVERT: A 464 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7743 (tm-30) REVERT: A 747 ILE cc_start: 0.9008 (mp) cc_final: 0.8770 (mp) REVERT: A 749 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9244 (tt) REVERT: A 773 ASP cc_start: 0.8987 (t0) cc_final: 0.8694 (t0) REVERT: A 833 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.8964 (pp) REVERT: A 1301 GLU cc_start: 0.8330 (tp30) cc_final: 0.8071 (mt-10) REVERT: A 1459 LYS cc_start: 0.7572 (ttmt) cc_final: 0.7186 (ttpt) REVERT: A 1474 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8753 (tt) REVERT: B 67 ASP cc_start: 0.8975 (t70) cc_final: 0.8745 (t70) REVERT: B 70 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8042 (mp0) REVERT: B 90 TYR cc_start: 0.7010 (p90) cc_final: 0.6167 (p90) REVERT: B 304 ASP cc_start: 0.8799 (m-30) cc_final: 0.8517 (t0) REVERT: B 430 MET cc_start: 0.8579 (tmm) cc_final: 0.8083 (tmm) REVERT: B 456 ASN cc_start: 0.8343 (t0) cc_final: 0.8139 (t0) REVERT: B 477 ASP cc_start: 0.6873 (t0) cc_final: 0.6567 (t0) REVERT: B 763 ASP cc_start: 0.8452 (m-30) cc_final: 0.8014 (p0) REVERT: B 778 TYR cc_start: 0.9064 (t80) cc_final: 0.8679 (t80) REVERT: B 787 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8777 (ppp) REVERT: B 842 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7691 (mm-30) REVERT: B 912 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8533 (mm-40) REVERT: B 1055 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8940 (pp) REVERT: C 127 THR cc_start: 0.9244 (p) cc_final: 0.9014 (t) REVERT: C 315 PHE cc_start: 0.8314 (t80) cc_final: 0.8052 (t80) REVERT: D 38 GLN cc_start: 0.8592 (tt0) cc_final: 0.8222 (tp40) REVERT: E 32 GLN cc_start: 0.8226 (tp40) cc_final: 0.8009 (tm-30) REVERT: E 66 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8494 (pm20) REVERT: E 110 PHE cc_start: 0.8506 (t80) cc_final: 0.7970 (t80) REVERT: E 119 SER cc_start: 0.8811 (m) cc_final: 0.8577 (t) REVERT: E 215 MET cc_start: 0.8844 (mmp) cc_final: 0.8604 (mmp) REVERT: F 122 MET cc_start: 0.9365 (mtt) cc_final: 0.9086 (mtt) REVERT: F 143 PHE cc_start: 0.8929 (p90) cc_final: 0.8636 (p90) REVERT: G 123 TYR cc_start: 0.8120 (m-10) cc_final: 0.7822 (m-80) REVERT: G 126 GLN cc_start: 0.8940 (pm20) cc_final: 0.8652 (pm20) REVERT: G 159 LYS cc_start: 0.7038 (tttm) cc_final: 0.6759 (tptp) REVERT: G 234 ARG cc_start: 0.7777 (ttt180) cc_final: 0.7437 (ttt180) REVERT: H 9 ILE cc_start: 0.9206 (mp) cc_final: 0.8954 (mm) REVERT: H 27 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8500 (mt-10) REVERT: H 103 LYS cc_start: 0.9361 (ttpt) cc_final: 0.8886 (ttmm) REVERT: H 115 TYR cc_start: 0.9044 (m-80) cc_final: 0.8522 (m-80) REVERT: I 29 GLU cc_start: 0.7900 (tt0) cc_final: 0.7469 (tp30) REVERT: I 41 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8565 (pm20) REVERT: I 64 LYS cc_start: 0.6993 (mmmt) cc_final: 0.6686 (tttt) REVERT: K 138 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8584 (mmtt) REVERT: N 29 PHE cc_start: 0.8346 (m-10) cc_final: 0.8078 (m-80) REVERT: N 134 ASP cc_start: 0.6292 (m-30) cc_final: 0.5374 (t70) REVERT: M 11 GLU cc_start: 0.7932 (tp30) cc_final: 0.7254 (pt0) REVERT: M 16 GLN cc_start: 0.7604 (tp-100) cc_final: 0.7356 (tp-100) REVERT: M 26 PHE cc_start: 0.7693 (m-80) cc_final: 0.7457 (m-80) REVERT: M 48 LYS cc_start: 0.4758 (tptt) cc_final: 0.4464 (tptt) REVERT: M 67 ASP cc_start: 0.8259 (t0) cc_final: 0.7628 (t0) outliers start: 115 outliers final: 73 residues processed: 649 average time/residue: 0.2194 time to fit residues: 234.4563 Evaluate side-chains 632 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 549 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain N residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 83 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 351 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 403 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 378 HIS ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A 840 ASN ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1454 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 702 ASN B 923 GLN B 952 HIS ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS N 170 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.087251 restraints weight = 61644.684| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.17 r_work: 0.2893 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 35356 Z= 0.326 Angle : 0.736 22.923 48090 Z= 0.371 Chirality : 0.049 0.184 5380 Planarity : 0.005 0.054 5944 Dihedral : 13.124 81.596 5375 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.08 % Allowed : 15.22 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.13), residues: 4092 helix: -0.43 (0.15), residues: 1268 sheet: -1.39 (0.20), residues: 657 loop : -1.03 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1039 TYR 0.024 0.002 TYR A 995 PHE 0.034 0.002 PHE B1044 TRP 0.029 0.002 TRP B 836 HIS 0.007 0.002 HIS A 795 Details of bonding type rmsd covalent geometry : bond 0.00775 (35332) covalent geometry : angle 0.71456 (48057) hydrogen bonds : bond 0.04392 ( 1138) hydrogen bonds : angle 5.31481 ( 3163) metal coordination : bond 0.01505 ( 24) metal coordination : angle 6.75709 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 545 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8795 (tp) REVERT: A 204 GLU cc_start: 0.8734 (pm20) cc_final: 0.8270 (pt0) REVERT: A 366 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8270 (ttm-80) REVERT: A 464 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7862 (tm-30) REVERT: A 562 LEU cc_start: 0.8998 (tm) cc_final: 0.8766 (tp) REVERT: A 747 ILE cc_start: 0.9095 (mp) cc_final: 0.8837 (tt) REVERT: A 749 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9246 (tt) REVERT: A 773 ASP cc_start: 0.9116 (t0) cc_final: 0.8838 (t0) REVERT: A 833 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.8956 (pp) REVERT: A 1459 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7477 (ttpt) REVERT: A 1474 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8756 (tt) REVERT: B 67 ASP cc_start: 0.9064 (t70) cc_final: 0.8848 (t70) REVERT: B 70 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8233 (mp0) REVERT: B 90 TYR cc_start: 0.7230 (p90) cc_final: 0.5822 (p90) REVERT: B 304 ASP cc_start: 0.8900 (m-30) cc_final: 0.8664 (t0) REVERT: B 430 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8214 (tmm) REVERT: B 448 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.7921 (ttm170) REVERT: B 456 ASN cc_start: 0.8587 (t0) cc_final: 0.8324 (t0) REVERT: B 477 ASP cc_start: 0.7373 (t0) cc_final: 0.7150 (t70) REVERT: B 778 TYR cc_start: 0.9232 (t80) cc_final: 0.9017 (t80) REVERT: B 787 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8444 (ptt) REVERT: B 815 ARG cc_start: 0.7122 (ptt90) cc_final: 0.6778 (ptt90) REVERT: B 842 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7957 (mm-30) REVERT: B 1039 MET cc_start: 0.9355 (mtm) cc_final: 0.8879 (mtm) REVERT: C 124 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8196 (mp0) REVERT: D 38 GLN cc_start: 0.8620 (tt0) cc_final: 0.8263 (tp40) REVERT: E 32 GLN cc_start: 0.8317 (tp40) cc_final: 0.8097 (tm-30) REVERT: E 66 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8608 (pp20) REVERT: E 196 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8784 (p) REVERT: F 122 MET cc_start: 0.9343 (mtt) cc_final: 0.9036 (mtt) REVERT: F 124 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8462 (mt-10) REVERT: G 123 TYR cc_start: 0.8389 (m-10) cc_final: 0.8107 (m-80) REVERT: G 126 GLN cc_start: 0.9055 (pm20) cc_final: 0.8722 (pm20) REVERT: G 159 LYS cc_start: 0.7152 (tttm) cc_final: 0.6789 (tptp) REVERT: H 27 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8696 (mt-10) REVERT: H 103 LYS cc_start: 0.9385 (ttpt) cc_final: 0.9008 (ttmm) REVERT: H 115 TYR cc_start: 0.9133 (m-80) cc_final: 0.8655 (m-80) REVERT: I 29 GLU cc_start: 0.7977 (tt0) cc_final: 0.7753 (tp30) REVERT: I 41 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8586 (pm20) REVERT: I 50 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8007 (t) REVERT: I 64 LYS cc_start: 0.7469 (mmmt) cc_final: 0.7120 (tttt) REVERT: K 138 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8606 (mmtt) REVERT: N 29 PHE cc_start: 0.8458 (m-10) cc_final: 0.8253 (m-80) REVERT: M 11 GLU cc_start: 0.7922 (tp30) cc_final: 0.7294 (pt0) REVERT: M 16 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7038 (tm-30) REVERT: M 67 ASP cc_start: 0.8371 (t0) cc_final: 0.7659 (t0) outliers start: 150 outliers final: 100 residues processed: 648 average time/residue: 0.2306 time to fit residues: 244.7411 Evaluate side-chains 622 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 511 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 375 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 274 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 379 optimal weight: 5.9990 chunk 382 optimal weight: 20.0000 chunk 400 optimal weight: 10.0000 chunk 297 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 378 HIS ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN A1088 HIS A1454 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 63 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 ASN G 216 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.089067 restraints weight = 61791.980| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.18 r_work: 0.2926 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35356 Z= 0.209 Angle : 0.645 19.016 48090 Z= 0.326 Chirality : 0.045 0.213 5380 Planarity : 0.004 0.067 5944 Dihedral : 13.051 81.814 5375 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.64 % Allowed : 16.28 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.13), residues: 4092 helix: -0.28 (0.15), residues: 1280 sheet: -1.36 (0.19), residues: 668 loop : -0.97 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 397 TYR 0.025 0.002 TYR E 187 PHE 0.029 0.002 PHE B1044 TRP 0.030 0.001 TRP B 836 HIS 0.008 0.001 HIS N 170 Details of bonding type rmsd covalent geometry : bond 0.00498 (35332) covalent geometry : angle 0.62682 (48057) hydrogen bonds : bond 0.03869 ( 1138) hydrogen bonds : angle 5.11460 ( 3163) metal coordination : bond 0.01033 ( 24) metal coordination : angle 5.76581 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 546 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8787 (tp) REVERT: A 321 LYS cc_start: 0.9284 (tttt) cc_final: 0.8966 (tttm) REVERT: A 366 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8233 (ttm-80) REVERT: A 453 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8672 (tp) REVERT: A 464 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7831 (tm-30) REVERT: A 747 ILE cc_start: 0.9041 (mp) cc_final: 0.8815 (tt) REVERT: A 749 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9258 (tt) REVERT: A 773 ASP cc_start: 0.9115 (t0) cc_final: 0.8872 (t0) REVERT: A 833 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.8992 (pp) REVERT: A 1459 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7350 (ttpt) REVERT: A 1474 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8749 (tt) REVERT: B 67 ASP cc_start: 0.9007 (t70) cc_final: 0.8751 (t70) REVERT: B 70 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8178 (mp0) REVERT: B 90 TYR cc_start: 0.7047 (p90) cc_final: 0.5654 (p90) REVERT: B 430 MET cc_start: 0.8559 (tmm) cc_final: 0.8214 (tmm) REVERT: B 448 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.7901 (ttm170) REVERT: B 456 ASN cc_start: 0.8541 (t0) cc_final: 0.8254 (t0) REVERT: B 477 ASP cc_start: 0.7060 (t0) cc_final: 0.6846 (t70) REVERT: B 561 ILE cc_start: 0.8762 (mp) cc_final: 0.8472 (mt) REVERT: B 778 TYR cc_start: 0.9142 (t80) cc_final: 0.8773 (t80) REVERT: B 787 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8375 (ptt) REVERT: B 815 ARG cc_start: 0.7142 (ptt90) cc_final: 0.6870 (ptt90) REVERT: B 912 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8633 (mm-40) REVERT: B 1039 MET cc_start: 0.9366 (mtm) cc_final: 0.8904 (mtm) REVERT: C 48 ASP cc_start: 0.7784 (t0) cc_final: 0.7581 (t0) REVERT: C 124 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8158 (mp0) REVERT: D 38 GLN cc_start: 0.8583 (tt0) cc_final: 0.8212 (tp40) REVERT: E 32 GLN cc_start: 0.8326 (tp40) cc_final: 0.8089 (tm-30) REVERT: E 196 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8782 (p) REVERT: F 122 MET cc_start: 0.9400 (mtt) cc_final: 0.9121 (mtt) REVERT: G 85 GLU cc_start: 0.8697 (pt0) cc_final: 0.8317 (pt0) REVERT: G 126 GLN cc_start: 0.9046 (pm20) cc_final: 0.8704 (pm20) REVERT: G 159 LYS cc_start: 0.7153 (tttm) cc_final: 0.6795 (tptp) REVERT: H 14 GLU cc_start: 0.8537 (pp20) cc_final: 0.8212 (pp20) REVERT: H 27 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8695 (mt-10) REVERT: H 103 LYS cc_start: 0.9371 (ttpt) cc_final: 0.8922 (ttmm) REVERT: H 115 TYR cc_start: 0.9078 (m-80) cc_final: 0.8565 (m-80) REVERT: I 15 ASP cc_start: 0.8769 (t70) cc_final: 0.8543 (t0) REVERT: I 50 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8014 (t) REVERT: I 61 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7202 (ttm-80) REVERT: I 64 LYS cc_start: 0.7422 (mmmt) cc_final: 0.7116 (tttt) REVERT: M 11 GLU cc_start: 0.7736 (tp30) cc_final: 0.7259 (pt0) REVERT: M 16 GLN cc_start: 0.7782 (tp-100) cc_final: 0.6984 (tm-30) REVERT: M 63 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7244 (mm-30) REVERT: M 67 ASP cc_start: 0.8373 (t0) cc_final: 0.7673 (t0) outliers start: 134 outliers final: 89 residues processed: 636 average time/residue: 0.2085 time to fit residues: 218.6437 Evaluate side-chains 619 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 520 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 221 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 307 optimal weight: 0.6980 chunk 226 optimal weight: 9.9990 chunk 261 optimal weight: 0.5980 chunk 235 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 210 optimal weight: 0.3980 chunk 198 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1454 HIS ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS M 71 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.093513 restraints weight = 60999.139| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.19 r_work: 0.3005 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35356 Z= 0.108 Angle : 0.579 15.839 48090 Z= 0.297 Chirality : 0.043 0.155 5380 Planarity : 0.004 0.053 5944 Dihedral : 12.878 82.294 5375 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.66 % Allowed : 17.64 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.13), residues: 4092 helix: 0.05 (0.15), residues: 1275 sheet: -1.05 (0.20), residues: 616 loop : -0.83 (0.14), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 61 TYR 0.024 0.001 TYR A 995 PHE 0.024 0.001 PHE B1044 TRP 0.026 0.001 TRP B 836 HIS 0.008 0.001 HIS N 170 Details of bonding type rmsd covalent geometry : bond 0.00241 (35332) covalent geometry : angle 0.56811 (48057) hydrogen bonds : bond 0.03306 ( 1138) hydrogen bonds : angle 4.79546 ( 3163) metal coordination : bond 0.00551 ( 24) metal coordination : angle 4.35288 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 592 time to evaluate : 0.942 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 43 HIS cc_start: 0.8760 (m-70) cc_final: 0.8340 (m170) REVERT: A 130 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8555 (tp) REVERT: A 213 ASN cc_start: 0.8836 (t0) cc_final: 0.8625 (t0) REVERT: A 366 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8116 (ttm-80) REVERT: A 400 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8122 (m-40) REVERT: A 749 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9254 (tt) REVERT: A 833 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.8962 (pp) REVERT: A 928 MET cc_start: 0.8966 (ptp) cc_final: 0.8725 (ptp) REVERT: A 1459 LYS cc_start: 0.7533 (ttmt) cc_final: 0.7187 (ttpt) REVERT: A 1474 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8763 (tt) REVERT: B 67 ASP cc_start: 0.8960 (t70) cc_final: 0.8688 (t70) REVERT: B 70 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8029 (mp0) REVERT: B 90 TYR cc_start: 0.6888 (p90) cc_final: 0.5816 (p90) REVERT: B 456 ASN cc_start: 0.8421 (t0) cc_final: 0.8167 (t0) REVERT: B 477 ASP cc_start: 0.6848 (t0) cc_final: 0.6607 (t0) REVERT: B 778 TYR cc_start: 0.9006 (t80) cc_final: 0.8500 (t80) REVERT: B 787 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8792 (ppp) REVERT: B 909 ARG cc_start: 0.8805 (mmt90) cc_final: 0.8486 (mmt-90) REVERT: B 912 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8498 (mm-40) REVERT: B 935 ASP cc_start: 0.8499 (m-30) cc_final: 0.8099 (m-30) REVERT: B 1039 MET cc_start: 0.9307 (mtm) cc_final: 0.9060 (mtm) REVERT: B 1057 MET cc_start: 0.8862 (mmt) cc_final: 0.8623 (mmt) REVERT: C 47 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.6791 (mm) REVERT: C 93 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8989 (pm20) REVERT: C 124 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8196 (mp0) REVERT: D 38 GLN cc_start: 0.8577 (tt0) cc_final: 0.8208 (tp40) REVERT: F 143 PHE cc_start: 0.9120 (p90) cc_final: 0.8705 (p90) REVERT: G 85 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: G 123 TYR cc_start: 0.8512 (m-80) cc_final: 0.7975 (m-80) REVERT: G 159 LYS cc_start: 0.7112 (tttm) cc_final: 0.6839 (tptp) REVERT: H 103 LYS cc_start: 0.9273 (ttpt) cc_final: 0.8867 (ttmm) REVERT: H 115 TYR cc_start: 0.9015 (m-80) cc_final: 0.8518 (m-80) REVERT: H 123 MET cc_start: 0.8879 (ttp) cc_final: 0.8602 (ttp) REVERT: I 29 GLU cc_start: 0.7992 (tp30) cc_final: 0.7664 (tp30) REVERT: I 50 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7975 (t) REVERT: I 61 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.7086 (ttm-80) REVERT: I 64 LYS cc_start: 0.7424 (mmmt) cc_final: 0.7172 (tttt) REVERT: N 57 LYS cc_start: 0.7717 (tmtt) cc_final: 0.6805 (ptpt) REVERT: N 175 TYR cc_start: 0.6513 (m-80) cc_final: 0.6280 (m-80) REVERT: M 11 GLU cc_start: 0.7680 (tp30) cc_final: 0.7234 (pt0) REVERT: M 16 GLN cc_start: 0.7484 (tp-100) cc_final: 0.6946 (tp40) outliers start: 98 outliers final: 63 residues processed: 652 average time/residue: 0.2160 time to fit residues: 231.2226 Evaluate side-chains 616 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 541 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 195 optimal weight: 7.9990 chunk 336 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 106 optimal weight: 0.4980 chunk 119 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 274 optimal weight: 10.0000 chunk 253 optimal weight: 0.0970 chunk 332 optimal weight: 6.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 538 ASN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1454 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS K 99 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.092813 restraints weight = 61125.015| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.18 r_work: 0.2991 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35356 Z= 0.125 Angle : 0.580 14.713 48090 Z= 0.297 Chirality : 0.043 0.201 5380 Planarity : 0.004 0.059 5944 Dihedral : 12.812 82.753 5373 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.53 % Allowed : 17.94 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.13), residues: 4092 helix: 0.22 (0.15), residues: 1279 sheet: -1.10 (0.20), residues: 641 loop : -0.77 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 634 TYR 0.022 0.001 TYR G 73 PHE 0.025 0.001 PHE B1044 TRP 0.022 0.001 TRP B 836 HIS 0.007 0.001 HIS N 170 Details of bonding type rmsd covalent geometry : bond 0.00293 (35332) covalent geometry : angle 0.56975 (48057) hydrogen bonds : bond 0.03370 ( 1138) hydrogen bonds : angle 4.74822 ( 3163) metal coordination : bond 0.00658 ( 24) metal coordination : angle 4.17290 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 551 time to evaluate : 1.958 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 43 HIS cc_start: 0.8740 (m-70) cc_final: 0.8283 (m170) REVERT: A 130 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8433 (tp) REVERT: A 213 ASN cc_start: 0.8882 (t0) cc_final: 0.8653 (t0) REVERT: A 366 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8058 (ttm-80) REVERT: A 562 LEU cc_start: 0.8777 (tm) cc_final: 0.8563 (tp) REVERT: A 589 MET cc_start: 0.9009 (mmm) cc_final: 0.8499 (mmm) REVERT: A 749 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9242 (tt) REVERT: A 833 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.8888 (pp) REVERT: A 1459 LYS cc_start: 0.7542 (ttmt) cc_final: 0.7189 (ttpt) REVERT: A 1474 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8779 (tt) REVERT: B 67 ASP cc_start: 0.8920 (t70) cc_final: 0.8650 (t70) REVERT: B 70 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8097 (mp0) REVERT: B 90 TYR cc_start: 0.6913 (p90) cc_final: 0.5668 (p90) REVERT: B 430 MET cc_start: 0.8504 (tmm) cc_final: 0.8200 (tmm) REVERT: B 456 ASN cc_start: 0.8450 (t0) cc_final: 0.8172 (t0) REVERT: B 477 ASP cc_start: 0.6917 (t0) cc_final: 0.6645 (t0) REVERT: B 561 ILE cc_start: 0.8685 (mp) cc_final: 0.8434 (mt) REVERT: B 778 TYR cc_start: 0.9015 (t80) cc_final: 0.8635 (t80) REVERT: B 787 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8778 (ppp) REVERT: B 912 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8486 (mm-40) REVERT: B 935 ASP cc_start: 0.8584 (m-30) cc_final: 0.8242 (m-30) REVERT: B 1039 MET cc_start: 0.9288 (mtm) cc_final: 0.8910 (mtm) REVERT: B 1057 MET cc_start: 0.8844 (mmt) cc_final: 0.8617 (mmt) REVERT: C 93 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.9014 (pm20) REVERT: C 124 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8170 (mp0) REVERT: D 38 GLN cc_start: 0.8608 (tt0) cc_final: 0.8247 (tp40) REVERT: F 122 MET cc_start: 0.9310 (mtm) cc_final: 0.8989 (mtt) REVERT: F 143 PHE cc_start: 0.9075 (p90) cc_final: 0.8754 (p90) REVERT: G 85 GLU cc_start: 0.8518 (pt0) cc_final: 0.8206 (pt0) REVERT: G 123 TYR cc_start: 0.8444 (m-80) cc_final: 0.7893 (m-80) REVERT: G 159 LYS cc_start: 0.7109 (tttm) cc_final: 0.6834 (tptp) REVERT: H 103 LYS cc_start: 0.9297 (ttpt) cc_final: 0.8887 (ttmm) REVERT: H 115 TYR cc_start: 0.9027 (m-80) cc_final: 0.8611 (m-80) REVERT: I 50 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8030 (t) REVERT: N 57 LYS cc_start: 0.7723 (tmtt) cc_final: 0.6780 (ptpt) REVERT: N 134 ASP cc_start: 0.5342 (m-30) cc_final: 0.3942 (t70) REVERT: N 175 TYR cc_start: 0.6474 (m-80) cc_final: 0.6268 (m-80) REVERT: M 11 GLU cc_start: 0.7671 (tp30) cc_final: 0.7221 (pt0) REVERT: M 16 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7494 (tp-100) REVERT: M 67 ASP cc_start: 0.8341 (t0) cc_final: 0.7592 (t0) outliers start: 93 outliers final: 66 residues processed: 609 average time/residue: 0.2336 time to fit residues: 235.1780 Evaluate side-chains 606 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 531 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 980 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 202 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 325 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 285 optimal weight: 10.0000 chunk 305 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1454 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS H 35 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.091341 restraints weight = 61134.114| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.15 r_work: 0.2966 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35356 Z= 0.163 Angle : 0.606 15.230 48090 Z= 0.310 Chirality : 0.044 0.206 5380 Planarity : 0.004 0.067 5944 Dihedral : 12.838 82.724 5373 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.56 % Allowed : 18.08 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.13), residues: 4092 helix: 0.28 (0.15), residues: 1272 sheet: -1.07 (0.20), residues: 650 loop : -0.78 (0.14), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 634 TYR 0.023 0.001 TYR G 73 PHE 0.027 0.001 PHE B1044 TRP 0.023 0.001 TRP B 836 HIS 0.006 0.001 HIS N 170 Details of bonding type rmsd covalent geometry : bond 0.00388 (35332) covalent geometry : angle 0.59474 (48057) hydrogen bonds : bond 0.03522 ( 1138) hydrogen bonds : angle 4.79010 ( 3163) metal coordination : bond 0.00808 ( 24) metal coordination : angle 4.55886 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 535 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.8748 (m-70) cc_final: 0.8287 (m170) REVERT: A 130 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8660 (tp) REVERT: A 213 ASN cc_start: 0.8935 (t0) cc_final: 0.8702 (t0) REVERT: A 366 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8088 (ttm-80) REVERT: A 562 LEU cc_start: 0.8829 (tm) cc_final: 0.8615 (tp) REVERT: A 589 MET cc_start: 0.9068 (mmm) cc_final: 0.8566 (mmm) REVERT: A 749 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9290 (tt) REVERT: A 833 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9006 (pp) REVERT: A 1301 GLU cc_start: 0.8505 (tp30) cc_final: 0.8146 (mt-10) REVERT: A 1459 LYS cc_start: 0.7680 (ttmt) cc_final: 0.7311 (ttpt) REVERT: A 1474 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8798 (tt) REVERT: B 67 ASP cc_start: 0.8934 (t70) cc_final: 0.8660 (t70) REVERT: B 70 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8136 (mp0) REVERT: B 430 MET cc_start: 0.8498 (tmm) cc_final: 0.8202 (tmm) REVERT: B 456 ASN cc_start: 0.8477 (t0) cc_final: 0.8163 (t0) REVERT: B 477 ASP cc_start: 0.6973 (t0) cc_final: 0.6753 (t0) REVERT: B 561 ILE cc_start: 0.8719 (mp) cc_final: 0.8479 (mt) REVERT: B 778 TYR cc_start: 0.9139 (t80) cc_final: 0.8783 (t80) REVERT: B 787 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8838 (ppp) REVERT: B 912 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8567 (mm-40) REVERT: B 935 ASP cc_start: 0.8586 (m-30) cc_final: 0.8287 (m-30) REVERT: B 1039 MET cc_start: 0.9335 (mtm) cc_final: 0.8920 (mtm) REVERT: C 93 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.9009 (pm20) REVERT: C 124 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8196 (mp0) REVERT: D 38 GLN cc_start: 0.8628 (tt0) cc_final: 0.8264 (tp40) REVERT: F 122 MET cc_start: 0.9349 (mtm) cc_final: 0.9035 (mtt) REVERT: F 143 PHE cc_start: 0.9106 (p90) cc_final: 0.8765 (p90) REVERT: G 85 GLU cc_start: 0.8499 (pt0) cc_final: 0.8213 (pt0) REVERT: G 123 TYR cc_start: 0.8452 (m-80) cc_final: 0.7932 (m-80) REVERT: G 159 LYS cc_start: 0.7109 (tttm) cc_final: 0.6847 (tptp) REVERT: G 234 ARG cc_start: 0.7677 (ttt180) cc_final: 0.7192 (mtp180) REVERT: H 103 LYS cc_start: 0.9316 (ttpt) cc_final: 0.8891 (ttmm) REVERT: H 115 TYR cc_start: 0.9034 (m-80) cc_final: 0.8606 (m-80) REVERT: H 136 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8509 (mmtt) REVERT: I 29 GLU cc_start: 0.8015 (tp30) cc_final: 0.7762 (tp30) REVERT: I 32 GLN cc_start: 0.8366 (mt0) cc_final: 0.7890 (mt0) REVERT: I 50 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.8006 (t) REVERT: I 64 LYS cc_start: 0.7471 (mmmt) cc_final: 0.7110 (ptmt) REVERT: N 57 LYS cc_start: 0.7684 (tmtt) cc_final: 0.6721 (ptpt) REVERT: N 175 TYR cc_start: 0.6498 (m-80) cc_final: 0.6286 (m-80) REVERT: M 11 GLU cc_start: 0.7515 (tp30) cc_final: 0.7188 (pt0) REVERT: M 16 GLN cc_start: 0.7771 (tp-100) cc_final: 0.7429 (tp-100) REVERT: M 67 ASP cc_start: 0.8047 (t0) cc_final: 0.7333 (t0) outliers start: 94 outliers final: 72 residues processed: 594 average time/residue: 0.2259 time to fit residues: 222.5177 Evaluate side-chains 599 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 518 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 227 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 151 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 chunk 331 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1454 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.089868 restraints weight = 61338.596| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.16 r_work: 0.2943 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 35356 Z= 0.214 Angle : 0.641 16.200 48090 Z= 0.326 Chirality : 0.046 0.200 5380 Planarity : 0.004 0.064 5944 Dihedral : 12.897 82.839 5373 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.53 % Allowed : 17.99 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.13), residues: 4092 helix: 0.22 (0.15), residues: 1276 sheet: -1.08 (0.20), residues: 636 loop : -0.81 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 634 TYR 0.021 0.002 TYR G 73 PHE 0.029 0.002 PHE B1044 TRP 0.025 0.001 TRP B 836 HIS 0.005 0.001 HIS N 170 Details of bonding type rmsd covalent geometry : bond 0.00510 (35332) covalent geometry : angle 0.62797 (48057) hydrogen bonds : bond 0.03728 ( 1138) hydrogen bonds : angle 4.87052 ( 3163) metal coordination : bond 0.00989 ( 24) metal coordination : angle 4.95791 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9795.45 seconds wall clock time: 168 minutes 30.79 seconds (10110.79 seconds total)