Starting phenix.real_space_refine on Tue Sep 15 01:32:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hko_0238/09_2026/6hko_0238.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hko_0238/09_2026/6hko_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6hko_0238/09_2026/6hko_0238.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hko_0238/09_2026/6hko_0238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hko_0238/09_2026/6hko_0238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hko_0238/09_2026/6hko_0238.map" model { file = "/net/cci-nas-00/data/ceres_data/6hko_0238/09_2026/6hko_0238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hko_0238/09_2026/6hko_0238.cif" } 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): 0.25s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 7.54, per 1000 atoms: 0.22 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: 3.09 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.57 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: 9.73 Time building geometry restraints manager: 4.12 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=" C3' DC T 37 " pdb=" C2' DC T 37 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.44e+01 ... (remaining 35327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 46773 2.44 - 4.88: 1107 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=" O4' DC T 18 " pdb=" C4' DC T 18 " pdb=" C3' DC T 18 " ideal model delta sigma weight residual 106.00 102.97 3.03 6.00e-01 2.78e+00 2.55e+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=" O4' DC T 11 " pdb=" C4' DC T 11 " pdb=" C3' DC T 11 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.06e+01 ... (remaining 48052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 20035 17.47 - 34.93: 937 34.93 - 52.40: 287 52.40 - 69.87: 71 69.87 - 87.33: 14 Dihedral angle restraints: 21344 sinusoidal: 9259 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=" O5' A R 12 " pdb=" C5' A R 12 " pdb=" C4' A R 12 " pdb=" C3' A R 12 " ideal model delta sinusoidal sigma weight residual 60.00 93.35 -33.35 3 6.40e+00 2.44e-02 3.06e+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 ... (remaining 21341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4765 0.090 - 0.180: 566 0.180 - 0.269: 46 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: 1.510 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: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 42.260 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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= 0.362 Angle : 1.016 44.935 48090 Z= 0.518 Chirality : 0.059 0.449 5380 Planarity : 0.007 0.073 5944 Dihedral : 12.176 87.332 13532 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 are 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/Z covalent geometry : bond 0.00624 / 0.30 (35332) covalent geometry : angle 0.91577 / 0.51 (48057) hydrogen bonds : bond 0.29848 / 19.56 ( 1138) hydrogen bonds : angle 10.82045 / 7.43 ( 3163) metal coordination : bond 0.22738 / 15.81 ( 24) metal coordination : angle 16.81238 / 10.80 ( 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 : 1.323 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: 0.5181 (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: 0.2595 time to fit residues: 466.4602 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 : 1.396 ------------------------------------------------------------------------------- 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... A 93 GLN A 213 ASN A 559 ASN A 642 ASN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN 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 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN B 368 GLN B 456 ASN B 669 GLN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 HIS 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 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN G 121 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS G 216 HIS G 237 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 = 0.3558 r_free = 0.3558 target = 0.122199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.093000 restraints weight = 61890.254| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.20 r_work: 0.2992 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35356 Z= 0.222 Angle : 0.754 29.465 48090 Z= 0.387 Chirality : 0.048 0.218 5380 Planarity : 0.006 0.054 5944 Dihedral : 13.062 78.239 5320 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.43 % Rotamer: Outliers : 2.85 % Allowed : 10.63 % Favored : 86.52 % 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 are not related in a simple way. whole: -3.15 (0.11), residues: 4092 helix: -2.58 (0.11), residues: 1270 sheet: -1.90 (0.19), residues: 627 loop : -1.78 (0.12), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 109 TYR 0.030 0.002 TYR B1184 PHE 0.036 0.002 PHE B1044 TRP 0.024 0.002 TRP B 836 HIS 0.008 0.001 HIS G 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (35332) covalent geometry : angle 0.72509 / 0.39 (48057) hydrogen bonds : bond 0.06294 / 4.09 ( 1138) hydrogen bonds : angle 6.51032 / 4.47 ( 3163) metal coordination : bond 0.01287 / 0.95 ( 24) metal coordination : angle 7.88629 / 6.36 ( 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: 105 poor density : 697 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 LEU cc_start: 0.8952 (mt) cc_final: 0.8745 (mp) REVERT: A 439 ASP cc_start: 0.8582 (t0) cc_final: 0.8271 (t0) REVERT: A 833 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9067 (pp) REVERT: A 1004 GLU cc_start: 0.8853 (tp30) cc_final: 0.8421 (mm-30) REVERT: A 1300 ASN cc_start: 0.8090 (t0) cc_final: 0.7581 (t0) REVERT: A 1459 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7386 (ttpt) REVERT: A 1529 MET cc_start: 0.9152 (mmm) cc_final: 0.8637 (mmt) REVERT: A 1588 MET cc_start: 0.9114 (tpt) cc_final: 0.8872 (tpt) REVERT: B 67 ASP cc_start: 0.8941 (t70) cc_final: 0.8542 (t70) REVERT: B 190 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8696 (pp) REVERT: B 215 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8888 (ptm) REVERT: B 255 ASP cc_start: 0.8683 (t70) cc_final: 0.8445 (t0) REVERT: B 288 ILE cc_start: 0.9539 (mm) cc_final: 0.9282 (mt) REVERT: B 298 LYS cc_start: 0.8841 (mttt) cc_final: 0.8638 (mptt) REVERT: B 304 ASP cc_start: 0.8972 (m-30) cc_final: 0.8646 (t0) REVERT: B 456 ASN cc_start: 0.8624 (t0) cc_final: 0.8108 (t0) REVERT: B 943 ILE cc_start: 0.8713 (pt) cc_final: 0.8354 (mt) REVERT: B 1134 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7887 (mmm160) REVERT: C 185 VAL cc_start: 0.9029 (p) cc_final: 0.8823 (m) REVERT: D 84 SER cc_start: 0.7540 (p) cc_final: 0.7338 (m) REVERT: E 25 ASP cc_start: 0.8922 (m-30) cc_final: 0.8655 (m-30) REVERT: E 32 GLN cc_start: 0.8391 (tp40) cc_final: 0.8062 (tm-30) REVERT: E 50 MET cc_start: 0.7844 (tpt) cc_final: 0.7584 (ptp) REVERT: E 75 MET cc_start: 0.9203 (mtp) cc_final: 0.8996 (mtm) REVERT: E 119 SER cc_start: 0.8870 (m) cc_final: 0.8599 (t) REVERT: E 187 TYR cc_start: 0.9277 (t80) cc_final: 0.8856 (t80) REVERT: F 77 ASP cc_start: 0.9045 (p0) cc_final: 0.8808 (p0) REVERT: G 75 ASN cc_start: 0.8915 (t0) cc_final: 0.8565 (m-40) REVERT: G 123 TYR cc_start: 0.8316 (m-10) cc_final: 0.7974 (m-80) REVERT: G 126 GLN cc_start: 0.8872 (pm20) cc_final: 0.8473 (pm20) REVERT: G 159 LYS cc_start: 0.7132 (tttm) cc_final: 0.6851 (tptp) REVERT: H 9 ILE cc_start: 0.9134 (mp) cc_final: 0.8897 (mm) REVERT: H 27 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8708 (mt-10) REVERT: H 103 LYS cc_start: 0.9309 (ttpt) cc_final: 0.8950 (ttmm) REVERT: I 29 GLU cc_start: 0.7765 (tt0) cc_final: 0.7255 (tp30) REVERT: J 68 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8650 (ttmt) REVERT: K 124 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9175 (tp) REVERT: N 79 THR cc_start: 0.8365 (t) cc_final: 0.8150 (m) REVERT: N 80 MET cc_start: 0.7795 (ppp) cc_final: 0.7434 (ppp) REVERT: N 134 ASP cc_start: 0.5914 (m-30) cc_final: 0.5236 (t70) REVERT: M 10 ILE cc_start: 0.7202 (mm) cc_final: 0.6913 (mm) REVERT: M 11 GLU cc_start: 0.8087 (tp30) cc_final: 0.7823 (tp30) REVERT: M 16 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7442 (tp-100) REVERT: M 48 LYS cc_start: 0.4870 (tptt) cc_final: 0.4522 (tptt) REVERT: M 67 ASP cc_start: 0.8228 (t0) cc_final: 0.8004 (t0) REVERT: M 88 ILE cc_start: 0.8474 (tt) cc_final: 0.7937 (tt) REVERT: M 91 TYR cc_start: 0.8000 (m-80) cc_final: 0.7762 (m-80) REVERT: M 135 LYS cc_start: 0.8048 (tptt) cc_final: 0.7749 (mtpt) outliers start: 105 outliers final: 51 residues processed: 766 average time/residue: 0.2334 time to fit residues: 290.9723 Evaluate side-chains 645 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 590 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 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 764 SER Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 811 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 878 ARG Chi-restraints excluded: chain A residue 941 SER 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 16 PHE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 337 VAL 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 883 GLU 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 E residue 131 THR Chi-restraints excluded: chain F residue 82 THR 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 H residue 37 LYS Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain K residue 97 SER 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 N residue 171 PHE Chi-restraints excluded: chain M residue 37 THR 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: 6.9990 chunk 373 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 227 optimal weight: 5.9990 chunk 221 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN A 880 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN A1088 HIS A1141 GLN A1454 HIS A1581 HIS B 39 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 921 HIS 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 K 70 HIS ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.091974 restraints weight = 61675.437| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.19 r_work: 0.2972 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35356 Z= 0.194 Angle : 0.678 21.503 48090 Z= 0.347 Chirality : 0.047 0.199 5380 Planarity : 0.005 0.071 5944 Dihedral : 12.895 79.524 5319 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.34 % Allowed : 12.01 % Favored : 84.64 % 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 are not related in a simple way. whole: -2.35 (0.12), residues: 4092 helix: -1.55 (0.13), residues: 1290 sheet: -1.61 (0.19), residues: 632 loop : -1.47 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 651 TYR 0.024 0.002 TYR A 995 PHE 0.032 0.002 PHE B1044 TRP 0.021 0.001 TRP B 836 HIS 0.017 0.001 HIS A1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (35332) covalent geometry : angle 0.65763 / 0.35 (48057) hydrogen bonds : bond 0.04840 / 3.13 ( 1138) hydrogen bonds : angle 5.80366 / 3.98 ( 3163) metal coordination : bond 0.00802 / 0.60 ( 24) metal coordination : angle 6.30349 / 4.97 ( 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 752 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 629 time to evaluate : 1.351 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 130 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8597 (tp) REVERT: A 204 GLU cc_start: 0.8744 (pm20) cc_final: 0.8289 (pt0) REVERT: A 439 ASP cc_start: 0.8619 (t0) cc_final: 0.8217 (t0) REVERT: A 635 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8812 (ttt) REVERT: A 747 ILE cc_start: 0.9147 (mp) cc_final: 0.8900 (mp) REVERT: A 749 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9201 (tt) REVERT: A 773 ASP cc_start: 0.8850 (t0) cc_final: 0.8624 (t0) REVERT: A 833 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9028 (pp) REVERT: A 1230 SER cc_start: 0.9264 (m) cc_final: 0.8778 (p) REVERT: A 1459 LYS cc_start: 0.7691 (ttmt) cc_final: 0.7274 (ttpt) REVERT: A 1474 LEU cc_start: 0.9054 (tt) cc_final: 0.8739 (tt) REVERT: A 1588 MET cc_start: 0.9066 (tpt) cc_final: 0.8833 (tpt) REVERT: B 67 ASP cc_start: 0.9056 (t70) cc_final: 0.8647 (t70) REVERT: B 70 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8077 (mp0) REVERT: B 90 TYR cc_start: 0.6322 (p90) cc_final: 0.5875 (p90) REVERT: B 190 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8719 (pp) REVERT: B 255 ASP cc_start: 0.8747 (t70) cc_final: 0.8545 (t0) REVERT: B 304 ASP cc_start: 0.8881 (m-30) cc_final: 0.8627 (t0) REVERT: B 456 ASN cc_start: 0.8458 (t0) cc_final: 0.8008 (t0) REVERT: B 473 GLN cc_start: 0.7964 (pt0) cc_final: 0.6722 (tp-100) REVERT: B 943 ILE cc_start: 0.8757 (pt) cc_final: 0.8330 (mt) REVERT: C 299 ILE cc_start: 0.9317 (mt) cc_final: 0.9085 (mm) REVERT: D 26 GLN cc_start: 0.8484 (tm-30) cc_final: 0.7862 (tm-30) REVERT: E 29 PHE cc_start: 0.9065 (t80) cc_final: 0.8775 (t80) REVERT: E 32 GLN cc_start: 0.8335 (tp40) cc_final: 0.8102 (tm-30) REVERT: E 66 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8554 (pm20) REVERT: E 119 SER cc_start: 0.8877 (m) cc_final: 0.8604 (t) REVERT: E 187 TYR cc_start: 0.9275 (t80) cc_final: 0.8999 (t80) REVERT: E 196 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8769 (p) REVERT: F 143 PHE cc_start: 0.9068 (p90) cc_final: 0.8745 (p90) REVERT: G 75 ASN cc_start: 0.8943 (t0) cc_final: 0.8674 (m110) REVERT: G 123 TYR cc_start: 0.8352 (m-10) cc_final: 0.7957 (m-80) REVERT: G 126 GLN cc_start: 0.8989 (pm20) cc_final: 0.8620 (pm20) REVERT: G 159 LYS cc_start: 0.7110 (tttm) cc_final: 0.6830 (tptp) REVERT: H 9 ILE cc_start: 0.9251 (mp) cc_final: 0.8968 (mm) REVERT: H 14 GLU cc_start: 0.8489 (pp20) cc_final: 0.7915 (pp20) REVERT: H 27 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8587 (mt-10) REVERT: H 34 ASP cc_start: 0.8234 (p0) cc_final: 0.7963 (m-30) REVERT: H 80 ARG cc_start: 0.8517 (tpp80) cc_final: 0.8308 (mmm-85) REVERT: H 103 LYS cc_start: 0.9331 (ttpt) cc_final: 0.8938 (ttmm) REVERT: H 115 TYR cc_start: 0.8966 (m-80) cc_final: 0.8383 (m-80) REVERT: I 29 GLU cc_start: 0.7858 (tt0) cc_final: 0.7341 (tp30) REVERT: J 68 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8689 (ttmt) REVERT: K 138 LYS cc_start: 0.9083 (mptt) cc_final: 0.8627 (mmtm) REVERT: N 29 PHE cc_start: 0.8366 (m-10) cc_final: 0.8060 (m-80) REVERT: N 80 MET cc_start: 0.7837 (ppp) cc_final: 0.7452 (ppp) REVERT: N 134 ASP cc_start: 0.6156 (m-30) cc_final: 0.5304 (t70) REVERT: M 11 GLU cc_start: 0.8042 (tp30) cc_final: 0.7104 (mt-10) REVERT: M 16 GLN cc_start: 0.7720 (tp-100) cc_final: 0.6537 (tp-100) REVERT: M 56 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7009 (mt-10) REVERT: M 67 ASP cc_start: 0.8167 (t0) cc_final: 0.7674 (t0) REVERT: M 82 ASN cc_start: 0.6561 (t0) cc_final: 0.6247 (t0) REVERT: M 92 LYS cc_start: 0.8856 (tttp) cc_final: 0.8642 (mttm) outliers start: 123 outliers final: 70 residues processed: 713 average time/residue: 0.2262 time to fit residues: 265.7397 Evaluate side-chains 646 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 568 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 555 LYS 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 849 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1272 VAL 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 121 VAL Chi-restraints excluded: chain B residue 124 SER 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 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 402 VAL Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 737 SER Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 806 THR 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 1033 TYR Chi-restraints excluded: chain B residue 1054 SER 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 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 232 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 8 ILE Chi-restraints excluded: chain I residue 24 LEU 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 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 37 THR Chi-restraints excluded: chain M residue 56 GLU Chi-restraints excluded: chain M residue 98 SER 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: 9.9990 chunk 138 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 chunk 299 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 ASN ** 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 547 HIS B 702 ASN B 923 GLN 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 63 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 GLN N 170 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.119378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089895 restraints weight = 61501.080| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.17 r_work: 0.2939 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 35356 Z= 0.237 Angle : 0.679 20.792 48090 Z= 0.347 Chirality : 0.047 0.205 5380 Planarity : 0.005 0.058 5944 Dihedral : 12.886 79.648 5319 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.72 % Allowed : 13.35 % Favored : 82.93 % 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 are not related in a simple way. whole: -1.96 (0.13), residues: 4092 helix: -1.02 (0.14), residues: 1288 sheet: -1.62 (0.19), residues: 661 loop : -1.30 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1130 TYR 0.023 0.002 TYR A 995 PHE 0.033 0.002 PHE B1044 TRP 0.025 0.001 TRP B 836 HIS 0.006 0.001 HIS B 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 (35332) covalent geometry : angle 0.66038 / 0.35 (48057) hydrogen bonds : bond 0.04447 / 2.87 ( 1138) hydrogen bonds : angle 5.55791 / 3.82 ( 3163) metal coordination : bond 0.00968 / 0.68 ( 24) metal coordination : angle 5.98972 / 4.74 ( 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 722 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 585 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.8759 (pm20) cc_final: 0.8288 (pt0) REVERT: A 366 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8022 (ttm-80) REVERT: A 439 ASP cc_start: 0.8659 (t0) cc_final: 0.8364 (t0) REVERT: A 749 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9232 (tt) REVERT: A 773 ASP cc_start: 0.8958 (t0) cc_final: 0.8677 (t0) REVERT: A 833 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.8982 (pp) REVERT: A 1230 SER cc_start: 0.9266 (m) cc_final: 0.8866 (p) REVERT: A 1250 GLN cc_start: 0.8653 (mt0) cc_final: 0.8208 (mt0) REVERT: A 1459 LYS cc_start: 0.7743 (ttmt) cc_final: 0.7328 (ttpt) REVERT: A 1474 LEU cc_start: 0.9057 (tt) cc_final: 0.8741 (tt) REVERT: A 1631 ARG cc_start: 0.7863 (ttt180) cc_final: 0.7432 (ttm170) REVERT: B 67 ASP cc_start: 0.9085 (t70) cc_final: 0.8715 (t70) REVERT: B 70 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8144 (mp0) REVERT: B 255 ASP cc_start: 0.8734 (t70) cc_final: 0.8532 (t0) REVERT: B 304 ASP cc_start: 0.8892 (m-30) cc_final: 0.8624 (t0) REVERT: B 415 GLU cc_start: 0.8818 (tp30) cc_final: 0.8559 (tp30) REVERT: B 456 ASN cc_start: 0.8490 (t0) cc_final: 0.8253 (t0) REVERT: B 787 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8463 (ptt) REVERT: B 1039 MET cc_start: 0.9280 (mtm) cc_final: 0.8960 (mtm) REVERT: B 1184 TYR cc_start: 0.9045 (t80) cc_final: 0.8788 (t80) REVERT: C 127 THR cc_start: 0.9192 (p) cc_final: 0.8990 (t) REVERT: D 26 GLN cc_start: 0.8643 (tm-30) cc_final: 0.7841 (tm-30) REVERT: E 29 PHE cc_start: 0.9053 (t80) cc_final: 0.8770 (t80) REVERT: E 66 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: E 110 PHE cc_start: 0.8742 (t80) cc_final: 0.8368 (t80) REVERT: E 119 SER cc_start: 0.8875 (m) cc_final: 0.8588 (t) REVERT: E 187 TYR cc_start: 0.9329 (t80) cc_final: 0.9016 (t80) REVERT: E 215 MET cc_start: 0.8876 (mmp) cc_final: 0.8388 (mmp) REVERT: G 85 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: G 123 TYR cc_start: 0.8327 (m-10) cc_final: 0.7916 (m-80) REVERT: G 126 GLN cc_start: 0.8986 (pm20) cc_final: 0.8590 (pm20) REVERT: G 159 LYS cc_start: 0.7081 (tttm) cc_final: 0.6795 (tptp) REVERT: H 14 GLU cc_start: 0.8508 (pp20) cc_final: 0.7817 (pp20) REVERT: H 27 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8544 (mt-10) REVERT: H 80 ARG cc_start: 0.8544 (tpp80) cc_final: 0.8336 (mmm-85) REVERT: H 103 LYS cc_start: 0.9373 (ttpt) cc_final: 0.8961 (ttmm) REVERT: H 115 TYR cc_start: 0.9023 (m-80) cc_final: 0.8403 (m-80) REVERT: I 16 LEU cc_start: 0.8954 (tt) cc_final: 0.8656 (tt) REVERT: I 29 GLU cc_start: 0.7939 (tt0) cc_final: 0.7730 (tp30) REVERT: I 40 SER cc_start: 0.7879 (p) cc_final: 0.7101 (p) REVERT: I 41 GLN cc_start: 0.8675 (pm20) cc_final: 0.7880 (pm20) REVERT: K 68 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8162 (mm-30) REVERT: N 29 PHE cc_start: 0.8469 (m-10) cc_final: 0.8129 (m-80) REVERT: M 11 GLU cc_start: 0.8038 (tp30) cc_final: 0.6998 (pt0) REVERT: M 16 GLN cc_start: 0.7765 (tp-100) cc_final: 0.6988 (tp-100) REVERT: M 41 TYR cc_start: 0.7617 (m-10) cc_final: 0.7008 (m-10) REVERT: M 67 ASP cc_start: 0.8243 (t0) cc_final: 0.7612 (t0) outliers start: 137 outliers final: 91 residues processed: 673 average time/residue: 0.2265 time to fit residues: 250.1083 Evaluate side-chains 632 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 535 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 197 LEU 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 391 THR Chi-restraints excluded: chain A residue 395 LEU 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 543 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU 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 849 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1577 VAL Chi-restraints excluded: chain A residue 1611 MET 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 124 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 167 SER 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 300 SER 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 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 674 ILE 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 784 ASP 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 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 B residue 1189 LEU 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 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 77 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU 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 51 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 40 LEU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 98 SER 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: 10.0000 chunk 298 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 317 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 374 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 350 optimal weight: 0.0030 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN ** 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** A1293 HIS A1336 GLN A1454 HIS A1648 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN 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 ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS H 35 GLN K 102 ASN N 170 HIS M 71 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.092367 restraints weight = 61323.376| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.19 r_work: 0.2982 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35356 Z= 0.128 Angle : 0.607 23.078 48090 Z= 0.310 Chirality : 0.044 0.183 5380 Planarity : 0.004 0.055 5944 Dihedral : 12.742 80.237 5315 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.32 % Allowed : 14.92 % Favored : 81.76 % 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 are not related in a simple way. whole: -1.57 (0.13), residues: 4092 helix: -0.60 (0.14), residues: 1297 sheet: -1.43 (0.20), residues: 658 loop : -1.10 (0.14), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 109 TYR 0.023 0.001 TYR A 995 PHE 0.027 0.001 PHE B1044 TRP 0.022 0.001 TRP B 836 HIS 0.005 0.001 HIS B 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (35332) covalent geometry : angle 0.58836 / 0.31 (48057) hydrogen bonds : bond 0.03859 / 2.50 ( 1138) hydrogen bonds : angle 5.29954 / 3.64 ( 3163) metal coordination : bond 0.00967 / 0.72 ( 24) metal coordination : angle 5.78312 / 4.78 ( 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 724 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 602 time to evaluate : 1.375 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 204 GLU cc_start: 0.8744 (pm20) cc_final: 0.8266 (pt0) REVERT: A 366 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8040 (ttm-80) REVERT: A 439 ASP cc_start: 0.8654 (t0) cc_final: 0.8341 (t0) REVERT: A 562 LEU cc_start: 0.8754 (tm) cc_final: 0.8464 (tp) REVERT: A 747 ILE cc_start: 0.9036 (mp) cc_final: 0.8800 (mp) REVERT: A 773 ASP cc_start: 0.8970 (t0) cc_final: 0.8680 (t0) REVERT: A 833 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.8966 (pp) REVERT: A 1230 SER cc_start: 0.9271 (m) cc_final: 0.8937 (p) REVERT: A 1459 LYS cc_start: 0.7672 (ttmt) cc_final: 0.7274 (ttpt) REVERT: A 1474 LEU cc_start: 0.9022 (tt) cc_final: 0.8703 (tt) REVERT: A 1588 MET cc_start: 0.8975 (tpt) cc_final: 0.8574 (tpt) REVERT: A 1613 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8819 (ttp) REVERT: B 67 ASP cc_start: 0.9069 (t70) cc_final: 0.8602 (t70) REVERT: B 70 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8102 (mp0) REVERT: B 430 MET cc_start: 0.8443 (tmm) cc_final: 0.8143 (tmm) REVERT: B 456 ASN cc_start: 0.8420 (t0) cc_final: 0.8096 (t0) REVERT: B 778 TYR cc_start: 0.9070 (t80) cc_final: 0.8779 (t80) REVERT: B 912 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8558 (mm-40) REVERT: C 35 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8768 (mtmm) REVERT: C 127 THR cc_start: 0.9261 (p) cc_final: 0.9033 (t) REVERT: D 26 GLN cc_start: 0.8630 (tm-30) cc_final: 0.7995 (tm-30) REVERT: E 50 MET cc_start: 0.7786 (tpt) cc_final: 0.7548 (ptp) REVERT: E 66 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8507 (pm20) REVERT: E 119 SER cc_start: 0.8839 (m) cc_final: 0.8564 (t) REVERT: E 187 TYR cc_start: 0.9278 (t80) cc_final: 0.8944 (t80) REVERT: E 215 MET cc_start: 0.8822 (mmp) cc_final: 0.8398 (mmp) REVERT: F 122 MET cc_start: 0.9307 (mtm) cc_final: 0.9015 (mtt) REVERT: G 75 ASN cc_start: 0.9002 (t0) cc_final: 0.8705 (m110) REVERT: G 126 GLN cc_start: 0.8959 (pm20) cc_final: 0.8569 (pm20) REVERT: G 159 LYS cc_start: 0.7096 (tttm) cc_final: 0.6804 (tptp) REVERT: H 103 LYS cc_start: 0.9339 (ttpt) cc_final: 0.8886 (ttmm) REVERT: H 115 TYR cc_start: 0.9039 (m-80) cc_final: 0.8454 (m-80) REVERT: H 116 TYR cc_start: 0.8913 (m-80) cc_final: 0.8634 (m-80) REVERT: K 68 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8164 (mm-30) REVERT: N 29 PHE cc_start: 0.8402 (m-10) cc_final: 0.8114 (m-80) REVERT: M 11 GLU cc_start: 0.7866 (tp30) cc_final: 0.7010 (pt0) REVERT: M 16 GLN cc_start: 0.7782 (tp-100) cc_final: 0.6894 (tp-100) REVERT: M 41 TYR cc_start: 0.7408 (m-10) cc_final: 0.6853 (m-10) REVERT: M 67 ASP cc_start: 0.8257 (t0) cc_final: 0.7659 (t0) REVERT: M 92 LYS cc_start: 0.8850 (tttp) cc_final: 0.8630 (mttp) outliers start: 122 outliers final: 73 residues processed: 681 average time/residue: 0.2206 time to fit residues: 248.2485 Evaluate side-chains 622 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 543 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 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 391 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 678 VAL 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 982 VAL Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1613 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 SER 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 300 SER 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 626 ILE Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 784 ASP 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 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 B residue 1111 LEU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 73 SER 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 124 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 232 THR Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain I residue 24 LEU 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 J residue 7 CYS Chi-restraints excluded: chain K residue 111 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 53 LEU Chi-restraints excluded: chain M residue 71 GLN Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 83 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 351 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 403 optimal weight: 0.1980 chunk 256 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** A1088 HIS A1454 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN C 172 GLN C 301 ASN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS N 170 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090788 restraints weight = 61245.329| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.18 r_work: 0.2956 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35356 Z= 0.186 Angle : 0.624 20.712 48090 Z= 0.319 Chirality : 0.045 0.211 5380 Planarity : 0.004 0.055 5944 Dihedral : 12.717 80.536 5315 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.67 % Allowed : 15.36 % Favored : 80.97 % 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 are not related in a simple way. whole: -1.40 (0.13), residues: 4092 helix: -0.39 (0.14), residues: 1293 sheet: -1.39 (0.19), residues: 656 loop : -1.03 (0.14), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 909 TYR 0.031 0.002 TYR B 90 PHE 0.030 0.001 PHE B1044 TRP 0.020 0.001 TRP B 836 HIS 0.007 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (35332) covalent geometry : angle 0.60797 / 0.32 (48057) hydrogen bonds : bond 0.03893 / 2.51 ( 1138) hydrogen bonds : angle 5.21371 / 3.60 ( 3163) metal coordination : bond 0.00974 / 0.72 ( 24) metal coordination : angle 5.42872 / 4.43 ( 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 692 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 557 time to evaluate : 1.398 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 321 LYS cc_start: 0.9238 (tttt) cc_final: 0.8907 (tttm) REVERT: A 366 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8060 (ttm-80) REVERT: A 439 ASP cc_start: 0.8661 (t0) cc_final: 0.8378 (t0) REVERT: A 562 LEU cc_start: 0.8805 (tm) cc_final: 0.8544 (tp) REVERT: A 747 ILE cc_start: 0.9050 (mp) cc_final: 0.8832 (mp) REVERT: A 749 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9244 (tt) REVERT: A 773 ASP cc_start: 0.9040 (t0) cc_final: 0.8746 (t0) REVERT: A 833 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.8953 (pp) REVERT: A 1230 SER cc_start: 0.9262 (m) cc_final: 0.9047 (p) REVERT: A 1459 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7315 (ttpt) REVERT: A 1474 LEU cc_start: 0.9024 (tt) cc_final: 0.8716 (tt) REVERT: B 67 ASP cc_start: 0.9032 (t70) cc_final: 0.8629 (t70) REVERT: B 70 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8119 (mp0) REVERT: B 90 TYR cc_start: 0.7072 (p90) cc_final: 0.6173 (p90) REVERT: B 430 MET cc_start: 0.8598 (tmm) cc_final: 0.8264 (tmm) REVERT: B 456 ASN cc_start: 0.8424 (t0) cc_final: 0.8151 (t0) REVERT: B 503 VAL cc_start: 0.9416 (OUTLIER) cc_final: 0.9197 (m) REVERT: B 778 TYR cc_start: 0.9126 (t80) cc_final: 0.8868 (t80) REVERT: B 787 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8372 (ptt) REVERT: B 909 ARG cc_start: 0.8715 (mmt-90) cc_final: 0.8507 (mmt-90) REVERT: C 35 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8769 (mtmm) REVERT: C 127 THR cc_start: 0.9287 (p) cc_final: 0.9056 (t) REVERT: D 26 GLN cc_start: 0.8627 (tm-30) cc_final: 0.7979 (tm-30) REVERT: E 66 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: E 110 PHE cc_start: 0.8638 (t80) cc_final: 0.8163 (t80) REVERT: E 119 SER cc_start: 0.8799 (m) cc_final: 0.8579 (t) REVERT: E 187 TYR cc_start: 0.9329 (t80) cc_final: 0.9117 (t80) REVERT: E 215 MET cc_start: 0.8857 (mmp) cc_final: 0.8400 (mmp) REVERT: F 122 MET cc_start: 0.9330 (mtm) cc_final: 0.9076 (mtt) REVERT: G 123 TYR cc_start: 0.8275 (m-10) cc_final: 0.7959 (m-80) REVERT: G 126 GLN cc_start: 0.8968 (pm20) cc_final: 0.8566 (pm20) REVERT: G 159 LYS cc_start: 0.7122 (tttm) cc_final: 0.6838 (tptp) REVERT: H 27 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8633 (mt-10) REVERT: H 45 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8235 (tm-30) REVERT: H 103 LYS cc_start: 0.9363 (ttpt) cc_final: 0.8889 (ttmm) REVERT: H 115 TYR cc_start: 0.9061 (m-80) cc_final: 0.8490 (m-80) REVERT: H 116 TYR cc_start: 0.8993 (m-80) cc_final: 0.8748 (m-80) REVERT: I 29 GLU cc_start: 0.7738 (tp30) cc_final: 0.7394 (tp30) REVERT: K 138 LYS cc_start: 0.8996 (tptt) cc_final: 0.8479 (mmtt) REVERT: N 29 PHE cc_start: 0.8375 (m-10) cc_final: 0.8122 (m-80) REVERT: M 11 GLU cc_start: 0.7773 (tp30) cc_final: 0.7032 (pt0) REVERT: M 16 GLN cc_start: 0.7830 (tp-100) cc_final: 0.6910 (tp-100) REVERT: M 26 PHE cc_start: 0.7702 (m-80) cc_final: 0.7272 (m-80) REVERT: M 41 TYR cc_start: 0.7601 (m-10) cc_final: 0.7023 (m-10) REVERT: M 63 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7209 (mm-30) REVERT: M 67 ASP cc_start: 0.8279 (t0) cc_final: 0.7647 (t0) outliers start: 135 outliers final: 92 residues processed: 644 average time/residue: 0.2219 time to fit residues: 236.0967 Evaluate side-chains 638 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 539 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 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 413 LEU Chi-restraints excluded: chain A residue 415 ASP 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 866 LYS Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1577 VAL 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 124 SER 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 478 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 VAL 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 784 ASP 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 980 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 35 LYS 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 D residue 86 ILE 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 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 232 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU 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 J residue 7 CYS 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 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 53 LEU 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: 10.0000 chunk 274 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 379 optimal weight: 7.9990 chunk 382 optimal weight: 50.0000 chunk 400 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** A1088 HIS A1454 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 499 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 93 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN M 75 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.087946 restraints weight = 61985.677| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.16 r_work: 0.2907 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 35356 Z= 0.291 Angle : 0.711 21.905 48090 Z= 0.362 Chirality : 0.049 0.186 5380 Planarity : 0.005 0.068 5944 Dihedral : 12.815 80.562 5315 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.83 % Allowed : 15.74 % Favored : 80.43 % 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 are not related in a simple way. whole: -1.42 (0.13), residues: 4092 helix: -0.41 (0.14), residues: 1286 sheet: -1.44 (0.20), residues: 649 loop : -1.03 (0.14), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 909 TYR 0.023 0.002 TYR B1184 PHE 0.035 0.002 PHE B1044 TRP 0.026 0.002 TRP B 836 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.29 (35332) covalent geometry : angle 0.69346 / 0.36 (48057) hydrogen bonds : bond 0.04281 / 2.76 ( 1138) hydrogen bonds : angle 5.33529 / 3.69 ( 3163) metal coordination : bond 0.01327 / 0.96 ( 24) metal coordination : angle 6.05348 / 4.87 ( 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 685 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 544 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8810 (tp) REVERT: A 204 GLU cc_start: 0.8676 (pm20) cc_final: 0.8228 (pt0) REVERT: A 366 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8200 (ttm-80) REVERT: A 439 ASP cc_start: 0.8739 (t0) cc_final: 0.8479 (t0) REVERT: A 562 LEU cc_start: 0.8926 (tm) cc_final: 0.8673 (tp) REVERT: A 747 ILE cc_start: 0.9095 (mp) cc_final: 0.8882 (mp) REVERT: A 749 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9253 (tt) REVERT: A 773 ASP cc_start: 0.9093 (t0) cc_final: 0.8815 (t0) REVERT: A 833 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.8945 (pp) REVERT: A 1230 SER cc_start: 0.9257 (m) cc_final: 0.9004 (p) REVERT: A 1459 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7474 (ttpt) REVERT: A 1474 LEU cc_start: 0.9039 (tt) cc_final: 0.8741 (tt) REVERT: A 1631 ARG cc_start: 0.8021 (ttt180) cc_final: 0.7702 (ttm170) REVERT: B 67 ASP cc_start: 0.9101 (t70) cc_final: 0.8683 (t70) REVERT: B 90 TYR cc_start: 0.7284 (p90) cc_final: 0.6117 (p90) REVERT: B 430 MET cc_start: 0.8481 (tmm) cc_final: 0.8122 (tmm) REVERT: B 456 ASN cc_start: 0.8515 (t0) cc_final: 0.8247 (t0) REVERT: B 778 TYR cc_start: 0.9205 (t80) cc_final: 0.9000 (t80) REVERT: B 787 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8464 (ptt) REVERT: B 912 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8692 (mm-40) REVERT: B 1134 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7971 (mmm160) REVERT: B 1184 TYR cc_start: 0.9238 (t80) cc_final: 0.9021 (t80) REVERT: C 35 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8777 (mtmm) REVERT: C 124 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8193 (mp0) REVERT: D 26 GLN cc_start: 0.8681 (tm-30) cc_final: 0.7976 (tm-30) REVERT: E 66 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8607 (pp20) REVERT: E 110 PHE cc_start: 0.8801 (t80) cc_final: 0.8314 (t80) REVERT: E 187 TYR cc_start: 0.9367 (t80) cc_final: 0.9056 (t80) REVERT: F 122 MET cc_start: 0.9367 (mtm) cc_final: 0.9117 (mtt) REVERT: G 85 GLU cc_start: 0.8572 (pt0) cc_final: 0.8074 (pt0) REVERT: G 123 TYR cc_start: 0.8363 (m-10) cc_final: 0.8158 (m-80) REVERT: G 126 GLN cc_start: 0.8994 (pm20) cc_final: 0.8605 (pm20) REVERT: G 159 LYS cc_start: 0.7146 (tttm) cc_final: 0.6779 (tptp) REVERT: H 27 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8708 (mt-10) REVERT: H 45 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8282 (tm-30) REVERT: H 96 VAL cc_start: 0.9247 (p) cc_final: 0.9020 (t) REVERT: H 103 LYS cc_start: 0.9382 (ttpt) cc_final: 0.8903 (ttmm) REVERT: H 115 TYR cc_start: 0.9103 (m-80) cc_final: 0.8510 (m-80) REVERT: H 138 GLU cc_start: 0.9137 (pm20) cc_final: 0.8857 (pm20) REVERT: K 138 LYS cc_start: 0.9000 (tptt) cc_final: 0.8749 (mptt) REVERT: N 29 PHE cc_start: 0.8463 (m-10) cc_final: 0.8227 (m-80) REVERT: M 11 GLU cc_start: 0.7782 (tp30) cc_final: 0.7181 (pt0) REVERT: M 16 GLN cc_start: 0.7749 (tp-100) cc_final: 0.7326 (tp-100) REVERT: M 41 TYR cc_start: 0.7803 (m-10) cc_final: 0.7271 (m-10) REVERT: M 63 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7248 (mm-30) REVERT: M 67 ASP cc_start: 0.8387 (t0) cc_final: 0.7742 (t0) outliers start: 141 outliers final: 100 residues processed: 638 average time/residue: 0.2274 time to fit residues: 238.8489 Evaluate side-chains 625 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 517 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 40 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 413 LEU Chi-restraints excluded: chain A residue 415 ASP 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 735 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 764 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 982 VAL Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1577 VAL Chi-restraints excluded: chain A residue 1611 MET 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 124 SER Chi-restraints excluded: chain B residue 167 SER 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 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 478 LEU Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 674 ILE 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 784 ASP 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 980 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 35 LYS 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 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 77 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU 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 J residue 7 CYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 51 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 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 53 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: 0.9980 chunk 144 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 307 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 235 optimal weight: 0.9980 chunk 321 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 427 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 301 ASN C 323 ASN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.091879 restraints weight = 61126.212| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.18 r_work: 0.2973 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35356 Z= 0.122 Angle : 0.612 18.322 48090 Z= 0.313 Chirality : 0.044 0.174 5380 Planarity : 0.004 0.090 5944 Dihedral : 12.705 81.304 5315 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.58 % Allowed : 16.96 % Favored : 80.46 % 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 are not related in a simple way. whole: -1.14 (0.13), residues: 4092 helix: -0.12 (0.15), residues: 1292 sheet: -1.32 (0.20), residues: 658 loop : -0.89 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 397 TYR 0.023 0.001 TYR A 995 PHE 0.026 0.001 PHE B1044 TRP 0.017 0.001 TRP B 836 HIS 0.006 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (35332) covalent geometry : angle 0.59825 / 0.31 (48057) hydrogen bonds : bond 0.03617 / 2.34 ( 1138) hydrogen bonds : angle 5.05386 / 3.48 ( 3163) metal coordination : bond 0.00643 / 0.47 ( 24) metal coordination : angle 4.98743 / 4.05 ( 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 669 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 574 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.8949 (t0) cc_final: 0.8743 (t0) REVERT: A 366 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8131 (ttm-80) REVERT: A 439 ASP cc_start: 0.8606 (t0) cc_final: 0.8376 (t0) REVERT: A 562 LEU cc_start: 0.8825 (tm) cc_final: 0.8591 (tp) REVERT: A 747 ILE cc_start: 0.8987 (mp) cc_final: 0.8765 (mp) REVERT: A 749 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9255 (tt) REVERT: A 773 ASP cc_start: 0.9091 (t0) cc_final: 0.8847 (t0) REVERT: A 833 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.8970 (pp) REVERT: A 1459 LYS cc_start: 0.7640 (ttmt) cc_final: 0.7273 (ttpt) REVERT: A 1474 LEU cc_start: 0.9028 (tt) cc_final: 0.8761 (tt) REVERT: B 67 ASP cc_start: 0.9049 (t70) cc_final: 0.8683 (t70) REVERT: B 90 TYR cc_start: 0.7068 (p90) cc_final: 0.6129 (p90) REVERT: B 430 MET cc_start: 0.8423 (tmm) cc_final: 0.8104 (tmm) REVERT: B 444 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8130 (tmm160) REVERT: B 456 ASN cc_start: 0.8426 (t0) cc_final: 0.8176 (t0) REVERT: B 778 TYR cc_start: 0.9063 (t80) cc_final: 0.8719 (t80) REVERT: B 787 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8810 (ppp) REVERT: B 815 ARG cc_start: 0.7122 (ptt90) cc_final: 0.6727 (ptt90) REVERT: B 912 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8504 (mm-40) REVERT: B 1039 MET cc_start: 0.9290 (mtm) cc_final: 0.8897 (mtm) REVERT: C 35 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8748 (mtmm) REVERT: C 124 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8120 (mp0) REVERT: D 26 GLN cc_start: 0.8658 (tm-30) cc_final: 0.7954 (tm-30) REVERT: D 38 GLN cc_start: 0.8648 (tt0) cc_final: 0.8268 (tp40) REVERT: D 89 LEU cc_start: 0.8348 (mt) cc_final: 0.8068 (mt) REVERT: E 110 PHE cc_start: 0.8616 (t80) cc_final: 0.8103 (t80) REVERT: E 187 TYR cc_start: 0.9327 (t80) cc_final: 0.9020 (t80) REVERT: F 122 MET cc_start: 0.9327 (mtm) cc_final: 0.9078 (mtt) REVERT: G 85 GLU cc_start: 0.8544 (pt0) cc_final: 0.8041 (pt0) REVERT: G 123 TYR cc_start: 0.8294 (m-10) cc_final: 0.8064 (m-80) REVERT: G 126 GLN cc_start: 0.8978 (pm20) cc_final: 0.8587 (pm20) REVERT: G 159 LYS cc_start: 0.7096 (tttm) cc_final: 0.6817 (tptp) REVERT: H 96 VAL cc_start: 0.9056 (p) cc_final: 0.8821 (t) REVERT: H 103 LYS cc_start: 0.9323 (ttpt) cc_final: 0.8870 (ttmm) REVERT: H 115 TYR cc_start: 0.9060 (m-80) cc_final: 0.8418 (m-80) REVERT: H 138 GLU cc_start: 0.9097 (pm20) cc_final: 0.8698 (pm20) REVERT: I 29 GLU cc_start: 0.8019 (tp30) cc_final: 0.7796 (tp30) REVERT: K 138 LYS cc_start: 0.8989 (tptt) cc_final: 0.8635 (mmtm) REVERT: M 11 GLU cc_start: 0.7795 (tp30) cc_final: 0.7251 (pt0) REVERT: M 16 GLN cc_start: 0.7649 (tp-100) cc_final: 0.7303 (tp-100) REVERT: M 41 TYR cc_start: 0.7730 (m-10) cc_final: 0.7242 (m-80) REVERT: M 67 ASP cc_start: 0.8272 (t0) cc_final: 0.7621 (t0) outliers start: 95 outliers final: 66 residues processed: 635 average time/residue: 0.2183 time to fit residues: 228.4638 Evaluate side-chains 611 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 539 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU 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 378 HIS Chi-restraints excluded: chain A residue 395 LEU 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 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 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 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 121 VAL 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 300 SER Chi-restraints excluded: chain B residue 374 LEU 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 734 CYS Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 787 MET 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 980 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 35 LYS 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 124 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 54 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 3 VAL 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 J residue 7 CYS 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 53 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: 0.2980 chunk 336 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 162 optimal weight: 8.9990 chunk 274 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 chunk 332 optimal weight: 0.3980 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 ASN ** 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** A1088 HIS A1454 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS C 172 GLN ** 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 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS H 52 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 = 0.3518 r_free = 0.3518 target = 0.119306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089712 restraints weight = 61476.044| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.17 r_work: 0.2938 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35356 Z= 0.207 Angle : 0.645 18.086 48090 Z= 0.329 Chirality : 0.046 0.199 5380 Planarity : 0.004 0.096 5944 Dihedral : 12.716 81.702 5315 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.80 % Allowed : 17.02 % Favored : 80.18 % 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 are not related in a simple way. whole: -1.10 (0.13), residues: 4092 helix: -0.04 (0.15), residues: 1279 sheet: -1.36 (0.19), residues: 663 loop : -0.88 (0.14), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 397 TYR 0.026 0.002 TYR G 73 PHE 0.031 0.002 PHE B1044 TRP 0.020 0.001 TRP B 836 HIS 0.026 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (35332) covalent geometry : angle 0.63099 / 0.33 (48057) hydrogen bonds : bond 0.03863 / 2.50 ( 1138) hydrogen bonds : angle 5.05554 / 3.49 ( 3163) metal coordination : bond 0.00949 / 0.68 ( 24) metal coordination : angle 5.14733 / 4.14 ( 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 639 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 536 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8776 (tp) REVERT: A 213 ASN cc_start: 0.8985 (t0) cc_final: 0.8760 (t0) REVERT: A 366 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8157 (ttm-80) REVERT: A 398 ASP cc_start: 0.8618 (m-30) cc_final: 0.8406 (m-30) REVERT: A 562 LEU cc_start: 0.8872 (tm) cc_final: 0.8641 (tp) REVERT: A 747 ILE cc_start: 0.8999 (mp) cc_final: 0.8726 (tt) REVERT: A 749 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9255 (tt) REVERT: A 773 ASP cc_start: 0.9113 (t0) cc_final: 0.8876 (t0) REVERT: A 833 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.8954 (pp) REVERT: A 1459 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7330 (ttpt) REVERT: A 1474 LEU cc_start: 0.9033 (tt) cc_final: 0.8752 (tt) REVERT: B 67 ASP cc_start: 0.9069 (t70) cc_final: 0.8656 (t70) REVERT: B 90 TYR cc_start: 0.7144 (p90) cc_final: 0.6132 (p90) REVERT: B 306 LEU cc_start: 0.8910 (tp) cc_final: 0.8586 (tt) REVERT: B 430 MET cc_start: 0.8391 (tmm) cc_final: 0.8054 (tmm) REVERT: B 456 ASN cc_start: 0.8458 (t0) cc_final: 0.8204 (t0) REVERT: B 692 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9071 (m) REVERT: B 778 TYR cc_start: 0.9147 (t80) cc_final: 0.8812 (t80) REVERT: B 787 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8395 (ptt) REVERT: B 815 ARG cc_start: 0.7028 (ptt90) cc_final: 0.6693 (ptt90) REVERT: B 912 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8561 (mm-40) REVERT: C 35 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8656 (mtmt) REVERT: C 124 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8170 (mp0) REVERT: D 26 GLN cc_start: 0.8668 (tm-30) cc_final: 0.7943 (tm-30) REVERT: D 38 GLN cc_start: 0.8673 (tt0) cc_final: 0.8301 (tp40) REVERT: D 89 LEU cc_start: 0.8195 (mt) cc_final: 0.7928 (mt) REVERT: E 110 PHE cc_start: 0.8714 (t80) cc_final: 0.8244 (t80) REVERT: E 187 TYR cc_start: 0.9358 (t80) cc_final: 0.9141 (t80) REVERT: F 122 MET cc_start: 0.9352 (mtm) cc_final: 0.9130 (mtt) REVERT: G 39 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8943 (p) REVERT: G 123 TYR cc_start: 0.8355 (m-10) cc_final: 0.8100 (m-80) REVERT: G 126 GLN cc_start: 0.8988 (pm20) cc_final: 0.8437 (pm20) REVERT: G 159 LYS cc_start: 0.7118 (tttm) cc_final: 0.6841 (tptp) REVERT: H 14 GLU cc_start: 0.8607 (pp20) cc_final: 0.8178 (pp20) REVERT: H 96 VAL cc_start: 0.9194 (p) cc_final: 0.8948 (t) REVERT: H 103 LYS cc_start: 0.9347 (ttpt) cc_final: 0.8890 (ttmm) REVERT: H 115 TYR cc_start: 0.9032 (m-80) cc_final: 0.8484 (m-80) REVERT: I 29 GLU cc_start: 0.7987 (tp30) cc_final: 0.7776 (tp30) REVERT: K 138 LYS cc_start: 0.8977 (tptt) cc_final: 0.8617 (mmtm) REVERT: M 11 GLU cc_start: 0.7723 (tp30) cc_final: 0.7247 (pt0) REVERT: M 16 GLN cc_start: 0.7635 (tp-100) cc_final: 0.6992 (tp-100) REVERT: M 23 VAL cc_start: 0.8209 (t) cc_final: 0.7992 (p) REVERT: M 41 TYR cc_start: 0.7709 (m-10) cc_final: 0.7405 (m-80) REVERT: M 67 ASP cc_start: 0.8334 (t0) cc_final: 0.7649 (t0) outliers start: 103 outliers final: 82 residues processed: 604 average time/residue: 0.2170 time to fit residues: 217.0998 Evaluate side-chains 618 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 527 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 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 390 LEU Chi-restraints excluded: chain A residue 395 LEU 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 587 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 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1508 VAL 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 300 SER Chi-restraints excluded: chain B residue 374 LEU 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 692 THR 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 784 ASP 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 943 ILE Chi-restraints excluded: chain B residue 980 ASP Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 35 LYS 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 D residue 81 ASN 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 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 39 VAL 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 107 VAL Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 3 VAL 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 J residue 7 CYS 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 53 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: 6.9990 chunk 80 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 325 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 285 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** A1088 HIS A1454 HIS ** B 50 ASN ** 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.089739 restraints weight = 61502.647| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.16 r_work: 0.2938 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 35356 Z= 0.222 Angle : 0.749 59.200 48090 Z= 0.408 Chirality : 0.048 1.043 5380 Planarity : 0.005 0.168 5944 Dihedral : 12.718 81.705 5315 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.75 % Allowed : 17.10 % Favored : 80.16 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: -1.10 (0.13), residues: 4092 helix: -0.03 (0.15), residues: 1279 sheet: -1.35 (0.19), residues: 663 loop : -0.88 (0.14), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 397 TYR 0.028 0.002 TYR G 73 PHE 0.031 0.001 PHE B1044 TRP 0.019 0.001 TRP B 836 HIS 0.018 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (35332) covalent geometry : angle 0.73662 / 0.41 (48057) hydrogen bonds : bond 0.03868 / 2.50 ( 1138) hydrogen bonds : angle 5.05462 / 3.49 ( 3163) metal coordination : bond 0.00936 / 0.67 ( 24) metal coordination : angle 5.13835 / 4.13 ( 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 633 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 532 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8773 (tp) REVERT: A 213 ASN cc_start: 0.8982 (t0) cc_final: 0.8761 (t0) REVERT: A 366 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8154 (ttm-80) REVERT: A 398 ASP cc_start: 0.8573 (m-30) cc_final: 0.8350 (m-30) REVERT: A 562 LEU cc_start: 0.8875 (tm) cc_final: 0.8646 (tp) REVERT: A 747 ILE cc_start: 0.8997 (mp) cc_final: 0.8726 (tt) REVERT: A 749 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9251 (tt) REVERT: A 773 ASP cc_start: 0.9111 (t0) cc_final: 0.8874 (t0) REVERT: A 833 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.8960 (pp) REVERT: A 1459 LYS cc_start: 0.7721 (ttmt) cc_final: 0.7347 (ttpt) REVERT: A 1474 LEU cc_start: 0.9031 (tt) cc_final: 0.8746 (tt) REVERT: B 67 ASP cc_start: 0.9069 (t70) cc_final: 0.8658 (t70) REVERT: B 90 TYR cc_start: 0.7142 (p90) cc_final: 0.6129 (p90) REVERT: B 306 LEU cc_start: 0.8914 (tp) cc_final: 0.8587 (tt) REVERT: B 430 MET cc_start: 0.8385 (tmm) cc_final: 0.8055 (tmm) REVERT: B 456 ASN cc_start: 0.8457 (t0) cc_final: 0.8217 (t0) REVERT: B 692 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.9069 (m) REVERT: B 778 TYR cc_start: 0.9149 (t80) cc_final: 0.8843 (t80) REVERT: B 787 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8379 (ptt) REVERT: B 815 ARG cc_start: 0.7094 (ptt90) cc_final: 0.6750 (ptt90) REVERT: B 912 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8555 (mm-40) REVERT: C 35 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8656 (mtmt) REVERT: C 93 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.9025 (pm20) REVERT: C 124 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8164 (mp0) REVERT: D 26 GLN cc_start: 0.8669 (tm-30) cc_final: 0.7944 (tm-30) REVERT: D 38 GLN cc_start: 0.8678 (tt0) cc_final: 0.8308 (tp40) REVERT: D 89 LEU cc_start: 0.8206 (mt) cc_final: 0.7929 (mt) REVERT: E 110 PHE cc_start: 0.8711 (t80) cc_final: 0.8245 (t80) REVERT: E 187 TYR cc_start: 0.9364 (t80) cc_final: 0.9144 (t80) REVERT: F 122 MET cc_start: 0.9354 (mtm) cc_final: 0.9125 (mtt) REVERT: G 39 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8950 (p) REVERT: G 123 TYR cc_start: 0.8372 (m-10) cc_final: 0.8101 (m-80) REVERT: G 126 GLN cc_start: 0.8984 (pm20) cc_final: 0.8435 (pm20) REVERT: G 159 LYS cc_start: 0.7122 (tttm) cc_final: 0.6844 (tptp) REVERT: H 96 VAL cc_start: 0.9195 (p) cc_final: 0.8946 (t) REVERT: H 103 LYS cc_start: 0.9337 (ttpt) cc_final: 0.8884 (ttmm) REVERT: H 115 TYR cc_start: 0.9036 (m-80) cc_final: 0.8484 (m-80) REVERT: H 138 GLU cc_start: 0.9111 (pm20) cc_final: 0.8677 (pm20) REVERT: I 29 GLU cc_start: 0.7991 (tp30) cc_final: 0.7775 (tp30) REVERT: K 138 LYS cc_start: 0.8993 (tptt) cc_final: 0.8637 (mmtm) REVERT: M 11 GLU cc_start: 0.7716 (tp30) cc_final: 0.7251 (pt0) REVERT: M 16 GLN cc_start: 0.7638 (tp-100) cc_final: 0.6997 (tp-100) REVERT: M 41 TYR cc_start: 0.7747 (m-10) cc_final: 0.7443 (m-80) REVERT: M 67 ASP cc_start: 0.8331 (t0) cc_final: 0.7647 (t0) outliers start: 101 outliers final: 87 residues processed: 598 average time/residue: 0.2172 time to fit residues: 214.8664 Evaluate side-chains 626 residues out of total 3679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 529 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 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 390 LEU Chi-restraints excluded: chain A residue 395 LEU 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 587 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 781 LEU 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 973 GLU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1508 VAL 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 300 SER Chi-restraints excluded: chain B residue 374 LEU 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 680 GLU Chi-restraints excluded: chain B residue 692 THR 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 784 ASP 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 943 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 980 ASP Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 93 GLN 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 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 39 VAL 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 107 VAL Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 7 LEU 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 J residue 7 CYS Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 40 LEU 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 53 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: 1.9990 chunk 178 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 116 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 331 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** A1088 HIS A1454 HIS ** B 50 ASN ** 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089727 restraints weight = 61237.573| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.17 r_work: 0.2938 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 35356 Z= 0.222 Angle : 0.749 59.200 48090 Z= 0.408 Chirality : 0.048 1.043 5380 Planarity : 0.005 0.168 5944 Dihedral : 12.718 81.705 5315 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.64 % Allowed : 17.23 % Favored : 80.13 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: -1.10 (0.13), residues: 4092 helix: -0.03 (0.15), residues: 1279 sheet: -1.35 (0.19), residues: 663 loop : -0.88 (0.14), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 397 TYR 0.028 0.002 TYR G 73 PHE 0.031 0.001 PHE B1044 TRP 0.019 0.001 TRP B 836 HIS 0.018 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (35332) covalent geometry : angle 0.73662 / 0.41 (48057) hydrogen bonds : bond 0.03868 / 2.50 ( 1138) hydrogen bonds : angle 5.05462 / 3.49 ( 3163) metal coordination : bond 0.00936 / 0.67 ( 24) metal coordination : angle 5.13835 / 4.13 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10181.46 seconds wall clock time: 174 minutes 58.91 seconds (10498.91 seconds total)