Starting phenix.real_space_refine on Thu Nov 20 17:48:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7du2_30865/11_2025/7du2_30865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7du2_30865/11_2025/7du2_30865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7du2_30865/11_2025/7du2_30865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7du2_30865/11_2025/7du2_30865.map" model { file = "/net/cci-nas-00/data/ceres_data/7du2_30865/11_2025/7du2_30865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7du2_30865/11_2025/7du2_30865.cif" } resolution = 3.35 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= 0.001 sd= 0.065 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 36 5.49 5 Mg 1 5.21 5 S 249 5.16 5 C 23095 2.51 5 N 6366 2.21 5 O 6859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36616 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 10152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1293, 10152 Classifications: {'peptide': 1293} Link IDs: {'PTRANS': 60, 'TRANS': 1232} Chain breaks: 5 Chain: "B" Number of atoms: 8254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8254 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 47, 'TRANS': 996} Chain breaks: 6 Chain: "C" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2641 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 17, 'TRANS': 312} Chain breaks: 1 Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "P" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Chain: "E" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1590 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain breaks: 2 Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "H" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1002 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 2 Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "O" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3546 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Q" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 724 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1272 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain breaks: 2 Chain: "N" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 697 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain breaks: 1 Chain: "I" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 340 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "X" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "Y" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "R" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} 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: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 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: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 534 SG CYS A 69 37.114 116.929 102.648 1.00 96.02 S ATOM 556 SG CYS A 72 39.723 120.654 103.407 1.00 94.46 S ATOM 604 SG CYS A 79 40.355 117.388 101.110 1.00 88.70 S ATOM 1236 SG CYS A 156 70.720 101.445 138.825 1.00118.39 S ATOM 1262 SG CYS A 159 68.454 102.675 141.276 1.00121.42 S ATOM 17993 SG CYS B1080 52.590 123.736 109.949 1.00 81.64 S ATOM 18012 SG CYS B1083 53.162 122.878 113.406 1.00 81.49 S ATOM 18078 SG CYS B1092 49.345 122.184 110.556 1.00 86.49 S ATOM 18106 SG CYS B1095 50.974 125.773 114.312 1.00 88.09 S ATOM 23248 SG CYS L 19 15.681 76.308 66.250 1.00 81.26 S ATOM 23410 SG CYS L 39 16.216 71.055 68.141 1.00 97.98 S ATOM 24369 SG CYS P 287 44.367 116.956 137.878 1.00121.28 S ATOM 27843 SG CYS J 7 51.989 82.339 42.122 1.00 54.01 S ATOM 27867 SG CYS J 10 55.193 84.642 38.723 1.00 57.92 S ATOM 28131 SG CYS J 44 55.248 81.631 40.751 1.00 57.10 S ATOM 28137 SG CYS J 45 52.330 81.199 38.745 1.00 54.89 S ATOM 35552 SG CYS I 5 80.387 40.108 126.364 1.00122.02 S ATOM 35700 SG CYS I 25 78.034 43.451 129.299 1.00125.31 S Time building chain proxies: 8.91, per 1000 atoms: 0.24 Number of scatterers: 36616 At special positions: 0 Unit cell: (135.966, 193.936, 193.936, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 249 16.00 P 36 15.00 Mg 1 11.99 O 6859 8.00 N 6366 7.00 C 23095 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: 3.51 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 307 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN A1902 " pdb="ZN ZN A1902 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 72 " pdb=" ZN A1903 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 25 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 15 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8486 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 51 sheets defined 37.1% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.573A pdb=" N GLN A 31 " --> pdb=" O MET A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.566A pdb=" N LYS A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 removed outlier: 4.430A pdb=" N LEU A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 removed outlier: 3.743A pdb=" N LEU A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASN A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 246 through 249 removed outlier: 3.589A pdb=" N ASP A 249 " --> pdb=" O LYS A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 279 through 296 removed outlier: 3.728A pdb=" N LYS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 320 removed outlier: 3.920A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 400 through 409 removed outlier: 3.576A pdb=" N GLN A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.507A pdb=" N SER A 472 " --> pdb=" O HIS A 469 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 473 " --> pdb=" O LYS A 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 469 through 473' Processing helix chain 'A' and resid 512 through 521 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.774A pdb=" N LEU A 551 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.659A pdb=" N CYS A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.713A pdb=" N ILE A 600 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 603 " --> pdb=" O GLN A 599 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.523A pdb=" N GLY A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 695 removed outlier: 3.841A pdb=" N ARG A 685 " --> pdb=" O SER A 681 " (cutoff:3.500A) Proline residue: A 688 - end of helix removed outlier: 3.801A pdb=" N ASN A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 733 removed outlier: 3.891A pdb=" N LEU A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 731 " --> pdb=" O TYR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 771 removed outlier: 3.707A pdb=" N LYS A 754 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 761 " --> pdb=" O SER A 757 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 768 " --> pdb=" O GLY A 764 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 783 removed outlier: 3.668A pdb=" N CYS A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 removed outlier: 3.735A pdb=" N ILE A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 877 removed outlier: 3.859A pdb=" N GLU A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 932 removed outlier: 3.728A pdb=" N VAL A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 952 Processing helix chain 'A' and resid 964 through 987 removed outlier: 3.610A pdb=" N GLU A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 979 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 removed outlier: 3.552A pdb=" N TYR A1001 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1025 removed outlier: 3.611A pdb=" N ASP A1020 " --> pdb=" O GLU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1047 removed outlier: 3.528A pdb=" N GLN A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) Proline residue: A1044 - end of helix Processing helix chain 'A' and resid 1066 through 1076 removed outlier: 3.591A pdb=" N GLU A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1106 Processing helix chain 'A' and resid 1111 through 1114 Processing helix chain 'A' and resid 1133 through 1140 removed outlier: 3.580A pdb=" N ILE A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1154 Processing helix chain 'A' and resid 1186 through 1196 removed outlier: 4.278A pdb=" N GLU A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A1195 " --> pdb=" O PHE A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1237 Processing helix chain 'A' and resid 1250 through 1259 removed outlier: 3.668A pdb=" N THR A1257 " --> pdb=" O GLU A1253 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1278 removed outlier: 3.501A pdb=" N ILE A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A1271 " --> pdb=" O ILE A1267 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A1274 " --> pdb=" O GLU A1270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 3.839A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP A1292 " --> pdb=" O MET A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1310 removed outlier: 3.607A pdb=" N LEU A1308 " --> pdb=" O THR A1304 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A1309 " --> pdb=" O ARG A1305 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A1310 " --> pdb=" O PHE A1306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1304 through 1310' Processing helix chain 'A' and resid 1314 through 1320 removed outlier: 3.698A pdb=" N LEU A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1334 removed outlier: 3.525A pdb=" N LEU A1328 " --> pdb=" O THR A1324 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A1331 " --> pdb=" O HIS A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1350 Processing helix chain 'B' and resid 28 through 38 removed outlier: 3.650A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 53 removed outlier: 3.611A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 removed outlier: 3.659A pdb=" N CYS B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.654A pdb=" N ALA B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 removed outlier: 3.644A pdb=" N ILE B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.837A pdb=" N ILE B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 264 Processing helix chain 'B' and resid 265 through 275 removed outlier: 5.274A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 292 removed outlier: 3.879A pdb=" N GLY B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 4.013A pdb=" N ALA B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 removed outlier: 3.640A pdb=" N ILE B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.595A pdb=" N LEU B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 385 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 406 No H-bonds generated for 'chain 'B' and resid 404 through 406' Processing helix chain 'B' and resid 407 through 421 removed outlier: 4.006A pdb=" N ILE B 411 " --> pdb=" O ARG B 407 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.940A pdb=" N MET B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.684A pdb=" N ASN B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 566 removed outlier: 3.556A pdb=" N LEU B 555 " --> pdb=" O ASP B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.707A pdb=" N ALA B 615 " --> pdb=" O MET B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 627 removed outlier: 3.639A pdb=" N PHE B 624 " --> pdb=" O ASN B 620 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 625 " --> pdb=" O PHE B 621 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 removed outlier: 3.689A pdb=" N CYS B 641 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.910A pdb=" N LEU B 664 " --> pdb=" O PRO B 661 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 665 " --> pdb=" O PHE B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 692 removed outlier: 3.783A pdb=" N ASN B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR B 685 " --> pdb=" O PRO B 681 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 688 " --> pdb=" O THR B 684 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 729 removed outlier: 3.621A pdb=" N LEU B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 765 Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 932 through 938 removed outlier: 4.435A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 937 " --> pdb=" O GLY B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 4.012A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 950 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 954 " --> pdb=" O LYS B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 977 removed outlier: 4.458A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 975 " --> pdb=" O ASP B 971 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 977 " --> pdb=" O CYS B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1019 Processing helix chain 'B' and resid 1048 through 1058 removed outlier: 3.550A pdb=" N CYS B1054 " --> pdb=" O MET B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1069 removed outlier: 3.913A pdb=" N LEU B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1118 Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 72 through 83 removed outlier: 3.525A pdb=" N ARG C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 258 through 262 removed outlier: 4.037A pdb=" N ILE C 262 " --> pdb=" O PRO C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.819A pdb=" N LEU C 280 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 292 through 295 removed outlier: 3.829A pdb=" N LYS C 295 " --> pdb=" O LYS C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 292 through 295' Processing helix chain 'C' and resid 317 through 343 removed outlier: 3.923A pdb=" N SER C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 4.001A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.751A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU G 29 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS G 32 " --> pdb=" O GLU G 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 61 removed outlier: 4.218A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 125 removed outlier: 3.780A pdb=" N ASN K 101 " --> pdb=" O GLN K 97 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 206 removed outlier: 3.936A pdb=" N GLN P 205 " --> pdb=" O ASN P 201 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG P 206 " --> pdb=" O PRO P 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 201 through 206' Processing helix chain 'P' and resid 219 through 228 removed outlier: 3.571A pdb=" N VAL P 228 " --> pdb=" O GLY P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 241 through 246 Processing helix chain 'P' and resid 246 through 254 removed outlier: 3.530A pdb=" N MET P 250 " --> pdb=" O GLY P 246 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA P 254 " --> pdb=" O MET P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 290 removed outlier: 3.702A pdb=" N LEU P 289 " --> pdb=" O ALA P 285 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS P 290 " --> pdb=" O PRO P 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 285 through 290' Processing helix chain 'P' and resid 291 through 295 Processing helix chain 'P' and resid 303 through 306 Processing helix chain 'P' and resid 307 through 314 removed outlier: 3.758A pdb=" N THR P 311 " --> pdb=" O CYS P 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 24 removed outlier: 4.010A pdb=" N HIS E 22 " --> pdb=" O MET E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.502A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 83 through 90 removed outlier: 3.958A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 97 Processing helix chain 'E' and resid 113 through 121 removed outlier: 4.053A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 136 removed outlier: 3.577A pdb=" N LEU E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 removed outlier: 3.674A pdb=" N THR E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 74 removed outlier: 3.545A pdb=" N ARG F 64 " --> pdb=" O TYR F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 removed outlier: 3.503A pdb=" N LYS F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 17 Processing helix chain 'J' and resid 18 through 27 removed outlier: 3.855A pdb=" N ALA J 27 " --> pdb=" O GLY J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 removed outlier: 4.257A pdb=" N LEU J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 51 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'J' and resid 61 through 63 No H-bonds generated for 'chain 'J' and resid 61 through 63' Processing helix chain 'O' and resid 3 through 17 removed outlier: 3.528A pdb=" N GLN O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 32 Processing helix chain 'O' and resid 35 through 43 Processing helix chain 'O' and resid 46 through 60 Processing helix chain 'O' and resid 78 through 83 removed outlier: 4.118A pdb=" N VAL O 82 " --> pdb=" O GLN O 78 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU O 83 " --> pdb=" O CYS O 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 78 through 83' Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'O' and resid 87 through 99 removed outlier: 3.543A pdb=" N THR O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR O 95 " --> pdb=" O TYR O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 113 Processing helix chain 'O' and resid 118 through 133 removed outlier: 4.284A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP O 127 " --> pdb=" O LYS O 123 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 154 removed outlier: 3.571A pdb=" N VAL O 149 " --> pdb=" O SER O 145 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA O 152 " --> pdb=" O PHE O 148 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR O 154 " --> pdb=" O ARG O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 257 removed outlier: 3.709A pdb=" N PHE O 242 " --> pdb=" O ASN O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 273 removed outlier: 3.601A pdb=" N SER O 264 " --> pdb=" O ASP O 260 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU O 265 " --> pdb=" O GLN O 261 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE O 266 " --> pdb=" O THR O 262 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL O 267 " --> pdb=" O SER O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 289 through 296 removed outlier: 3.602A pdb=" N ILE O 293 " --> pdb=" O SER O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 317 removed outlier: 3.539A pdb=" N ASP O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 358 removed outlier: 3.678A pdb=" N LEU O 342 " --> pdb=" O LEU O 338 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR O 347 " --> pdb=" O ALA O 343 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 367 removed outlier: 3.735A pdb=" N CYS O 362 " --> pdb=" O PHE O 358 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) Processing helix chain 'O' and resid 387 through 401 removed outlier: 3.653A pdb=" N ASP O 393 " --> pdb=" O LYS O 389 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET O 394 " --> pdb=" O GLU O 390 " (cutoff:3.500A) Processing helix chain 'O' and resid 429 through 453 removed outlier: 3.622A pdb=" N LEU O 435 " --> pdb=" O ALA O 431 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA O 444 " --> pdb=" O TYR O 440 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG O 449 " --> pdb=" O ASN O 445 " (cutoff:3.500A) Processing helix chain 'O' and resid 454 through 456 No H-bonds generated for 'chain 'O' and resid 454 through 456' Processing helix chain 'O' and resid 457 through 465 removed outlier: 3.754A pdb=" N LEU O 461 " --> pdb=" O ASN O 457 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU O 462 " --> pdb=" O LYS O 458 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS O 463 " --> pdb=" O ARG O 459 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER O 464 " --> pdb=" O LEU O 460 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN O 465 " --> pdb=" O LEU O 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 457 through 465' Processing helix chain 'O' and resid 492 through 516 removed outlier: 3.653A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL O 516 " --> pdb=" O SER O 512 " (cutoff:3.500A) Processing helix chain 'O' and resid 516 through 530 removed outlier: 3.987A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 62 removed outlier: 4.104A pdb=" N THR Q 50 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY Q 53 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU Q 58 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN Q 62 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 77 removed outlier: 3.864A pdb=" N PHE Q 74 " --> pdb=" O ARG Q 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 28 removed outlier: 3.525A pdb=" N LYS D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 removed outlier: 3.864A pdb=" N SER D 37 " --> pdb=" O LYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 56 removed outlier: 3.610A pdb=" N THR D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR D 56 " --> pdb=" O TYR D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 77 removed outlier: 4.138A pdb=" N VAL D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 93 through 99 removed outlier: 3.762A pdb=" N ILE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'M' and resid 70 through 76 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'N' and resid 252 through 261 Processing helix chain 'N' and resid 342 through 344 No H-bonds generated for 'chain 'N' and resid 342 through 344' Processing sheet with id=AA1, first strand: chain 'A' and resid 1337 through 1339 removed outlier: 4.914A pdb=" N ILE A 15 " --> pdb=" O SER B1129 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N SER B1129 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.420A pdb=" N ILE A 34 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASP A 87 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N LEU A 88 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N LEU A 256 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N LEU A 90 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG A 254 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 361 removed outlier: 3.650A pdb=" N VAL A 361 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU B1045 " --> pdb=" O VAL A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 1021 through 1023 removed outlier: 4.092A pdb=" N THR A 367 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 458 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE A 486 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 368 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N PHE A 488 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER A 370 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 395 removed outlier: 4.204A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 617 through 620 removed outlier: 6.472A pdb=" N THR A 639 " --> pdb=" O MET A 646 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 883 through 884 removed outlier: 3.777A pdb=" N CYS A 883 " --> pdb=" O ARG A 891 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 891 " --> pdb=" O CYS A 883 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1210 through 1213 removed outlier: 6.250A pdb=" N ARG A1245 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 7.232A pdb=" N THR A1108 " --> pdb=" O VAL A1201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1118 through 1122 removed outlier: 3.639A pdb=" N LEU A1122 " --> pdb=" O ASP A1125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1166 through 1168 removed outlier: 3.828A pdb=" N VAL A1173 " --> pdb=" O HIS A1168 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1297 through 1298 removed outlier: 3.820A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 58 through 59 removed outlier: 4.528A pdb=" N LEU A1362 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB7, first strand: chain 'B' and resid 110 through 113 removed outlier: 3.526A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB9, first strand: chain 'B' and resid 360 through 363 removed outlier: 6.230A pdb=" N ILE B 180 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 189 through 191 removed outlier: 4.094A pdb=" N ILE B 190 " --> pdb=" O GLY B 200 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA B 201 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 218 through 219 Processing sheet with id=AC3, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC4, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 548 removed outlier: 4.702A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 709 through 712 Processing sheet with id=AC7, first strand: chain 'B' and resid 739 through 741 Processing sheet with id=AC8, first strand: chain 'B' and resid 909 through 911 Processing sheet with id=AC9, first strand: chain 'B' and resid 776 through 778 Processing sheet with id=AD1, first strand: chain 'B' and resid 820 through 821 Processing sheet with id=AD2, first strand: chain 'B' and resid 825 through 832 removed outlier: 6.394A pdb=" N VAL B 826 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR B 858 " --> pdb=" O VAL B 826 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 828 " --> pdb=" O ILE B 856 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 830 " --> pdb=" O VAL B 854 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 896 through 897 Processing sheet with id=AD4, first strand: chain 'B' and resid 986 through 987 Processing sheet with id=AD5, first strand: chain 'B' and resid 1075 through 1080 removed outlier: 3.631A pdb=" N ILE B1106 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B1077 " --> pdb=" O LEU B1104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 13 through 15 removed outlier: 10.375A pdb=" N ARG C 301 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N THR C 240 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N ARG C 303 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 10.662A pdb=" N ASP C 238 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N HIS C 305 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AD8, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.125A pdb=" N GLU C 207 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASN C 96 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASP C 209 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL C 94 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU C 211 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL C 92 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.571A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 228 through 230 removed outlier: 7.131A pdb=" N GLU C 311 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.989A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE G 51 " --> pdb=" O ARG G 73 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.989A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL G 8 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL D 3 " --> pdb=" O VAL G 8 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 83 through 87 removed outlier: 4.796A pdb=" N GLU G 83 " --> pdb=" O PHE G 150 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE G 150 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER G 189 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AE6, first strand: chain 'K' and resid 26 through 27 Processing sheet with id=AE7, first strand: chain 'E' and resid 61 through 62 Processing sheet with id=AE8, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE9, first strand: chain 'E' and resid 103 through 105 Processing sheet with id=AF1, first strand: chain 'H' and resid 146 through 147 removed outlier: 4.220A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H 125 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE H 40 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.674A pdb=" N GLN O 66 " --> pdb=" O GLU O 74 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 116 through 117 Processing sheet with id=AF4, first strand: chain 'M' and resid 124 through 125 removed outlier: 3.685A pdb=" N LYS N 328 " --> pdb=" O LEU N 340 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL N 337 " --> pdb=" O THR N 349 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR N 349 " --> pdb=" O VAL N 337 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 105 through 106 removed outlier: 8.393A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER N 362 " --> pdb=" O LEU N 376 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 118 through 119 1162 hydrogen bonds defined for protein. 3213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.02 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 13606 1.37 - 1.56: 23285 1.56 - 1.76: 74 1.76 - 1.95: 378 1.95 - 2.14: 12 Bond restraints: 37355 Sorted by residual: bond pdb=" C PRO I 29 " pdb=" O PRO I 29 " ideal model delta sigma weight residual 1.235 1.184 0.051 7.90e-03 1.60e+04 4.12e+01 bond pdb=" CA GLN B 692 " pdb=" C GLN B 692 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.41e-02 5.03e+03 3.04e+01 bond pdb=" N LEU M 45 " pdb=" CA LEU M 45 " ideal model delta sigma weight residual 1.458 1.492 -0.034 6.30e-03 2.52e+04 2.90e+01 bond pdb=" CA TYR B 357 " pdb=" C TYR B 357 " ideal model delta sigma weight residual 1.523 1.447 0.076 1.56e-02 4.11e+03 2.40e+01 bond pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 2.280 2.134 0.146 3.00e-02 1.11e+03 2.38e+01 ... (remaining 37350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 48856 3.36 - 6.72: 1512 6.72 - 10.09: 153 10.09 - 13.45: 13 13.45 - 16.81: 25 Bond angle restraints: 50559 Sorted by residual: angle pdb="FE3 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.51 -16.81 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE3 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.51 -16.81 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.48 -16.78 1.50e+00 4.44e-01 1.25e+02 angle pdb="FE2 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.48 -16.78 1.50e+00 4.44e-01 1.25e+02 angle pdb=" N ARG A 59 " pdb=" CA ARG A 59 " pdb=" C ARG A 59 " ideal model delta sigma weight residual 113.38 99.66 13.72 1.23e+00 6.61e-01 1.24e+02 ... (remaining 50554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 22037 35.71 - 71.42: 767 71.42 - 107.13: 31 107.13 - 142.84: 1 142.84 - 178.55: 1 Dihedral angle restraints: 22837 sinusoidal: 9723 harmonic: 13114 Sorted by residual: dihedral pdb=" C LEU B 809 " pdb=" N LEU B 809 " pdb=" CA LEU B 809 " pdb=" CB LEU B 809 " ideal model delta harmonic sigma weight residual -122.60 -145.73 23.13 0 2.50e+00 1.60e-01 8.56e+01 dihedral pdb=" N LEU B 809 " pdb=" C LEU B 809 " pdb=" CA LEU B 809 " pdb=" CB LEU B 809 " ideal model delta harmonic sigma weight residual 122.80 145.47 -22.67 0 2.50e+00 1.60e-01 8.22e+01 dihedral pdb=" C ILE M 77 " pdb=" N ILE M 77 " pdb=" CA ILE M 77 " pdb=" CB ILE M 77 " ideal model delta harmonic sigma weight residual -122.00 -141.38 19.38 0 2.50e+00 1.60e-01 6.01e+01 ... (remaining 22834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 5467 0.195 - 0.389: 220 0.389 - 0.584: 20 0.584 - 0.778: 1 0.778 - 0.973: 5 Chirality restraints: 5713 Sorted by residual: chirality pdb=" CA LEU B 809 " pdb=" N LEU B 809 " pdb=" C LEU B 809 " pdb=" CB LEU B 809 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb="FE4 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " both_signs ideal model delta sigma weight residual False 10.55 9.72 0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb="FE1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb=" S4 SF4 P 401 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.83 2.00e-01 2.50e+01 1.71e+01 ... (remaining 5710 not shown) Planarity restraints: 6357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 162 " -0.024 2.00e-02 2.50e+03 4.81e-02 2.32e+01 pdb=" C LEU C 162 " 0.083 2.00e-02 2.50e+03 pdb=" O LEU C 162 " -0.031 2.00e-02 2.50e+03 pdb=" N TYR C 163 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1111 " 0.023 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C GLY A1111 " -0.081 2.00e-02 2.50e+03 pdb=" O GLY A1111 " 0.030 2.00e-02 2.50e+03 pdb=" N GLU A1112 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 617 " -0.022 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C GLY B 617 " 0.080 2.00e-02 2.50e+03 pdb=" O GLY B 617 " -0.031 2.00e-02 2.50e+03 pdb=" N TYR B 618 " -0.027 2.00e-02 2.50e+03 ... (remaining 6354 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 1011 2.64 - 3.20: 33386 3.20 - 3.77: 58791 3.77 - 4.33: 79070 4.33 - 4.90: 127578 Nonbonded interactions: 299836 Sorted by model distance: nonbonded pdb=" N ASP C 183 " pdb=" OD1 ASP C 183 " model vdw 2.073 3.120 nonbonded pdb=" O ALA A 161 " pdb="ZN ZN A1903 " model vdw 2.102 2.230 nonbonded pdb=" O THR M 107 " pdb=" OG1 THR M 107 " model vdw 2.132 3.040 nonbonded pdb=" CD2 LEU N 357 " pdb=" NE2 GLN N 358 " model vdw 2.145 3.540 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A1901 " model vdw 2.156 2.170 ... (remaining 299831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.060 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 46.250 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 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:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 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 : 0.016 0.935 37375 Z= 0.695 Angle : 1.510 56.168 50580 Z= 0.908 Chirality : 0.091 0.973 5713 Planarity : 0.008 0.080 6357 Dihedral : 17.067 178.552 14351 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.85 % Favored : 89.49 % Rotamer: Outliers : 4.73 % Allowed : 13.33 % Favored : 81.94 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.10), residues: 4426 helix: -3.86 (0.08), residues: 1495 sheet: -2.92 (0.20), residues: 506 loop : -2.76 (0.11), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 78 TYR 0.043 0.003 TYR M 114 PHE 0.037 0.003 PHE B 662 TRP 0.025 0.003 TRP P 217 HIS 0.013 0.002 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.01200 (37355) covalent geometry : angle 1.42010 (50559) hydrogen bonds : bond 0.28968 ( 1155) hydrogen bonds : angle 10.65495 ( 3213) metal coordination : bond 0.43683 ( 20) metal coordination : angle 25.28235 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 1017 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TYR cc_start: 0.7564 (m-80) cc_final: 0.6979 (m-80) REVERT: A 429 LYS cc_start: 0.8470 (mmtt) cc_final: 0.8209 (mmtm) REVERT: A 440 MET cc_start: 0.7691 (mtt) cc_final: 0.7324 (mtt) REVERT: A 514 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 908 ASP cc_start: 0.8093 (m-30) cc_final: 0.7878 (m-30) REVERT: A 1115 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: A 1255 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 1321 PHE cc_start: 0.8889 (t80) cc_final: 0.8688 (t80) REVERT: B 190 ILE cc_start: 0.7856 (tp) cc_final: 0.7606 (pt) REVERT: B 236 ILE cc_start: 0.8303 (pt) cc_final: 0.8091 (mm) REVERT: B 243 MET cc_start: 0.7476 (tpp) cc_final: 0.7124 (mmp) REVERT: B 354 ARG cc_start: 0.6687 (ptm160) cc_final: 0.5866 (ptm160) REVERT: B 520 VAL cc_start: 0.7812 (m) cc_final: 0.7540 (m) REVERT: B 527 CYS cc_start: 0.6999 (m) cc_final: 0.6790 (m) REVERT: C 275 VAL cc_start: 0.6910 (OUTLIER) cc_final: 0.6569 (p) REVERT: G 9 ASP cc_start: 0.6870 (t0) cc_final: 0.6652 (t0) REVERT: G 45 CYS cc_start: 0.7508 (m) cc_final: 0.6871 (m) REVERT: G 129 TRP cc_start: 0.6468 (m-10) cc_final: 0.6219 (m100) REVERT: P 203 MET cc_start: 0.7935 (mpp) cc_final: 0.7473 (mmm) REVERT: E 128 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6959 (mm-30) REVERT: F 80 MET cc_start: 0.7769 (mmt) cc_final: 0.7504 (mmt) REVERT: H 56 PHE cc_start: 0.8341 (p90) cc_final: 0.7899 (p90) REVERT: O 50 VAL cc_start: 0.9067 (t) cc_final: 0.8823 (p) REVERT: O 385 MET cc_start: 0.5563 (mmm) cc_final: 0.4667 (tpt) REVERT: O 398 MET cc_start: 0.7602 (mmp) cc_final: 0.7134 (mmt) REVERT: O 448 GLU cc_start: 0.7968 (tp30) cc_final: 0.7760 (pp20) REVERT: O 461 LEU cc_start: 0.7679 (pp) cc_final: 0.7452 (mp) REVERT: D 43 ASN cc_start: 0.5377 (OUTLIER) cc_final: 0.4242 (m110) REVERT: M 193 TYR cc_start: 0.2353 (OUTLIER) cc_final: 0.1318 (m-80) outliers start: 188 outliers final: 59 residues processed: 1125 average time/residue: 0.2494 time to fit residues: 445.1460 Evaluate side-chains 660 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 597 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 423 LEU Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 193 TYR Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain N residue 328 LYS Chi-restraints excluded: chain N residue 329 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 358 GLN Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain N residue 375 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 36 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 4.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 422 GLN A 511 GLN A 543 GLN A 662 ASN A 693 ASN A 738 GLN A 791 ASN A 943 ASN A1364 HIS B 129 ASN ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 434 GLN B 472 GLN B 608 ASN B 639 ASN B 692 GLN B 806 HIS B 825 GLN B 887 GLN B1014 HIS B1100 HIS C 42 GLN C 59 ASN C 127 GLN K 38 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN L 26 ASN P 274 ASN E 35 GLN O 14 GLN O 49 GLN O 113 ASN O 337 ASN O 379 GLN O 437 HIS ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 457 ASN O 507 ASN D 13 ASN D 26 GLN D 40 GLN D 43 ASN D 61 GLN D 88 ASN M 29 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 HIS ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.126548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.098161 restraints weight = 91716.989| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.07 r_work: 0.3463 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 37375 Z= 0.177 Angle : 0.866 27.103 50580 Z= 0.427 Chirality : 0.049 0.273 5713 Planarity : 0.007 0.077 6357 Dihedral : 12.252 177.010 5418 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.16 % Favored : 91.62 % Rotamer: Outliers : 3.90 % Allowed : 18.49 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.69 (0.11), residues: 4426 helix: -2.27 (0.11), residues: 1573 sheet: -2.72 (0.20), residues: 523 loop : -2.50 (0.12), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 33 TYR 0.033 0.002 TYR D 47 PHE 0.028 0.002 PHE K 96 TRP 0.029 0.003 TRP G 201 HIS 0.012 0.001 HIS D 76 Details of bonding type rmsd covalent geometry : bond 0.00401 (37355) covalent geometry : angle 0.83372 (50559) hydrogen bonds : bond 0.04999 ( 1155) hydrogen bonds : angle 6.04992 ( 3213) metal coordination : bond 0.01849 ( 20) metal coordination : angle 11.58207 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 712 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.5548 (t80) cc_final: 0.5027 (t80) REVERT: A 65 LYS cc_start: 0.8795 (tptp) cc_final: 0.8435 (tttt) REVERT: A 97 TYR cc_start: 0.7897 (m-80) cc_final: 0.7519 (m-80) REVERT: A 227 PHE cc_start: 0.8594 (m-10) cc_final: 0.8385 (m-10) REVERT: A 281 MET cc_start: 0.8014 (mmm) cc_final: 0.7770 (mmm) REVERT: A 429 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7747 (mmtm) REVERT: A 514 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7627 (mt-10) REVERT: A 623 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8643 (pp30) REVERT: A 749 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8038 (mm-30) REVERT: A 1115 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: A 1159 ARG cc_start: 0.8973 (mtt180) cc_final: 0.8237 (tpt90) REVERT: A 1178 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6470 (tmt170) REVERT: A 1255 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8347 (tm-30) REVERT: A 1317 MET cc_start: 0.8322 (tpt) cc_final: 0.7977 (tpt) REVERT: B 236 ILE cc_start: 0.8372 (pt) cc_final: 0.8121 (pt) REVERT: B 243 MET cc_start: 0.8056 (tpp) cc_final: 0.7530 (mmp) REVERT: B 254 MET cc_start: 0.8206 (mmt) cc_final: 0.7925 (mmt) REVERT: B 354 ARG cc_start: 0.6699 (ptm160) cc_final: 0.6315 (ptm160) REVERT: B 527 CYS cc_start: 0.7172 (m) cc_final: 0.6961 (m) REVERT: B 530 GLU cc_start: 0.8399 (pp20) cc_final: 0.8132 (pp20) REVERT: B 588 ASP cc_start: 0.8471 (t0) cc_final: 0.8073 (t0) REVERT: B 639 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.7914 (m-40) REVERT: B 801 LYS cc_start: 0.8490 (mppt) cc_final: 0.8255 (mmmt) REVERT: B 870 MET cc_start: 0.7712 (tmm) cc_final: 0.7144 (tmm) REVERT: C 56 MET cc_start: 0.7996 (tmm) cc_final: 0.7779 (tmm) REVERT: C 96 ASN cc_start: 0.7988 (p0) cc_final: 0.7766 (p0) REVERT: C 336 PHE cc_start: 0.9008 (m-80) cc_final: 0.8753 (m-80) REVERT: G 6 GLU cc_start: 0.7546 (mp0) cc_final: 0.7259 (mp0) REVERT: G 7 MET cc_start: 0.8225 (mtp) cc_final: 0.7971 (mtt) REVERT: G 45 CYS cc_start: 0.7952 (m) cc_final: 0.7583 (m) REVERT: G 159 ASP cc_start: 0.6930 (t0) cc_final: 0.6485 (t70) REVERT: K 60 MET cc_start: 0.8799 (tpp) cc_final: 0.8505 (tpp) REVERT: L 27 GLU cc_start: 0.6784 (tp30) cc_final: 0.6315 (tp30) REVERT: L 28 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8393 (pt) REVERT: L 29 LYS cc_start: 0.7065 (ptpp) cc_final: 0.6794 (ptpp) REVERT: L 34 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8189 (mp) REVERT: P 205 GLN cc_start: 0.5405 (OUTLIER) cc_final: 0.4349 (pt0) REVERT: P 266 HIS cc_start: 0.8069 (m-70) cc_final: 0.7521 (p90) REVERT: P 267 MET cc_start: 0.6609 (mmm) cc_final: 0.6275 (mmm) REVERT: E 108 GLN cc_start: 0.8567 (mm110) cc_final: 0.8336 (mt0) REVERT: E 121 MET cc_start: 0.8036 (tmm) cc_final: 0.6831 (tmm) REVERT: E 125 TYR cc_start: 0.6773 (m-80) cc_final: 0.5947 (m-10) REVERT: E 128 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7646 (mm-30) REVERT: E 131 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8754 (mm) REVERT: F 84 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8002 (mm-30) REVERT: H 8 ASP cc_start: 0.6078 (m-30) cc_final: 0.5788 (m-30) REVERT: H 87 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7906 (mp10) REVERT: J 54 ASP cc_start: 0.8440 (t70) cc_final: 0.7881 (p0) REVERT: O 385 MET cc_start: 0.6425 (mmm) cc_final: 0.5144 (tpt) REVERT: O 398 MET cc_start: 0.7593 (mmp) cc_final: 0.7331 (mmt) REVERT: O 408 GLU cc_start: 0.5178 (OUTLIER) cc_final: 0.4580 (tt0) REVERT: O 448 GLU cc_start: 0.7932 (tp30) cc_final: 0.7294 (pp20) REVERT: Q 52 GLU cc_start: 0.8226 (pp20) cc_final: 0.7894 (pp20) REVERT: Q 58 LEU cc_start: 0.7328 (tt) cc_final: 0.6984 (mp) REVERT: Q 68 MET cc_start: 0.6229 (ppp) cc_final: 0.6022 (ppp) REVERT: Q 71 MET cc_start: 0.6267 (mmp) cc_final: 0.6051 (mmt) REVERT: D 4 LYS cc_start: 0.7934 (ttpp) cc_final: 0.7561 (mptt) REVERT: D 5 ASP cc_start: 0.7348 (t0) cc_final: 0.7050 (t0) REVERT: D 24 LYS cc_start: 0.8239 (pptt) cc_final: 0.8009 (pptt) REVERT: D 59 ARG cc_start: 0.6924 (pmt-80) cc_final: 0.6062 (ptt-90) REVERT: D 76 HIS cc_start: 0.6698 (t-170) cc_final: 0.6293 (t70) REVERT: M 29 GLN cc_start: 0.8345 (mt0) cc_final: 0.7768 (mt0) REVERT: M 45 LEU cc_start: 0.8882 (tp) cc_final: 0.8677 (mt) REVERT: M 58 LEU cc_start: 0.6543 (mt) cc_final: 0.6174 (mt) REVERT: M 132 ILE cc_start: 0.7319 (mm) cc_final: 0.6841 (mm) REVERT: M 149 HIS cc_start: 0.8290 (m90) cc_final: 0.8043 (m-70) REVERT: M 191 GLN cc_start: 0.8950 (pm20) cc_final: 0.7894 (tp40) REVERT: N 264 GLU cc_start: 0.8069 (mp0) cc_final: 0.5272 (tp30) REVERT: N 365 LEU cc_start: 0.8032 (tt) cc_final: 0.7634 (tp) REVERT: I 37 LYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5645 (tptp) outliers start: 155 outliers final: 77 residues processed: 803 average time/residue: 0.2301 time to fit residues: 302.5826 Evaluate side-chains 643 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 556 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 70 ARG Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 375 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 362 optimal weight: 0.9990 chunk 380 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 309 optimal weight: 8.9990 chunk 359 optimal weight: 1.9990 chunk 297 optimal weight: 0.0040 chunk 316 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 257 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 158 HIS ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A1371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS B 289 ASN B 417 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS B 703 ASN ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 14 GLN O 16 HIS O 146 ASN O 244 GLN O 286 GLN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 451 GLN D 18 GLN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN M 44 HIS ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 ASN M 121 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.119317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090521 restraints weight = 90808.317| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.02 r_work: 0.3320 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 37375 Z= 0.184 Angle : 0.774 20.096 50580 Z= 0.385 Chirality : 0.047 0.245 5713 Planarity : 0.005 0.078 6357 Dihedral : 11.499 178.828 5350 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.74 % Favored : 91.05 % Rotamer: Outliers : 4.38 % Allowed : 20.42 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.83 (0.12), residues: 4426 helix: -1.24 (0.12), residues: 1568 sheet: -2.53 (0.21), residues: 498 loop : -2.18 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 90 TYR 0.028 0.002 TYR D 52 PHE 0.024 0.002 PHE B 662 TRP 0.022 0.002 TRP M 205 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00417 (37355) covalent geometry : angle 0.74887 (50559) hydrogen bonds : bond 0.04368 ( 1155) hydrogen bonds : angle 5.36185 ( 3213) metal coordination : bond 0.01203 ( 20) metal coordination : angle 9.66678 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 600 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.6391 (t80) cc_final: 0.5504 (t80) REVERT: A 97 TYR cc_start: 0.7864 (m-80) cc_final: 0.7137 (m-80) REVERT: A 128 TYR cc_start: 0.8579 (t80) cc_final: 0.8214 (t80) REVERT: A 281 MET cc_start: 0.8157 (mmm) cc_final: 0.7950 (mmm) REVERT: A 461 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8666 (pp) REVERT: A 749 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8171 (mm-30) REVERT: A 790 ILE cc_start: 0.8987 (mm) cc_final: 0.8737 (mt) REVERT: A 1115 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: A 1119 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: A 1159 ARG cc_start: 0.8963 (mtt180) cc_final: 0.8173 (tpt90) REVERT: A 1178 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6779 (tmt170) REVERT: A 1198 LYS cc_start: 0.8686 (ptpt) cc_final: 0.8279 (mtmt) REVERT: A 1255 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8501 (tm-30) REVERT: A 1317 MET cc_start: 0.8533 (tpt) cc_final: 0.8056 (tpt) REVERT: B 236 ILE cc_start: 0.8337 (pt) cc_final: 0.7959 (mm) REVERT: B 243 MET cc_start: 0.8145 (tpp) cc_final: 0.7595 (mmp) REVERT: B 254 MET cc_start: 0.8402 (mmt) cc_final: 0.8188 (mmt) REVERT: B 530 GLU cc_start: 0.8418 (pp20) cc_final: 0.8030 (pp20) REVERT: B 588 ASP cc_start: 0.8469 (t0) cc_final: 0.8130 (t0) REVERT: B 794 MET cc_start: 0.8579 (tpp) cc_final: 0.8189 (mpp) REVERT: B 870 MET cc_start: 0.7958 (tmm) cc_final: 0.7541 (tmm) REVERT: B 1003 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8681 (t80) REVERT: B 1004 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8755 (t80) REVERT: C 27 THR cc_start: 0.8914 (p) cc_final: 0.8677 (t) REVERT: C 33 TYR cc_start: 0.8251 (m-80) cc_final: 0.7990 (m-80) REVERT: C 56 MET cc_start: 0.8290 (tmm) cc_final: 0.7925 (tmm) REVERT: C 191 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7591 (ptt-90) REVERT: C 336 PHE cc_start: 0.9087 (m-80) cc_final: 0.8853 (m-80) REVERT: G 6 GLU cc_start: 0.7750 (mp0) cc_final: 0.7449 (mp0) REVERT: G 7 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7897 (mtt) REVERT: G 34 LEU cc_start: 0.8995 (mt) cc_final: 0.8580 (tp) REVERT: G 40 TYR cc_start: 0.7494 (t80) cc_final: 0.7180 (t80) REVERT: G 45 CYS cc_start: 0.8298 (m) cc_final: 0.7659 (m) REVERT: G 50 ASP cc_start: 0.7624 (m-30) cc_final: 0.7382 (m-30) REVERT: G 129 TRP cc_start: 0.7160 (m-10) cc_final: 0.6877 (m100) REVERT: K 64 GLU cc_start: 0.8271 (mp0) cc_final: 0.8057 (mt-10) REVERT: K 120 ASP cc_start: 0.8982 (t0) cc_final: 0.8775 (t70) REVERT: L 27 GLU cc_start: 0.7053 (tp30) cc_final: 0.6811 (tp30) REVERT: L 28 ILE cc_start: 0.8737 (pt) cc_final: 0.8451 (pt) REVERT: L 29 LYS cc_start: 0.7487 (ptpp) cc_final: 0.7213 (ptpp) REVERT: L 34 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8377 (mp) REVERT: P 205 GLN cc_start: 0.5218 (OUTLIER) cc_final: 0.3978 (pt0) REVERT: P 217 TRP cc_start: 0.5805 (t-100) cc_final: 0.5503 (t-100) REVERT: P 266 HIS cc_start: 0.8009 (m-70) cc_final: 0.7417 (p-80) REVERT: P 267 MET cc_start: 0.6408 (mmm) cc_final: 0.5976 (mmm) REVERT: E 121 MET cc_start: 0.8050 (tmm) cc_final: 0.7241 (tmm) REVERT: E 125 TYR cc_start: 0.7122 (m-80) cc_final: 0.6567 (m-10) REVERT: E 128 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7668 (mm-30) REVERT: E 131 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9030 (tp) REVERT: E 163 TYR cc_start: 0.8800 (m-80) cc_final: 0.8546 (m-80) REVERT: H 8 ASP cc_start: 0.6648 (m-30) cc_final: 0.6270 (m-30) REVERT: J 41 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8520 (mmtm) REVERT: O 139 MET cc_start: 0.4010 (ttp) cc_final: 0.3395 (tmm) REVERT: O 236 GLN cc_start: 0.7623 (pt0) cc_final: 0.7010 (pm20) REVERT: O 385 MET cc_start: 0.6468 (mmm) cc_final: 0.5318 (tpt) REVERT: O 398 MET cc_start: 0.7912 (mmp) cc_final: 0.7623 (mmt) REVERT: O 423 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7470 (pp) REVERT: O 448 GLU cc_start: 0.8121 (tp30) cc_final: 0.7500 (pp20) REVERT: O 526 TYR cc_start: 0.7710 (t80) cc_final: 0.7473 (t80) REVERT: Q 52 GLU cc_start: 0.8127 (pp20) cc_final: 0.7889 (pp20) REVERT: Q 55 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: Q 68 MET cc_start: 0.6733 (ppp) cc_final: 0.5074 (ppp) REVERT: D 4 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7813 (tppt) REVERT: D 18 GLN cc_start: 0.8692 (mt0) cc_final: 0.8249 (mt0) REVERT: D 59 ARG cc_start: 0.7043 (pmt-80) cc_final: 0.6275 (ptt-90) REVERT: D 67 ARG cc_start: 0.5396 (tpt170) cc_final: 0.5091 (mmm160) REVERT: D 74 LYS cc_start: -0.0228 (mmtt) cc_final: -0.0889 (mmtt) REVERT: M 27 LEU cc_start: 0.7561 (tp) cc_final: 0.7122 (tp) REVERT: M 29 GLN cc_start: 0.8407 (mt0) cc_final: 0.8171 (mt0) REVERT: M 149 HIS cc_start: 0.8358 (m90) cc_final: 0.8118 (m-70) REVERT: M 189 ARG cc_start: 0.4837 (tmt170) cc_final: 0.4247 (tmt170) REVERT: M 191 GLN cc_start: 0.8986 (pm20) cc_final: 0.8088 (tp40) REVERT: M 205 TRP cc_start: 0.7835 (m100) cc_final: 0.7483 (m100) REVERT: N 253 GLU cc_start: 0.7895 (mp0) cc_final: 0.7672 (mp0) REVERT: N 264 GLU cc_start: 0.8211 (mp0) cc_final: 0.5624 (tp30) REVERT: N 382 LYS cc_start: 0.7277 (ttmt) cc_final: 0.6954 (mtpt) outliers start: 174 outliers final: 93 residues processed: 716 average time/residue: 0.2230 time to fit residues: 264.5250 Evaluate side-chains 644 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 538 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1119 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain P residue 311 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 423 LEU Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 375 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 361 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 338 optimal weight: 6.9990 chunk 298 optimal weight: 0.0470 chunk 430 optimal weight: 5.9990 chunk 258 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 347 optimal weight: 3.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN A1371 ASN B 413 ASN B 472 GLN B 542 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS K 38 HIS K 45 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** 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 = 0.3843 r_free = 0.3843 target = 0.115488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.086573 restraints weight = 89528.656| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.98 r_work: 0.3257 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 37375 Z= 0.183 Angle : 0.739 23.370 50580 Z= 0.364 Chirality : 0.046 0.270 5713 Planarity : 0.005 0.076 6357 Dihedral : 11.249 178.740 5335 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.68 % Favored : 91.14 % Rotamer: Outliers : 4.43 % Allowed : 21.55 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.12), residues: 4426 helix: -0.79 (0.13), residues: 1576 sheet: -2.49 (0.21), residues: 510 loop : -2.14 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 90 TYR 0.044 0.002 TYR D 47 PHE 0.062 0.002 PHE B 278 TRP 0.023 0.002 TRP G 201 HIS 0.016 0.001 HIS M 130 Details of bonding type rmsd covalent geometry : bond 0.00430 (37355) covalent geometry : angle 0.70932 (50559) hydrogen bonds : bond 0.03927 ( 1155) hydrogen bonds : angle 5.10337 ( 3213) metal coordination : bond 0.01017 ( 20) metal coordination : angle 10.17957 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 575 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.6468 (t80) cc_final: 0.5556 (t80) REVERT: A 65 LYS cc_start: 0.8768 (tptp) cc_final: 0.8370 (tttt) REVERT: A 126 LEU cc_start: 0.8615 (mp) cc_final: 0.8341 (mp) REVERT: A 128 TYR cc_start: 0.8647 (t80) cc_final: 0.8342 (t80) REVERT: A 241 ASN cc_start: 0.8697 (t0) cc_final: 0.8483 (t0) REVERT: A 440 MET cc_start: 0.8402 (mtt) cc_final: 0.7921 (mtt) REVERT: A 461 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8690 (pp) REVERT: A 544 ASP cc_start: 0.8666 (t0) cc_final: 0.8445 (t0) REVERT: A 749 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8292 (mm-30) REVERT: A 790 ILE cc_start: 0.9016 (mm) cc_final: 0.8779 (mt) REVERT: A 1115 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: A 1159 ARG cc_start: 0.8911 (mtt180) cc_final: 0.8147 (tpt90) REVERT: A 1178 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6882 (tmt170) REVERT: A 1198 LYS cc_start: 0.8700 (ptpt) cc_final: 0.8320 (mtmt) REVERT: A 1255 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 1317 MET cc_start: 0.8527 (tpt) cc_final: 0.8058 (tpt) REVERT: A 1375 ARG cc_start: 0.5913 (tmt170) cc_final: 0.5696 (tmt170) REVERT: B 236 ILE cc_start: 0.8317 (pt) cc_final: 0.7836 (mm) REVERT: B 243 MET cc_start: 0.8173 (tpp) cc_final: 0.7746 (mmp) REVERT: B 530 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7933 (pp20) REVERT: B 588 ASP cc_start: 0.8510 (t0) cc_final: 0.8214 (t0) REVERT: B 794 MET cc_start: 0.8494 (tpp) cc_final: 0.8209 (mpp) REVERT: B 801 LYS cc_start: 0.8842 (mmtm) cc_final: 0.8487 (mmmt) REVERT: B 1003 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.8725 (t80) REVERT: B 1004 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8764 (t80) REVERT: B 1012 LEU cc_start: 0.8669 (pt) cc_final: 0.8453 (mp) REVERT: B 1112 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8463 (tp) REVERT: C 27 THR cc_start: 0.8897 (p) cc_final: 0.8530 (t) REVERT: C 33 TYR cc_start: 0.8457 (m-80) cc_final: 0.8093 (m-80) REVERT: C 55 HIS cc_start: 0.7913 (t-90) cc_final: 0.7674 (t-90) REVERT: C 56 MET cc_start: 0.8469 (tmm) cc_final: 0.8120 (tmm) REVERT: G 6 GLU cc_start: 0.7757 (mp0) cc_final: 0.7523 (mp0) REVERT: G 7 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8063 (mtt) REVERT: G 45 CYS cc_start: 0.8450 (m) cc_final: 0.8097 (m) REVERT: G 129 TRP cc_start: 0.7026 (m-10) cc_final: 0.6783 (m100) REVERT: K 60 MET cc_start: 0.9032 (tpp) cc_final: 0.8702 (mmp) REVERT: K 104 MET cc_start: 0.8729 (ttm) cc_final: 0.8485 (ttm) REVERT: L 27 GLU cc_start: 0.7074 (tp30) cc_final: 0.6864 (tp30) REVERT: L 28 ILE cc_start: 0.8645 (pt) cc_final: 0.8284 (pt) REVERT: L 29 LYS cc_start: 0.7612 (ptpp) cc_final: 0.7177 (ptpp) REVERT: P 205 GLN cc_start: 0.5218 (OUTLIER) cc_final: 0.3456 (pm20) REVERT: P 217 TRP cc_start: 0.6067 (t-100) cc_final: 0.5848 (t-100) REVERT: P 266 HIS cc_start: 0.7986 (m-70) cc_final: 0.7499 (p-80) REVERT: P 267 MET cc_start: 0.6381 (mmm) cc_final: 0.5992 (mmm) REVERT: E 108 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: E 121 MET cc_start: 0.8058 (tmm) cc_final: 0.7350 (tmm) REVERT: E 125 TYR cc_start: 0.7074 (m-80) cc_final: 0.6641 (m-10) REVERT: E 128 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7739 (mm-30) REVERT: E 163 TYR cc_start: 0.8972 (m-80) cc_final: 0.8483 (m-80) REVERT: F 82 GLU cc_start: 0.8250 (pp20) cc_final: 0.7904 (pp20) REVERT: F 84 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8024 (mm-30) REVERT: O 139 MET cc_start: 0.3984 (ttp) cc_final: 0.3513 (tmm) REVERT: O 158 GLN cc_start: 0.5619 (pm20) cc_final: 0.5177 (pm20) REVERT: O 236 GLN cc_start: 0.7786 (pt0) cc_final: 0.7363 (pm20) REVERT: O 385 MET cc_start: 0.6353 (mmm) cc_final: 0.5458 (tpp) REVERT: O 398 MET cc_start: 0.8071 (mmp) cc_final: 0.7704 (mmt) REVERT: O 448 GLU cc_start: 0.8171 (tp30) cc_final: 0.7551 (pp20) REVERT: O 526 TYR cc_start: 0.7822 (t80) cc_final: 0.7556 (t80) REVERT: Q 55 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: Q 68 MET cc_start: 0.6820 (ppp) cc_final: 0.5564 (ppp) REVERT: D 59 ARG cc_start: 0.7069 (pmt-80) cc_final: 0.6291 (ptt-90) REVERT: D 74 LYS cc_start: -0.0143 (mmtt) cc_final: -0.0524 (mmtt) REVERT: D 85 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7693 (tp40) REVERT: M 27 LEU cc_start: 0.8200 (tp) cc_final: 0.7961 (tp) REVERT: M 134 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7560 (mm-40) REVERT: M 149 HIS cc_start: 0.8459 (m90) cc_final: 0.8249 (m-70) REVERT: M 189 ARG cc_start: 0.4951 (tmt170) cc_final: 0.4491 (tmt170) REVERT: M 191 GLN cc_start: 0.8904 (pm20) cc_final: 0.8142 (tp40) REVERT: N 253 GLU cc_start: 0.7848 (mp0) cc_final: 0.7629 (mp0) REVERT: N 264 GLU cc_start: 0.8172 (mp0) cc_final: 0.5628 (tp30) REVERT: I 4 PHE cc_start: 0.6242 (m-80) cc_final: 0.5723 (m-80) outliers start: 176 outliers final: 112 residues processed: 699 average time/residue: 0.2265 time to fit residues: 263.7531 Evaluate side-chains 650 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 527 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain P residue 311 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 21 optimal weight: 5.9990 chunk 400 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 223 optimal weight: 0.7980 chunk 432 optimal weight: 10.0000 chunk 341 optimal weight: 10.0000 chunk 403 optimal weight: 4.9990 chunk 147 optimal weight: 0.0170 chunk 136 optimal weight: 0.0870 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN B 544 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN B1118 GLN C 139 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS K 38 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN M 29 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.114026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085094 restraints weight = 89321.847| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.98 r_work: 0.3227 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 37375 Z= 0.159 Angle : 0.710 22.997 50580 Z= 0.349 Chirality : 0.046 0.448 5713 Planarity : 0.005 0.062 6357 Dihedral : 11.092 178.904 5333 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.79 % Favored : 91.05 % Rotamer: Outliers : 4.07 % Allowed : 22.79 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.26 (0.12), residues: 4426 helix: -0.48 (0.13), residues: 1569 sheet: -2.38 (0.21), residues: 515 loop : -2.04 (0.12), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 90 TYR 0.027 0.001 TYR P 219 PHE 0.038 0.001 PHE B 278 TRP 0.027 0.002 TRP G 201 HIS 0.037 0.001 HIS D 89 Details of bonding type rmsd covalent geometry : bond 0.00371 (37355) covalent geometry : angle 0.68173 (50559) hydrogen bonds : bond 0.03722 ( 1155) hydrogen bonds : angle 4.90852 ( 3213) metal coordination : bond 0.00877 ( 20) metal coordination : angle 9.72263 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 557 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.6314 (t80) cc_final: 0.5330 (t80) REVERT: A 126 LEU cc_start: 0.8601 (mp) cc_final: 0.8363 (mp) REVERT: A 128 TYR cc_start: 0.8652 (t80) cc_final: 0.8384 (t80) REVERT: A 281 MET cc_start: 0.8284 (mmm) cc_final: 0.8032 (mmm) REVERT: A 305 MET cc_start: 0.7954 (ppp) cc_final: 0.7302 (ppp) REVERT: A 440 MET cc_start: 0.8513 (mtt) cc_final: 0.8084 (mtt) REVERT: A 461 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8739 (pp) REVERT: A 544 ASP cc_start: 0.8648 (t0) cc_final: 0.8420 (t0) REVERT: A 749 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8397 (mm-30) REVERT: A 790 ILE cc_start: 0.9043 (mm) cc_final: 0.8826 (mt) REVERT: A 896 ASP cc_start: 0.8532 (m-30) cc_final: 0.8293 (m-30) REVERT: A 1115 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: A 1159 ARG cc_start: 0.8892 (mtt180) cc_final: 0.8114 (tpt90) REVERT: A 1178 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6861 (tmt170) REVERT: A 1255 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8669 (tm-30) REVERT: A 1317 MET cc_start: 0.8557 (tpt) cc_final: 0.8090 (tpt) REVERT: B 236 ILE cc_start: 0.8329 (pt) cc_final: 0.7861 (mm) REVERT: B 243 MET cc_start: 0.8223 (tpp) cc_final: 0.7781 (mmp) REVERT: B 530 GLU cc_start: 0.8418 (pp20) cc_final: 0.7438 (pp20) REVERT: B 588 ASP cc_start: 0.8498 (t0) cc_final: 0.8254 (t0) REVERT: B 794 MET cc_start: 0.8528 (tpp) cc_final: 0.8269 (mpp) REVERT: B 1003 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8729 (t80) REVERT: B 1004 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8777 (t80) REVERT: B 1042 ASP cc_start: 0.8680 (t0) cc_final: 0.8288 (t0) REVERT: B 1120 MET cc_start: 0.7841 (mtm) cc_final: 0.7593 (ptp) REVERT: C 28 ASP cc_start: 0.8361 (t0) cc_final: 0.7939 (t0) REVERT: C 55 HIS cc_start: 0.8065 (t-90) cc_final: 0.7796 (t-90) REVERT: C 56 MET cc_start: 0.8539 (tmm) cc_final: 0.8245 (tmm) REVERT: C 191 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7745 (ptt-90) REVERT: G 6 GLU cc_start: 0.7830 (mp0) cc_final: 0.7457 (mp0) REVERT: G 7 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8085 (mtt) REVERT: G 45 CYS cc_start: 0.8570 (m) cc_final: 0.8277 (m) REVERT: G 50 ASP cc_start: 0.7781 (m-30) cc_final: 0.7471 (m-30) REVERT: G 82 ASP cc_start: 0.5977 (t0) cc_final: 0.5732 (t70) REVERT: G 129 TRP cc_start: 0.7072 (m-10) cc_final: 0.6829 (m100) REVERT: K 60 MET cc_start: 0.9079 (tpp) cc_final: 0.8791 (mmt) REVERT: K 104 MET cc_start: 0.8712 (ttm) cc_final: 0.8451 (ttm) REVERT: L 27 GLU cc_start: 0.7109 (tp30) cc_final: 0.6843 (tp30) REVERT: P 205 GLN cc_start: 0.5001 (OUTLIER) cc_final: 0.3567 (pm20) REVERT: E 90 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7057 (p90) REVERT: E 108 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8305 (mt0) REVERT: E 121 MET cc_start: 0.8044 (tmm) cc_final: 0.7374 (tmm) REVERT: E 125 TYR cc_start: 0.7243 (m-80) cc_final: 0.6835 (m-10) REVERT: E 128 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7726 (mm-30) REVERT: F 84 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8048 (mm-30) REVERT: J 41 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8592 (mmtm) REVERT: O 106 ILE cc_start: 0.7820 (mt) cc_final: 0.7600 (mm) REVERT: O 139 MET cc_start: 0.4023 (ttp) cc_final: 0.3744 (tmm) REVERT: O 385 MET cc_start: 0.6011 (mmm) cc_final: 0.5285 (tpp) REVERT: O 448 GLU cc_start: 0.8333 (tp30) cc_final: 0.7796 (pp20) REVERT: Q 37 LEU cc_start: 0.7581 (mp) cc_final: 0.7352 (mt) REVERT: Q 55 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6669 (pm20) REVERT: Q 68 MET cc_start: 0.6941 (ppp) cc_final: 0.6028 (ppp) REVERT: Q 80 GLU cc_start: 0.5460 (mp0) cc_final: 0.5234 (mp0) REVERT: D 4 LYS cc_start: 0.8198 (ttpp) cc_final: 0.7848 (tppt) REVERT: D 59 ARG cc_start: 0.7196 (pmt-80) cc_final: 0.6347 (ptt-90) REVERT: D 74 LYS cc_start: -0.0043 (mmtt) cc_final: -0.0523 (mmtt) REVERT: D 100 MET cc_start: 0.5916 (ptp) cc_final: 0.5333 (ptp) REVERT: M 38 THR cc_start: 0.8116 (m) cc_final: 0.7693 (p) REVERT: M 149 HIS cc_start: 0.8520 (m90) cc_final: 0.8271 (m-70) REVERT: M 189 ARG cc_start: 0.5154 (tmt170) cc_final: 0.4686 (ttt90) REVERT: M 191 GLN cc_start: 0.8864 (pm20) cc_final: 0.8145 (tp40) REVERT: N 253 GLU cc_start: 0.7727 (mp0) cc_final: 0.7522 (mp0) REVERT: N 264 GLU cc_start: 0.8030 (mp0) cc_final: 0.6016 (pp20) REVERT: N 347 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7679 (t0) REVERT: I 4 PHE cc_start: 0.6019 (m-80) cc_final: 0.5698 (m-80) outliers start: 162 outliers final: 113 residues processed: 666 average time/residue: 0.2282 time to fit residues: 253.3389 Evaluate side-chains 632 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 507 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 90 TYR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 446 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 428 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 412 optimal weight: 7.9990 chunk 414 optimal weight: 0.0770 chunk 202 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 overall best weight: 2.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 ASN B1010 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN C 139 GLN C 166 HIS ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS K 38 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN E 129 GLN O 445 ASN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 89 HIS M 11 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.111908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.083022 restraints weight = 89039.421| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.97 r_work: 0.3180 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37375 Z= 0.171 Angle : 0.729 24.554 50580 Z= 0.354 Chirality : 0.046 0.312 5713 Planarity : 0.005 0.055 6357 Dihedral : 10.945 179.002 5329 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.43 % Favored : 91.41 % Rotamer: Outliers : 4.50 % Allowed : 22.96 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.12), residues: 4426 helix: -0.23 (0.13), residues: 1559 sheet: -2.25 (0.22), residues: 505 loop : -1.95 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 81 TYR 0.059 0.002 TYR D 47 PHE 0.019 0.001 PHE B 278 TRP 0.034 0.002 TRP G 201 HIS 0.017 0.001 HIS D 89 Details of bonding type rmsd covalent geometry : bond 0.00396 (37355) covalent geometry : angle 0.69987 (50559) hydrogen bonds : bond 0.03644 ( 1155) hydrogen bonds : angle 4.78416 ( 3213) metal coordination : bond 0.00999 ( 20) metal coordination : angle 10.09775 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 550 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.6418 (t80) cc_final: 0.5308 (t80) REVERT: A 65 LYS cc_start: 0.8817 (tptp) cc_final: 0.8437 (tttt) REVERT: A 128 TYR cc_start: 0.8669 (t80) cc_final: 0.8448 (t80) REVERT: A 158 HIS cc_start: 0.7287 (m90) cc_final: 0.7052 (m90) REVERT: A 305 MET cc_start: 0.7992 (ppp) cc_final: 0.7459 (ppp) REVERT: A 440 MET cc_start: 0.8542 (mtt) cc_final: 0.8205 (mtt) REVERT: A 544 ASP cc_start: 0.8630 (t0) cc_final: 0.8352 (t0) REVERT: A 749 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8513 (mm-30) REVERT: A 790 ILE cc_start: 0.9062 (mm) cc_final: 0.8850 (mt) REVERT: A 896 ASP cc_start: 0.8645 (m-30) cc_final: 0.8440 (m-30) REVERT: A 1178 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6768 (tmt170) REVERT: A 1209 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7864 (ptt-90) REVERT: A 1267 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9116 (mp) REVERT: A 1317 MET cc_start: 0.8589 (tpt) cc_final: 0.8261 (tpt) REVERT: A 1361 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8098 (mttt) REVERT: B 236 ILE cc_start: 0.8344 (pt) cc_final: 0.7958 (mm) REVERT: B 243 MET cc_start: 0.8303 (tpp) cc_final: 0.7741 (mmp) REVERT: B 354 ARG cc_start: 0.6436 (ptm160) cc_final: 0.6091 (ptm160) REVERT: B 445 TYR cc_start: 0.8770 (t80) cc_final: 0.8560 (t80) REVERT: B 530 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7618 (pp20) REVERT: B 904 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8264 (ptpt) REVERT: B 1003 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8683 (t80) REVERT: B 1004 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8855 (t80) REVERT: B 1042 ASP cc_start: 0.8702 (t0) cc_final: 0.8306 (t0) REVERT: C 28 ASP cc_start: 0.8155 (t0) cc_final: 0.7911 (t0) REVERT: C 55 HIS cc_start: 0.8129 (t-90) cc_final: 0.7862 (t-90) REVERT: C 56 MET cc_start: 0.8621 (tmm) cc_final: 0.8372 (tmm) REVERT: C 191 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7740 (ptt-90) REVERT: G 7 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8122 (mtt) REVERT: G 25 SER cc_start: 0.8578 (m) cc_final: 0.8308 (t) REVERT: G 45 CYS cc_start: 0.8758 (m) cc_final: 0.8506 (m) REVERT: G 129 TRP cc_start: 0.7153 (m-10) cc_final: 0.6862 (m100) REVERT: K 60 MET cc_start: 0.8997 (tpp) cc_final: 0.8709 (mmt) REVERT: K 102 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8009 (mt-10) REVERT: K 104 MET cc_start: 0.8739 (ttm) cc_final: 0.8499 (ttm) REVERT: L 27 GLU cc_start: 0.7278 (tp30) cc_final: 0.6971 (tp30) REVERT: L 32 ASP cc_start: 0.8641 (m-30) cc_final: 0.8187 (m-30) REVERT: L 34 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8642 (mp) REVERT: P 205 GLN cc_start: 0.5129 (OUTLIER) cc_final: 0.4073 (pm20) REVERT: E 90 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.6977 (p90) REVERT: E 121 MET cc_start: 0.8155 (tmm) cc_final: 0.7626 (tmm) REVERT: E 125 TYR cc_start: 0.7293 (m-80) cc_final: 0.6960 (m-10) REVERT: F 82 GLU cc_start: 0.8229 (pp20) cc_final: 0.7989 (pp20) REVERT: F 109 TYR cc_start: 0.9020 (m-80) cc_final: 0.8615 (m-10) REVERT: J 41 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8684 (mmtm) REVERT: O 85 MET cc_start: 0.8300 (mpp) cc_final: 0.7761 (mpp) REVERT: O 106 ILE cc_start: 0.7824 (mt) cc_final: 0.7520 (mm) REVERT: O 139 MET cc_start: 0.4251 (ttp) cc_final: 0.3995 (tmm) REVERT: O 385 MET cc_start: 0.6197 (mmm) cc_final: 0.5347 (tpp) REVERT: O 448 GLU cc_start: 0.8536 (tp30) cc_final: 0.7944 (tp30) REVERT: O 461 LEU cc_start: 0.7908 (mt) cc_final: 0.7459 (pp) REVERT: Q 55 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6768 (pm20) REVERT: Q 68 MET cc_start: 0.6895 (ppp) cc_final: 0.6610 (ppp) REVERT: D 4 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7887 (tppt) REVERT: D 22 ASP cc_start: 0.8215 (m-30) cc_final: 0.7938 (m-30) REVERT: D 59 ARG cc_start: 0.7242 (pmt-80) cc_final: 0.6963 (ppt170) REVERT: M 40 ASP cc_start: 0.7686 (t0) cc_final: 0.7360 (t0) REVERT: M 97 MET cc_start: 0.5440 (ttp) cc_final: 0.4957 (ptm) REVERT: M 143 ASP cc_start: 0.7905 (m-30) cc_final: 0.7663 (m-30) REVERT: M 146 ASP cc_start: 0.9021 (m-30) cc_final: 0.8812 (p0) REVERT: M 149 HIS cc_start: 0.8560 (m90) cc_final: 0.8350 (m-70) REVERT: M 189 ARG cc_start: 0.5200 (ttt180) cc_final: 0.4826 (ttt90) REVERT: M 191 GLN cc_start: 0.8828 (pm20) cc_final: 0.8148 (tp40) REVERT: N 253 GLU cc_start: 0.7779 (mp0) cc_final: 0.7543 (mp0) REVERT: N 264 GLU cc_start: 0.8168 (mp0) cc_final: 0.6104 (pp20) REVERT: N 347 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7610 (t0) REVERT: N 382 LYS cc_start: 0.7457 (ttmt) cc_final: 0.7106 (tttt) REVERT: I 27 THR cc_start: 0.7029 (p) cc_final: 0.6665 (t) outliers start: 179 outliers final: 117 residues processed: 671 average time/residue: 0.2344 time to fit residues: 260.0248 Evaluate side-chains 635 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 503 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1267 ILE Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain A residue 1361 LYS Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 904 LYS Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 90 TYR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain O residue 434 MET Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 76 optimal weight: 9.9990 chunk 227 optimal weight: 0.5980 chunk 128 optimal weight: 0.0070 chunk 159 optimal weight: 7.9990 chunk 370 optimal weight: 0.0020 chunk 360 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 197 optimal weight: 0.0870 chunk 317 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 HIS O 245 HIS ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.113182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084463 restraints weight = 88714.188| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.97 r_work: 0.3212 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 37375 Z= 0.125 Angle : 0.710 25.596 50580 Z= 0.344 Chirality : 0.045 0.309 5713 Planarity : 0.004 0.055 6357 Dihedral : 10.770 178.882 5324 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.27 % Favored : 91.57 % Rotamer: Outliers : 3.47 % Allowed : 24.42 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -1.90 (0.12), residues: 4426 helix: -0.05 (0.13), residues: 1553 sheet: -2.07 (0.22), residues: 501 loop : -1.94 (0.13), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 35 TYR 0.022 0.001 TYR P 219 PHE 0.023 0.001 PHE A 288 TRP 0.029 0.002 TRP M 205 HIS 0.022 0.001 HIS D 89 Details of bonding type rmsd covalent geometry : bond 0.00289 (37355) covalent geometry : angle 0.68120 (50559) hydrogen bonds : bond 0.03422 ( 1155) hydrogen bonds : angle 4.67393 ( 3213) metal coordination : bond 0.00704 ( 20) metal coordination : angle 9.88325 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 555 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7646 (mt) REVERT: A 53 TYR cc_start: 0.6239 (t80) cc_final: 0.5152 (t80) REVERT: A 158 HIS cc_start: 0.7295 (m90) cc_final: 0.7064 (m90) REVERT: A 281 MET cc_start: 0.8203 (mmm) cc_final: 0.7940 (mmm) REVERT: A 461 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8752 (pp) REVERT: A 544 ASP cc_start: 0.8590 (t0) cc_final: 0.8295 (t0) REVERT: A 749 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8491 (mm-30) REVERT: A 790 ILE cc_start: 0.9026 (mm) cc_final: 0.8822 (mt) REVERT: A 896 ASP cc_start: 0.8665 (m-30) cc_final: 0.8447 (m-30) REVERT: A 1178 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6906 (tmt170) REVERT: A 1267 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9113 (mp) REVERT: A 1317 MET cc_start: 0.8653 (tpt) cc_final: 0.8190 (tpt) REVERT: B 236 ILE cc_start: 0.8365 (pt) cc_final: 0.7857 (mm) REVERT: B 243 MET cc_start: 0.8251 (tpp) cc_final: 0.7693 (mmp) REVERT: B 354 ARG cc_start: 0.6491 (ptm160) cc_final: 0.6181 (ptm160) REVERT: B 445 TYR cc_start: 0.8678 (t80) cc_final: 0.8465 (t80) REVERT: B 530 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7585 (pp20) REVERT: B 1003 TYR cc_start: 0.9155 (OUTLIER) cc_final: 0.8556 (t80) REVERT: B 1004 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8779 (t80) REVERT: B 1042 ASP cc_start: 0.8619 (t0) cc_final: 0.8249 (t0) REVERT: B 1120 MET cc_start: 0.7843 (mtm) cc_final: 0.7567 (ptp) REVERT: C 55 HIS cc_start: 0.8055 (t-90) cc_final: 0.7781 (t-90) REVERT: C 191 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7744 (ptt-90) REVERT: C 306 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6736 (p90) REVERT: G 6 GLU cc_start: 0.7991 (mp0) cc_final: 0.7783 (mp0) REVERT: G 7 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8133 (mtt) REVERT: G 45 CYS cc_start: 0.8746 (m) cc_final: 0.8470 (m) REVERT: G 50 ASP cc_start: 0.7696 (m-30) cc_final: 0.7385 (m-30) REVERT: G 129 TRP cc_start: 0.7025 (m-10) cc_final: 0.6749 (m100) REVERT: G 184 TYR cc_start: 0.5547 (OUTLIER) cc_final: 0.4285 (m-80) REVERT: K 60 MET cc_start: 0.8974 (tpp) cc_final: 0.8710 (mmt) REVERT: K 89 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8305 (p) REVERT: K 102 GLU cc_start: 0.8632 (mm-30) cc_final: 0.7980 (mt-10) REVERT: L 32 ASP cc_start: 0.8642 (m-30) cc_final: 0.8306 (m-30) REVERT: P 205 GLN cc_start: 0.5071 (OUTLIER) cc_final: 0.4314 (pm20) REVERT: E 121 MET cc_start: 0.8107 (tmm) cc_final: 0.7566 (tmm) REVERT: E 125 TYR cc_start: 0.7279 (m-80) cc_final: 0.6860 (m-10) REVERT: F 109 TYR cc_start: 0.8996 (m-80) cc_final: 0.8714 (m-10) REVERT: H 33 GLU cc_start: 0.8494 (tp30) cc_final: 0.8280 (tt0) REVERT: O 85 MET cc_start: 0.8202 (mpp) cc_final: 0.7676 (mpp) REVERT: O 139 MET cc_start: 0.4336 (ttp) cc_final: 0.4112 (tmm) REVERT: O 385 MET cc_start: 0.6195 (mmm) cc_final: 0.5173 (tpp) REVERT: O 448 GLU cc_start: 0.8397 (tp30) cc_final: 0.7821 (tp30) REVERT: O 461 LEU cc_start: 0.7962 (mt) cc_final: 0.7518 (pp) REVERT: Q 55 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: Q 80 GLU cc_start: 0.4962 (mp0) cc_final: 0.4676 (mp0) REVERT: Q 115 LYS cc_start: 0.4411 (mttt) cc_final: 0.3250 (mttp) REVERT: D 4 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7868 (tppt) REVERT: D 22 ASP cc_start: 0.8171 (m-30) cc_final: 0.7914 (m-30) REVERT: D 59 ARG cc_start: 0.7183 (pmt-80) cc_final: 0.6880 (ppt170) REVERT: D 74 LYS cc_start: 0.0358 (mttt) cc_final: 0.0123 (mmtt) REVERT: M 97 MET cc_start: 0.5250 (ttp) cc_final: 0.4679 (ptm) REVERT: M 143 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: M 149 HIS cc_start: 0.8545 (m90) cc_final: 0.8309 (m-70) REVERT: M 189 ARG cc_start: 0.5143 (ttt180) cc_final: 0.4787 (ttt90) REVERT: M 191 GLN cc_start: 0.8777 (pm20) cc_final: 0.8069 (tp40) REVERT: M 205 TRP cc_start: 0.8032 (m100) cc_final: 0.7451 (m-90) REVERT: N 253 GLU cc_start: 0.7744 (mp0) cc_final: 0.7470 (mp0) REVERT: N 264 GLU cc_start: 0.8199 (mp0) cc_final: 0.5835 (tp30) REVERT: N 347 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7524 (t0) REVERT: N 382 LYS cc_start: 0.7433 (ttmt) cc_final: 0.7159 (tttt) REVERT: I 27 THR cc_start: 0.7026 (p) cc_final: 0.6819 (t) outliers start: 138 outliers final: 95 residues processed: 649 average time/residue: 0.2357 time to fit residues: 252.8289 Evaluate side-chains 622 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 511 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1267 ILE Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain O residue 434 MET Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 357 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 416 optimal weight: 10.0000 chunk 308 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 438 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 319 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 343 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN B1010 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 HIS ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.108998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.080140 restraints weight = 88661.813| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.99 r_work: 0.3134 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.6527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 37375 Z= 0.206 Angle : 0.771 30.244 50580 Z= 0.373 Chirality : 0.047 0.316 5713 Planarity : 0.005 0.053 6357 Dihedral : 10.793 179.433 5323 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.06 % Favored : 90.76 % Rotamer: Outliers : 3.92 % Allowed : 24.40 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.12), residues: 4426 helix: -0.06 (0.13), residues: 1556 sheet: -2.12 (0.22), residues: 504 loop : -1.92 (0.13), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 376 TYR 0.049 0.002 TYR D 47 PHE 0.021 0.002 PHE N 268 TRP 0.028 0.002 TRP G 200 HIS 0.011 0.001 HIS D 89 Details of bonding type rmsd covalent geometry : bond 0.00485 (37355) covalent geometry : angle 0.73403 (50559) hydrogen bonds : bond 0.03744 ( 1155) hydrogen bonds : angle 4.82841 ( 3213) metal coordination : bond 0.01072 ( 20) metal coordination : angle 11.52883 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 533 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.8777 (t80) cc_final: 0.8538 (t80) REVERT: A 281 MET cc_start: 0.8237 (mmm) cc_final: 0.8019 (mmm) REVERT: A 306 ILE cc_start: 0.8038 (tp) cc_final: 0.7790 (tt) REVERT: A 429 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8416 (mptt) REVERT: A 440 MET cc_start: 0.8669 (mtt) cc_final: 0.8281 (mtt) REVERT: A 461 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8763 (pp) REVERT: A 544 ASP cc_start: 0.8728 (t0) cc_final: 0.8436 (t0) REVERT: A 749 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8538 (mm-30) REVERT: A 896 ASP cc_start: 0.8751 (m-30) cc_final: 0.8525 (m-30) REVERT: A 1178 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6972 (tmt170) REVERT: A 1209 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7797 (tmm-80) REVERT: A 1317 MET cc_start: 0.8722 (tpt) cc_final: 0.8252 (tpt) REVERT: B 236 ILE cc_start: 0.8503 (pt) cc_final: 0.7976 (mm) REVERT: B 243 MET cc_start: 0.8346 (tpp) cc_final: 0.7797 (mmp) REVERT: B 254 MET cc_start: 0.8294 (mmt) cc_final: 0.7771 (mmp) REVERT: B 354 ARG cc_start: 0.6493 (ptm160) cc_final: 0.6171 (ptm160) REVERT: B 530 GLU cc_start: 0.8567 (pp20) cc_final: 0.7717 (pp20) REVERT: B 1003 TYR cc_start: 0.9244 (OUTLIER) cc_final: 0.8620 (t80) REVERT: B 1004 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8888 (t80) REVERT: B 1042 ASP cc_start: 0.8741 (t0) cc_final: 0.8278 (t0) REVERT: B 1120 MET cc_start: 0.7715 (mtm) cc_final: 0.7460 (ptp) REVERT: C 28 ASP cc_start: 0.8337 (t70) cc_final: 0.8062 (t70) REVERT: C 55 HIS cc_start: 0.8365 (t-90) cc_final: 0.7903 (t-90) REVERT: C 191 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7792 (ptt-90) REVERT: C 196 ASP cc_start: 0.9027 (t70) cc_final: 0.8747 (t0) REVERT: C 306 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6759 (p90) REVERT: G 7 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7996 (mtt) REVERT: G 9 ASP cc_start: 0.7835 (t0) cc_final: 0.7325 (m-30) REVERT: G 25 SER cc_start: 0.8640 (m) cc_final: 0.8393 (t) REVERT: G 129 TRP cc_start: 0.7115 (m-10) cc_final: 0.6430 (m100) REVERT: G 184 TYR cc_start: 0.5606 (OUTLIER) cc_final: 0.4372 (m-80) REVERT: K 89 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8369 (p) REVERT: K 102 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8040 (mt-10) REVERT: P 198 SER cc_start: 0.8164 (m) cc_final: 0.7943 (p) REVERT: P 205 GLN cc_start: 0.5326 (OUTLIER) cc_final: 0.4959 (pm20) REVERT: P 213 SER cc_start: 0.5899 (p) cc_final: 0.5620 (p) REVERT: P 222 GLU cc_start: 0.7823 (tp30) cc_final: 0.6852 (tt0) REVERT: P 303 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7575 (t) REVERT: E 121 MET cc_start: 0.8228 (tmm) cc_final: 0.7844 (tmm) REVERT: F 84 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7851 (mm-30) REVERT: H 33 GLU cc_start: 0.8595 (tp30) cc_final: 0.8366 (tt0) REVERT: O 385 MET cc_start: 0.6265 (mmm) cc_final: 0.5298 (tpp) REVERT: O 398 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8081 (mmt) REVERT: O 448 GLU cc_start: 0.8551 (tp30) cc_final: 0.8095 (tp30) REVERT: O 461 LEU cc_start: 0.7953 (mt) cc_final: 0.7526 (pp) REVERT: Q 55 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6947 (pm20) REVERT: Q 115 LYS cc_start: 0.4634 (mttt) cc_final: 0.3261 (mttp) REVERT: D 4 LYS cc_start: 0.8142 (ttpp) cc_final: 0.7861 (tppt) REVERT: D 22 ASP cc_start: 0.8295 (m-30) cc_final: 0.7953 (m-30) REVERT: D 59 ARG cc_start: 0.7464 (pmt-80) cc_final: 0.7217 (ppt170) REVERT: D 74 LYS cc_start: 0.0695 (mttt) cc_final: 0.0373 (mmtt) REVERT: M 53 GLN cc_start: 0.6997 (mp10) cc_final: 0.6703 (tt0) REVERT: M 97 MET cc_start: 0.5577 (ttp) cc_final: 0.4439 (ptm) REVERT: M 114 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: M 149 HIS cc_start: 0.8577 (m90) cc_final: 0.8364 (m-70) REVERT: M 191 GLN cc_start: 0.8828 (pm20) cc_final: 0.8151 (tp40) REVERT: N 253 GLU cc_start: 0.7780 (mp0) cc_final: 0.7475 (mp0) REVERT: N 264 GLU cc_start: 0.8261 (mp0) cc_final: 0.6261 (pp20) REVERT: N 328 LYS cc_start: 0.8618 (tppt) cc_final: 0.8096 (tptp) REVERT: N 347 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7620 (t0) REVERT: N 349 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6768 (t) REVERT: N 350 MET cc_start: 0.7048 (mpp) cc_final: 0.6835 (mpp) REVERT: N 382 LYS cc_start: 0.7563 (ttmt) cc_final: 0.7267 (tttt) outliers start: 156 outliers final: 114 residues processed: 643 average time/residue: 0.2286 time to fit residues: 245.6956 Evaluate side-chains 635 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 503 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 232 MET Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain P residue 307 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain O residue 398 MET Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain O residue 434 MET Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain N residue 375 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 190 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 333 optimal weight: 0.7980 chunk 255 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 342 optimal weight: 5.9990 chunk 92 optimal weight: 0.0370 chunk 265 optimal weight: 0.9980 chunk 440 optimal weight: 6.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN B1118 GLN ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN E 108 GLN E 129 GLN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 GLN ** I 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.110425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.081738 restraints weight = 89114.845| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.97 r_work: 0.3156 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37375 Z= 0.142 Angle : 0.732 26.959 50580 Z= 0.353 Chirality : 0.045 0.329 5713 Planarity : 0.005 0.054 6357 Dihedral : 10.721 178.941 5321 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.25 % Favored : 91.55 % Rotamer: Outliers : 3.40 % Allowed : 24.75 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.13), residues: 4426 helix: 0.07 (0.13), residues: 1559 sheet: -2.01 (0.23), residues: 509 loop : -1.93 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 376 TYR 0.026 0.001 TYR P 219 PHE 0.029 0.001 PHE A 288 TRP 0.028 0.002 TRP G 200 HIS 0.006 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00334 (37355) covalent geometry : angle 0.70059 (50559) hydrogen bonds : bond 0.03485 ( 1155) hydrogen bonds : angle 4.69251 ( 3213) metal coordination : bond 0.00691 ( 20) metal coordination : angle 10.36239 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 531 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7667 (mt) REVERT: A 128 TYR cc_start: 0.8727 (t80) cc_final: 0.8473 (t80) REVERT: A 281 MET cc_start: 0.8254 (mmm) cc_final: 0.8020 (mmm) REVERT: A 429 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8434 (mptt) REVERT: A 440 MET cc_start: 0.8665 (mtt) cc_final: 0.8316 (mtt) REVERT: A 461 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8841 (pp) REVERT: A 544 ASP cc_start: 0.8626 (t0) cc_final: 0.8307 (t0) REVERT: A 749 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8536 (mm-30) REVERT: A 1178 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7016 (tmt170) REVERT: A 1209 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7886 (tmm-80) REVERT: A 1317 MET cc_start: 0.8631 (tpt) cc_final: 0.8185 (tpt) REVERT: B 236 ILE cc_start: 0.8329 (pt) cc_final: 0.7942 (mm) REVERT: B 243 MET cc_start: 0.8201 (tpp) cc_final: 0.7675 (mmp) REVERT: B 254 MET cc_start: 0.8280 (mmt) cc_final: 0.7696 (mmp) REVERT: B 354 ARG cc_start: 0.6534 (ptm160) cc_final: 0.6236 (ptm160) REVERT: B 430 LYS cc_start: 0.8217 (mttm) cc_final: 0.7850 (pttt) REVERT: B 445 TYR cc_start: 0.8690 (t80) cc_final: 0.8473 (t80) REVERT: B 530 GLU cc_start: 0.8519 (pp20) cc_final: 0.7604 (pp20) REVERT: B 1003 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8560 (t80) REVERT: B 1004 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8797 (t80) REVERT: B 1042 ASP cc_start: 0.8671 (t0) cc_final: 0.8308 (t0) REVERT: B 1120 MET cc_start: 0.7835 (mtm) cc_final: 0.7581 (ptp) REVERT: C 28 ASP cc_start: 0.8236 (t70) cc_final: 0.8006 (t70) REVERT: C 55 HIS cc_start: 0.8267 (t-90) cc_final: 0.7921 (t-90) REVERT: C 191 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7790 (ptt-90) REVERT: C 196 ASP cc_start: 0.8950 (t70) cc_final: 0.8699 (t0) REVERT: C 306 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6727 (p90) REVERT: G 7 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8054 (mtt) REVERT: G 9 ASP cc_start: 0.7696 (t0) cc_final: 0.7072 (m-30) REVERT: G 25 SER cc_start: 0.8632 (m) cc_final: 0.8387 (t) REVERT: G 129 TRP cc_start: 0.7003 (m-10) cc_final: 0.6367 (m100) REVERT: G 184 TYR cc_start: 0.5554 (OUTLIER) cc_final: 0.4260 (m-80) REVERT: K 47 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7783 (mm-30) REVERT: K 89 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8377 (p) REVERT: K 102 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8035 (mt-10) REVERT: L 32 ASP cc_start: 0.8690 (m-30) cc_final: 0.8390 (m-30) REVERT: P 205 GLN cc_start: 0.5318 (OUTLIER) cc_final: 0.4997 (pm20) REVERT: P 213 SER cc_start: 0.6153 (p) cc_final: 0.5868 (p) REVERT: P 303 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7565 (t) REVERT: E 121 MET cc_start: 0.8271 (tmm) cc_final: 0.7965 (tmm) REVERT: E 151 MET cc_start: 0.7730 (mmm) cc_final: 0.7339 (tpt) REVERT: J 41 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8554 (mmtt) REVERT: O 85 MET cc_start: 0.8091 (mpp) cc_final: 0.7837 (mpp) REVERT: O 385 MET cc_start: 0.6167 (mmm) cc_final: 0.5121 (tpp) REVERT: O 448 GLU cc_start: 0.8600 (tp30) cc_final: 0.8139 (tp30) REVERT: O 461 LEU cc_start: 0.7979 (mt) cc_final: 0.7529 (pp) REVERT: Q 55 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: D 22 ASP cc_start: 0.8278 (m-30) cc_final: 0.7934 (m-30) REVERT: D 59 ARG cc_start: 0.7402 (pmt-80) cc_final: 0.7161 (ppt170) REVERT: M 53 GLN cc_start: 0.6908 (mp10) cc_final: 0.6616 (tt0) REVERT: M 60 MET cc_start: 0.6374 (mmm) cc_final: 0.5785 (mmm) REVERT: M 97 MET cc_start: 0.5536 (ttp) cc_final: 0.4459 (ptm) REVERT: M 100 GLN cc_start: 0.8134 (tt0) cc_final: 0.7660 (tp40) REVERT: M 114 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: M 138 SER cc_start: 0.7043 (p) cc_final: 0.6535 (p) REVERT: M 149 HIS cc_start: 0.8592 (m90) cc_final: 0.8363 (m-70) REVERT: M 189 ARG cc_start: 0.5379 (ttt180) cc_final: 0.4822 (ttt90) REVERT: M 191 GLN cc_start: 0.8816 (pm20) cc_final: 0.8209 (tp40) REVERT: M 205 TRP cc_start: 0.8124 (m100) cc_final: 0.7294 (m-90) REVERT: N 253 GLU cc_start: 0.7770 (mp0) cc_final: 0.7448 (mp0) REVERT: N 264 GLU cc_start: 0.8304 (mp0) cc_final: 0.6402 (pp20) REVERT: N 347 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7664 (t0) REVERT: N 349 THR cc_start: 0.7077 (OUTLIER) cc_final: 0.6850 (t) REVERT: N 382 LYS cc_start: 0.7507 (ttmt) cc_final: 0.7245 (tttt) outliers start: 135 outliers final: 98 residues processed: 627 average time/residue: 0.2221 time to fit residues: 231.8092 Evaluate side-chains 622 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 507 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 270 GLN Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 446 optimal weight: 10.0000 chunk 303 optimal weight: 5.9990 chunk 405 optimal weight: 6.9990 chunk 349 optimal weight: 0.0040 chunk 153 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 342 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 378 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 overall best weight: 2.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN C 166 HIS ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN E 129 GLN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.109977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.081085 restraints weight = 89320.146| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.03 r_work: 0.3153 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.6718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 37375 Z= 0.197 Angle : 0.885 59.200 50580 Z= 0.464 Chirality : 0.045 0.346 5713 Planarity : 0.005 0.054 6357 Dihedral : 10.717 178.953 5321 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.43 % Favored : 91.37 % Rotamer: Outliers : 3.14 % Allowed : 25.23 % Favored : 71.63 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.13), residues: 4426 helix: 0.07 (0.13), residues: 1560 sheet: -2.00 (0.23), residues: 509 loop : -1.93 (0.13), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 449 TYR 0.028 0.002 TYR A 97 PHE 0.017 0.001 PHE B 662 TRP 0.027 0.002 TRP G 200 HIS 0.007 0.001 HIS O 27 Details of bonding type rmsd covalent geometry : bond 0.00442 (37355) covalent geometry : angle 0.85925 (50559) hydrogen bonds : bond 0.03502 ( 1155) hydrogen bonds : angle 4.69483 ( 3213) metal coordination : bond 0.00710 ( 20) metal coordination : angle 10.35289 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8852 Ramachandran restraints generated. 4426 Oldfield, 0 Emsley, 4426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 506 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7671 (mt) REVERT: A 128 TYR cc_start: 0.8747 (t80) cc_final: 0.8483 (t80) REVERT: A 281 MET cc_start: 0.8227 (mmm) cc_final: 0.7998 (mmm) REVERT: A 429 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8427 (mptt) REVERT: A 440 MET cc_start: 0.8663 (mtt) cc_final: 0.8321 (mtt) REVERT: A 461 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8817 (pp) REVERT: A 544 ASP cc_start: 0.8682 (t0) cc_final: 0.8379 (t0) REVERT: A 749 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8539 (mm-30) REVERT: A 1178 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6998 (tmt170) REVERT: A 1209 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7866 (tmm-80) REVERT: A 1317 MET cc_start: 0.8655 (tpt) cc_final: 0.8198 (tpt) REVERT: B 236 ILE cc_start: 0.8407 (pt) cc_final: 0.7937 (mm) REVERT: B 243 MET cc_start: 0.8219 (tpp) cc_final: 0.7690 (mmp) REVERT: B 254 MET cc_start: 0.8255 (mmt) cc_final: 0.7659 (mmp) REVERT: B 354 ARG cc_start: 0.6528 (ptm160) cc_final: 0.6229 (ptm160) REVERT: B 424 TRP cc_start: 0.7176 (m100) cc_final: 0.6405 (m100) REVERT: B 430 LYS cc_start: 0.8224 (mttm) cc_final: 0.7852 (pttt) REVERT: B 445 TYR cc_start: 0.8724 (t80) cc_final: 0.8502 (t80) REVERT: B 530 GLU cc_start: 0.8543 (pp20) cc_final: 0.7609 (pp20) REVERT: B 1003 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8596 (t80) REVERT: B 1004 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8828 (t80) REVERT: B 1042 ASP cc_start: 0.8691 (t0) cc_final: 0.8302 (t0) REVERT: B 1120 MET cc_start: 0.7814 (mtm) cc_final: 0.7559 (ptp) REVERT: C 28 ASP cc_start: 0.8272 (t70) cc_final: 0.8039 (t70) REVERT: C 55 HIS cc_start: 0.8290 (t-90) cc_final: 0.7917 (t-90) REVERT: C 191 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7800 (ptt-90) REVERT: C 196 ASP cc_start: 0.8984 (t70) cc_final: 0.8719 (t0) REVERT: C 306 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6759 (p90) REVERT: G 7 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8066 (mtt) REVERT: G 9 ASP cc_start: 0.7722 (t0) cc_final: 0.7095 (m-30) REVERT: G 25 SER cc_start: 0.8632 (m) cc_final: 0.8389 (t) REVERT: G 129 TRP cc_start: 0.7035 (m-10) cc_final: 0.6397 (m100) REVERT: G 184 TYR cc_start: 0.5546 (OUTLIER) cc_final: 0.4264 (m-80) REVERT: K 47 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7768 (mm-30) REVERT: K 89 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8402 (p) REVERT: K 102 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8042 (mt-10) REVERT: L 32 ASP cc_start: 0.8686 (m-30) cc_final: 0.8371 (m-30) REVERT: P 205 GLN cc_start: 0.5370 (OUTLIER) cc_final: 0.5025 (pm20) REVERT: P 213 SER cc_start: 0.6172 (p) cc_final: 0.5890 (p) REVERT: P 303 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7532 (t) REVERT: E 121 MET cc_start: 0.8302 (tmm) cc_final: 0.7980 (tmm) REVERT: E 151 MET cc_start: 0.7767 (mmm) cc_final: 0.7375 (tpt) REVERT: J 41 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8581 (mmtt) REVERT: O 85 MET cc_start: 0.8079 (mpp) cc_final: 0.7820 (mpp) REVERT: O 385 MET cc_start: 0.6166 (mmm) cc_final: 0.5124 (tpp) REVERT: O 448 GLU cc_start: 0.8621 (tp30) cc_final: 0.8153 (tp30) REVERT: O 461 LEU cc_start: 0.7987 (mt) cc_final: 0.7541 (pp) REVERT: Q 55 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: Q 115 LYS cc_start: 0.4812 (mttp) cc_final: 0.3403 (mttp) REVERT: D 22 ASP cc_start: 0.8273 (m-30) cc_final: 0.7931 (m-30) REVERT: D 59 ARG cc_start: 0.7438 (pmt-80) cc_final: 0.7199 (ppt170) REVERT: M 53 GLN cc_start: 0.6938 (mp10) cc_final: 0.6625 (tt0) REVERT: M 60 MET cc_start: 0.6408 (mmm) cc_final: 0.5872 (mmm) REVERT: M 97 MET cc_start: 0.5565 (ttp) cc_final: 0.4478 (ptm) REVERT: M 100 GLN cc_start: 0.8149 (tt0) cc_final: 0.7649 (tp40) REVERT: M 114 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: M 138 SER cc_start: 0.7070 (p) cc_final: 0.6536 (p) REVERT: M 149 HIS cc_start: 0.8606 (m90) cc_final: 0.8371 (m-70) REVERT: M 189 ARG cc_start: 0.5345 (ttt180) cc_final: 0.4796 (ttt90) REVERT: M 191 GLN cc_start: 0.8823 (pm20) cc_final: 0.8214 (tp40) REVERT: M 205 TRP cc_start: 0.8159 (m100) cc_final: 0.7307 (m-90) REVERT: N 253 GLU cc_start: 0.7764 (mp0) cc_final: 0.7435 (mp0) REVERT: N 264 GLU cc_start: 0.8299 (mp0) cc_final: 0.6395 (pp20) REVERT: N 347 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7659 (t0) REVERT: N 382 LYS cc_start: 0.7501 (ttmt) cc_final: 0.7248 (tttt) outliers start: 125 outliers final: 105 residues processed: 600 average time/residue: 0.2253 time to fit residues: 224.8588 Evaluate side-chains 627 residues out of total 3987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 506 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain P residue 205 GLN Chi-restraints excluded: chain P residue 277 ILE Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain P residue 303 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 168 ASN Chi-restraints excluded: chain O residue 235 TRP Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain O residue 408 GLU Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 347 ASP Chi-restraints excluded: chain N residue 375 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 39 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 443 optimal weight: 1.9990 chunk 442 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 429 optimal weight: 3.9990 chunk 320 optimal weight: 0.8980 chunk 217 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 390 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 240 optimal weight: 0.0270 chunk 168 optimal weight: 4.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN E 129 GLN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 HIS ** 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 = 0.3767 r_free = 0.3767 target = 0.110042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081351 restraints weight = 88498.471| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.01 r_work: 0.3164 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.6721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 37375 Z= 0.197 Angle : 0.885 59.200 50580 Z= 0.464 Chirality : 0.045 0.346 5713 Planarity : 0.005 0.055 6357 Dihedral : 10.717 178.953 5321 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.43 % Favored : 91.37 % Rotamer: Outliers : 3.04 % Allowed : 25.35 % Favored : 71.60 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.13), residues: 4426 helix: 0.07 (0.13), residues: 1560 sheet: -2.00 (0.23), residues: 509 loop : -1.93 (0.13), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 449 TYR 0.028 0.002 TYR A 97 PHE 0.017 0.001 PHE B 662 TRP 0.027 0.002 TRP G 200 HIS 0.007 0.001 HIS O 27 Details of bonding type rmsd covalent geometry : bond 0.00442 (37355) covalent geometry : angle 0.85926 (50559) hydrogen bonds : bond 0.03502 ( 1155) hydrogen bonds : angle 4.69483 ( 3213) metal coordination : bond 0.00710 ( 20) metal coordination : angle 10.35289 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10572.07 seconds wall clock time: 181 minutes 52.17 seconds (10912.17 seconds total)