Starting phenix.real_space_refine on Sat Mar 7 02:41:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dn3_30779/03_2026/7dn3_30779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dn3_30779/03_2026/7dn3_30779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dn3_30779/03_2026/7dn3_30779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dn3_30779/03_2026/7dn3_30779.map" model { file = "/net/cci-nas-00/data/ceres_data/7dn3_30779/03_2026/7dn3_30779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dn3_30779/03_2026/7dn3_30779.cif" } resolution = 3.5 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= 0.049 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 45 5.49 5 Mg 1 5.21 5 S 249 5.16 5 C 23212 2.51 5 N 6411 2.21 5 O 6928 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36856 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: "I" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 393 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 54} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 34 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: "X" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 327 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "Y" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 477 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "R" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 534 SG CYS A 69 98.362 67.954 107.805 1.00 96.02 S ATOM 556 SG CYS A 72 95.640 64.640 109.497 1.00 94.46 S ATOM 604 SG CYS A 79 95.192 67.076 106.302 1.00 88.70 S ATOM 1236 SG CYS A 156 63.353 93.706 135.896 1.00118.39 S ATOM 1262 SG CYS A 159 65.469 93.250 138.719 1.00121.42 S ATOM 17993 SG CYS B1080 82.403 63.720 115.962 1.00 81.64 S ATOM 18012 SG CYS B1083 81.680 65.573 118.972 1.00 81.49 S ATOM 18078 SG CYS B1092 85.646 65.364 116.253 1.00 86.49 S ATOM 18106 SG CYS B1095 83.758 63.067 120.814 1.00 88.09 S ATOM 22417 SG CYS I 5 55.633 148.605 105.275 1.00122.02 S ATOM 22565 SG CYS I 25 57.767 146.274 109.192 1.00125.31 S ATOM 23641 SG CYS L 19 122.426 95.761 62.177 1.00 81.26 S ATOM 23803 SG CYS L 39 121.911 101.343 62.390 1.00 97.98 S ATOM 24762 SG CYS P 287 89.383 78.467 141.011 1.00121.28 S ATOM 28236 SG CYS J 7 87.230 83.024 39.029 1.00 54.01 S ATOM 28260 SG CYS J 10 84.149 79.831 36.303 1.00 57.92 S ATOM 28524 SG CYS J 44 84.058 83.310 37.338 1.00 57.10 S ATOM 28530 SG CYS J 45 87.080 83.108 35.453 1.00 54.89 S Time building chain proxies: 7.70, per 1000 atoms: 0.21 Number of scatterers: 36856 At special positions: 0 Unit cell: (138.86, 183.38, 192.92, 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 45 15.00 Mg 1 11.99 O 6928 8.00 N 6411 7.00 C 23212 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: 3.29 Conformation dependent library (CDL) restraints added in 1.5 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 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8504 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 51 sheets defined 37.0% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 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: 4.429A 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: 3.742A pdb=" N LEU A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.474A 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: 3.506A pdb=" N SER A 472 " --> pdb=" O HIS A 469 " (cutoff:3.500A) removed outlier: 3.875A 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: 3.658A 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: 3.890A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.524A pdb=" N GLY A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 695 removed outlier: 3.842A 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: 3.889A 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: 3.636A 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: 3.592A pdb=" N LEU A 768 " --> pdb=" O GLY A 764 " (cutoff:3.500A) removed outlier: 3.752A 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: 3.736A 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: 4.175A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.606A 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: 3.672A 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: 3.611A pdb=" N GLU A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 979 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.612A pdb=" N ASP A1020 " --> pdb=" O GLU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1047 removed outlier: 3.529A 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: 3.569A 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: 3.581A 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: 3.570A 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: 3.845A 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: 3.602A pdb=" N ILE A1271 " --> pdb=" O ILE A1267 " (cutoff:3.500A) removed outlier: 3.510A 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: 3.840A 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: 3.608A 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: 3.697A 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: 3.685A pdb=" N LYS B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 4.340A 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: 3.655A pdb=" N ALA B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 removed outlier: 3.645A 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: 5.273A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.964A 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: 4.014A 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: 3.697A pdb=" N TYR B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.596A pdb=" N LEU B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.991A 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: 4.005A 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: 3.625A pdb=" N THR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.941A pdb=" N MET B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.638A 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: 3.683A pdb=" N ASN B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 566 removed outlier: 3.557A 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: 3.677A pdb=" N LEU B 625 " --> pdb=" O PHE B 621 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 removed outlier: 3.690A 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: 3.523A pdb=" N LEU B 665 " --> pdb=" O PHE B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 692 removed outlier: 3.784A 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: 3.840A 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: 4.436A 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: 3.791A 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: 3.734A 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: 3.914A 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: 3.924A pdb=" N SER C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.685A 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: 3.781A pdb=" N ASN K 101 " --> pdb=" O GLN K 97 " (cutoff:3.500A) removed outlier: 3.571A 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: 3.935A pdb=" N GLN P 205 " --> pdb=" O ASN P 201 " (cutoff:3.500A) removed outlier: 3.909A 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: 3.570A 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: 3.529A 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: 3.701A 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: 4.054A 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: 3.562A 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: 3.748A 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: 3.527A 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: 3.590A 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: 3.873A 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: 3.601A 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: 3.530A pdb=" N ALA O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 367 removed outlier: 3.734A 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: 3.652A pdb=" N ASP O 393 " --> pdb=" O LYS O 389 " (cutoff:3.500A) removed outlier: 3.743A 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: 3.629A 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: 4.090A 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: 3.695A 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: 3.986A 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: 3.660A 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: 3.865A 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: 4.307A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.696A 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: 4.913A 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: 9.853A 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: 4.064A 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: 7.814A 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: 8.177A pdb=" N PHE A 488 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.768A 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: 6.363A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 7.236A 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: 6.473A 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: 3.707A 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: 7.233A 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: 3.829A 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: 3.525A 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: 4.256A 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: 7.360A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 5.976A 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: 3.552A pdb=" N VAL B 828 " --> pdb=" O ILE B 856 " (cutoff:3.500A) removed outlier: 3.878A 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: 3.630A 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: 10.307A 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: 10.661A pdb=" N ASP C 238 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 6.348A 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: 6.126A pdb=" N GLU C 207 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 7.280A 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: 7.130A 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: 3.988A 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: 3.988A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 6.680A 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: 4.797A 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: 4.221A 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: 3.585A 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: 5.610A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE H 40 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 6.561A 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: 3.649A 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: 4.912A 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: 8.358A 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: 6.819A 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: 8.40 Time building geometry restraints manager: 4.30 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: 13668 1.37 - 1.56: 23467 1.56 - 1.76: 92 1.76 - 1.95: 378 1.95 - 2.14: 12 Bond restraints: 37617 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 4.20e+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 3.05e+01 bond pdb=" N LEU M 45 " pdb=" CA LEU M 45 " ideal model delta sigma weight residual 1.458 1.492 -0.033 6.30e-03 2.52e+04 2.82e+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 37612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 49220 3.36 - 6.72: 1537 6.72 - 10.09: 157 10.09 - 13.45: 16 13.45 - 16.81: 26 Bond angle restraints: 50956 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="FE2 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 90.48 -16.78 1.50e+00 4.44e-01 1.25e+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=" N ARG A 59 " pdb=" CA ARG A 59 " pdb=" C ARG A 59 " ideal model delta sigma weight residual 113.38 99.70 13.68 1.23e+00 6.61e-01 1.24e+02 ... (remaining 50951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 22161 35.52 - 71.04: 782 71.04 - 106.56: 32 106.56 - 142.08: 0 142.08 - 177.59: 1 Dihedral angle restraints: 22976 sinusoidal: 9833 harmonic: 13143 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 -145.70 23.10 0 2.50e+00 1.60e-01 8.53e+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 122.80 145.46 -22.66 0 2.50e+00 1.60e-01 8.21e+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 -141.35 19.35 0 2.50e+00 1.60e-01 5.99e+01 ... (remaining 22973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 5507 0.194 - 0.389: 226 0.389 - 0.583: 22 0.583 - 0.778: 1 0.778 - 0.972: 5 Chirality restraints: 5761 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 2.36e+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 5758 not shown) Planarity restraints: 6377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 162 " 0.024 2.00e-02 2.50e+03 4.78e-02 2.28e+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 4.70e-02 2.21e+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 4.60e-02 2.12e+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 6374 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 476 2.55 - 3.14: 29019 3.14 - 3.72: 58719 3.72 - 4.31: 81521 4.31 - 4.90: 132417 Nonbonded interactions: 302152 Sorted by model distance: nonbonded pdb=" O3' U R 9 " pdb="MG MG A1901 " model vdw 1.961 2.170 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 2.133 3.040 nonbonded pdb=" CD2 LEU N 357 " pdb=" NE2 GLN N 358 " model vdw 2.145 3.540 ... (remaining 302147 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 group one per residue 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: 2.110 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: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 40.700 Find NCS groups from input model: 0.180 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 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 37637 Z= 0.694 Angle : 1.517 56.145 50977 Z= 0.913 Chirality : 0.092 0.972 5761 Planarity : 0.008 0.080 6377 Dihedral : 17.046 177.595 14472 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.89 % Favored : 89.43 % Rotamer: Outliers : 4.73 % Allowed : 13.28 % Favored : 81.99 % 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: -4.77 (0.10), residues: 4437 helix: -3.86 (0.08), residues: 1495 sheet: -2.92 (0.20), residues: 506 loop : -2.77 (0.11), residues: 2436 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 0.036 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 0.01199 (37617) covalent geometry : angle 1.42786 (50956) hydrogen bonds : bond 0.28966 ( 1155) hydrogen bonds : angle 10.65580 ( 3213) metal coordination : bond 0.43706 ( 20) metal coordination : angle 25.28124 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 1133 time to evaluate : 1.528 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: 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 101 VAL cc_start: 0.8869 (t) cc_final: 0.8586 (p) REVERT: A 313 LEU cc_start: 0.8882 (tt) cc_final: 0.8641 (tt) REVERT: A 1190 GLN cc_start: 0.8311 (tp40) cc_final: 0.8033 (tp40) REVERT: B 317 ILE cc_start: 0.8322 (mm) cc_final: 0.7956 (tp) REVERT: B 521 GLU cc_start: 0.3960 (OUTLIER) cc_final: 0.3249 (tp30) REVERT: B 527 CYS cc_start: 0.6797 (m) cc_final: 0.6346 (m) REVERT: B 574 ILE cc_start: 0.6489 (OUTLIER) cc_final: 0.6242 (tt) REVERT: B 634 ASP cc_start: 0.5770 (p0) cc_final: 0.5484 (p0) REVERT: B 769 CYS cc_start: 0.4529 (m) cc_final: 0.4229 (m) REVERT: B 869 VAL cc_start: 0.6298 (OUTLIER) cc_final: 0.5801 (p) REVERT: C 87 MET cc_start: 0.6806 (mmm) cc_final: 0.6484 (mmm) REVERT: K 39 CYS cc_start: 0.5760 (p) cc_final: 0.5051 (p) REVERT: E 37 LEU cc_start: 0.7414 (tp) cc_final: 0.6877 (tp) REVERT: E 110 MET cc_start: 0.5770 (mtp) cc_final: 0.5526 (ttm) REVERT: O 41 HIS cc_start: 0.7706 (m90) cc_final: 0.7421 (m-70) REVERT: O 72 VAL cc_start: 0.7499 (t) cc_final: 0.6971 (p) REVERT: O 118 MET cc_start: 0.7129 (ttm) cc_final: 0.6357 (ttt) REVERT: O 415 HIS cc_start: 0.6927 (m-70) cc_final: 0.6637 (m170) REVERT: O 448 GLU cc_start: 0.8738 (tp30) cc_final: 0.8418 (pp20) REVERT: Q 32 LEU cc_start: 0.6495 (mt) cc_final: 0.5885 (pp) REVERT: Q 54 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8033 (tm-30) REVERT: N 360 LEU cc_start: 0.3914 (OUTLIER) cc_final: 0.3461 (tt) outliers start: 188 outliers final: 48 residues processed: 1248 average time/residue: 0.2362 time to fit residues: 464.5128 Evaluate side-chains 648 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 596 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 1099 ARG Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 869 VAL 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 181 GLN Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain G residue 152 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 Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain P residue 284 ARG Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 105 GLU 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 N residue 329 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS A 163 ASN A 374 ASN A 422 GLN A 511 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 144 ASN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 289 ASN B 434 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 608 ASN B 639 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN B1100 HIS C 42 GLN C 48 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS C 127 GLN C 143 GLN C 181 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS K 38 HIS K 85 GLN L 23 HIS P 274 ASN E 129 GLN E 132 GLN O 14 GLN O 16 HIS O 49 GLN ** O 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 ASN O 337 ASN O 377 GLN O 379 GLN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 415 HIS ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 457 ASN O 497 GLN O 507 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 112 GLN M 66 ASN M 121 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.090699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.076156 restraints weight = 185957.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.078105 restraints weight = 107809.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.079461 restraints weight = 71426.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.080373 restraints weight = 52037.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.081053 restraints weight = 40852.912| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 37637 Z= 0.202 Angle : 0.939 41.903 50977 Z= 0.455 Chirality : 0.050 0.280 5761 Planarity : 0.007 0.095 6377 Dihedral : 12.420 173.996 5531 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.68 % Favored : 91.10 % Rotamer: Outliers : 4.50 % Allowed : 19.77 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -3.70 (0.11), residues: 4437 helix: -2.28 (0.10), residues: 1587 sheet: -2.67 (0.20), residues: 521 loop : -2.53 (0.12), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 258 TYR 0.020 0.002 TYR D 14 PHE 0.029 0.002 PHE G 18 TRP 0.025 0.003 TRP C 40 HIS 0.012 0.002 HIS O 60 Details of bonding type rmsd covalent geometry : bond 0.00453 (37617) covalent geometry : angle 0.88317 (50956) hydrogen bonds : bond 0.05590 ( 1155) hydrogen bonds : angle 6.11641 ( 3213) metal coordination : bond 0.01813 ( 20) metal coordination : angle 15.78872 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 685 time to evaluate : 1.452 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: A 30 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7958 (pm20) REVERT: A 281 MET cc_start: 0.8922 (tpp) cc_final: 0.8661 (tpp) REVERT: A 305 MET cc_start: 0.7985 (ppp) cc_final: 0.7223 (ppp) REVERT: A 439 LYS cc_start: 0.9263 (mmtm) cc_final: 0.8487 (mmmm) REVERT: A 440 MET cc_start: 0.8234 (mmt) cc_final: 0.7904 (mmm) REVERT: A 505 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7815 (ptt) REVERT: A 646 MET cc_start: 0.8119 (tpp) cc_final: 0.7600 (mmp) REVERT: A 680 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8451 (tpp) REVERT: A 815 ASN cc_start: 0.8211 (m-40) cc_final: 0.7993 (m-40) REVERT: A 1020 ASP cc_start: 0.8833 (t0) cc_final: 0.8573 (t0) REVERT: A 1236 MET cc_start: 0.8295 (ptt) cc_final: 0.8064 (ptm) REVERT: A 1255 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8320 (tt0) REVERT: B 107 MET cc_start: 0.8471 (mtm) cc_final: 0.8267 (mtp) REVERT: B 317 ILE cc_start: 0.8734 (mm) cc_final: 0.8388 (tp) REVERT: B 434 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7178 (tm-30) REVERT: B 451 MET cc_start: 0.8826 (ttm) cc_final: 0.8546 (ttm) REVERT: B 527 CYS cc_start: 0.7524 (m) cc_final: 0.7261 (m) REVERT: B 540 PHE cc_start: 0.8067 (m-10) cc_final: 0.7628 (m-10) REVERT: B 625 LEU cc_start: 0.9347 (mp) cc_final: 0.9137 (mp) REVERT: B 634 ASP cc_start: 0.8186 (p0) cc_final: 0.7893 (p0) REVERT: B 769 CYS cc_start: 0.6429 (m) cc_final: 0.6133 (m) REVERT: B 1062 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7950 (mpp) REVERT: B 1116 GLU cc_start: 0.8674 (pt0) cc_final: 0.8451 (pt0) REVERT: B 1126 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8615 (mt) REVERT: C 87 MET cc_start: 0.8008 (mmm) cc_final: 0.7510 (mmt) REVERT: C 203 ARG cc_start: 0.8110 (mmp80) cc_final: 0.7805 (mmp80) REVERT: C 206 GLN cc_start: 0.8226 (mt0) cc_final: 0.7595 (mt0) REVERT: C 330 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8838 (ttm) REVERT: G 9 ASP cc_start: 0.7893 (t70) cc_final: 0.7510 (t0) REVERT: G 37 LYS cc_start: 0.7712 (mmmm) cc_final: 0.7249 (mmmm) REVERT: G 190 ILE cc_start: 0.6456 (mp) cc_final: 0.6136 (mt) REVERT: I 37 LYS cc_start: 0.8102 (tppp) cc_final: 0.7419 (tptt) REVERT: K 60 MET cc_start: 0.8795 (tpp) cc_final: 0.8591 (tpp) REVERT: L 44 MET cc_start: 0.7626 (mtp) cc_final: 0.6948 (mmm) REVERT: P 232 MET cc_start: 0.5687 (mmp) cc_final: 0.5416 (mmp) REVERT: P 257 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6768 (pp20) REVERT: E 23 ASP cc_start: 0.8139 (m-30) cc_final: 0.7744 (m-30) REVERT: E 110 MET cc_start: 0.7837 (mtp) cc_final: 0.6734 (ttm) REVERT: F 101 LYS cc_start: 0.7807 (mmtp) cc_final: 0.7592 (mmtt) REVERT: H 24 ARG cc_start: 0.7152 (mtm-85) cc_final: 0.6902 (mtm180) REVERT: O 54 LEU cc_start: 0.8727 (pp) cc_final: 0.8511 (mt) REVERT: O 72 VAL cc_start: 0.7672 (t) cc_final: 0.7296 (p) REVERT: O 404 MET cc_start: 0.7519 (mmm) cc_final: 0.7230 (mmm) REVERT: O 423 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7821 (pp) REVERT: O 448 GLU cc_start: 0.9348 (tp30) cc_final: 0.8370 (pp20) REVERT: Q 54 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8207 (tm-30) REVERT: Q 111 MET cc_start: 0.7090 (mmm) cc_final: 0.6519 (tmm) REVERT: D 26 GLN cc_start: 0.9579 (mm-40) cc_final: 0.9032 (pp30) REVERT: D 41 ASN cc_start: 0.8972 (m-40) cc_final: 0.8475 (t0) REVERT: D 42 LEU cc_start: 0.9026 (tm) cc_final: 0.8649 (pt) REVERT: D 89 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.7097 (t-90) REVERT: M 17 LEU cc_start: 0.5065 (pt) cc_final: 0.4442 (tt) REVERT: M 45 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9125 (mt) REVERT: M 49 ILE cc_start: 0.6869 (mt) cc_final: 0.6533 (mt) REVERT: M 99 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8707 (mmmt) REVERT: M 114 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: M 149 HIS cc_start: 0.8628 (m-70) cc_final: 0.8248 (m90) REVERT: M 202 GLU cc_start: 0.8849 (pt0) cc_final: 0.8502 (pt0) REVERT: N 352 THR cc_start: 0.2972 (OUTLIER) cc_final: 0.1664 (p) REVERT: N 356 PHE cc_start: 0.7626 (m-80) cc_final: 0.7187 (m-80) REVERT: N 363 VAL cc_start: 0.8028 (t) cc_final: 0.7795 (t) REVERT: N 382 LYS cc_start: 0.7895 (tttt) cc_final: 0.7631 (pttm) outliers start: 179 outliers final: 88 residues processed: 812 average time/residue: 0.2130 time to fit residues: 284.1994 Evaluate side-chains 643 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 543 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1062 MET Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain P residue 219 TYR Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 257 GLU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 386 ILE Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain O residue 423 LEU Chi-restraints excluded: chain O residue 445 ASN Chi-restraints excluded: chain O residue 497 GLN Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 81 ARG Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 64 GLU 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 D residue 116 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 329 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 352 THR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 8 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 268 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 435 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 400 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN A 794 GLN A 836 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS B 639 ASN B 642 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN G 23 ASN K 85 GLN K 101 ASN O 371 GLN O 402 ASN ** O 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN M 106 GLN ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.080212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.065864 restraints weight = 189217.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.067643 restraints weight = 107163.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.068865 restraints weight = 70792.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069721 restraints weight = 51926.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.070331 restraints weight = 41097.639| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 37637 Z= 0.242 Angle : 0.921 56.136 50977 Z= 0.438 Chirality : 0.049 0.347 5761 Planarity : 0.006 0.087 6377 Dihedral : 11.671 178.062 5462 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.29 % Favored : 90.49 % Rotamer: Outliers : 5.08 % Allowed : 19.99 % Favored : 74.92 % 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: -2.85 (0.12), residues: 4437 helix: -1.16 (0.12), residues: 1600 sheet: -2.28 (0.21), residues: 506 loop : -2.36 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 67 TYR 0.026 0.002 TYR B 445 PHE 0.036 0.002 PHE C 140 TRP 0.020 0.002 TRP C 40 HIS 0.026 0.002 HIS M 200 Details of bonding type rmsd covalent geometry : bond 0.00542 (37617) covalent geometry : angle 0.85419 (50956) hydrogen bonds : bond 0.04838 ( 1155) hydrogen bonds : angle 5.60432 ( 3213) metal coordination : bond 0.01768 ( 20) metal coordination : angle 16.97549 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 564 time to evaluate : 1.200 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: A 30 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8282 (pm20) REVERT: A 60 MET cc_start: 0.9309 (mmm) cc_final: 0.8273 (mmt) REVERT: A 144 LYS cc_start: 0.9530 (tppt) cc_final: 0.9299 (tptp) REVERT: A 281 MET cc_start: 0.9073 (tpp) cc_final: 0.8679 (tpp) REVERT: A 308 GLU cc_start: 0.8789 (pt0) cc_final: 0.8242 (pt0) REVERT: A 311 ASP cc_start: 0.9036 (m-30) cc_final: 0.8763 (p0) REVERT: A 406 LYS cc_start: 0.9464 (tppt) cc_final: 0.8794 (mmtm) REVERT: A 440 MET cc_start: 0.8479 (mmt) cc_final: 0.8151 (mmm) REVERT: A 646 MET cc_start: 0.8616 (tpp) cc_final: 0.8119 (mmp) REVERT: A 654 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.9116 (p) REVERT: A 815 ASN cc_start: 0.8525 (m-40) cc_final: 0.8245 (m-40) REVERT: A 852 MET cc_start: 0.9058 (mtp) cc_final: 0.8852 (mtp) REVERT: A 871 MET cc_start: 0.8835 (tmm) cc_final: 0.8549 (tmm) REVERT: A 915 LYS cc_start: 0.7640 (pttp) cc_final: 0.7283 (tptp) REVERT: A 1012 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8712 (tm-30) REVERT: A 1236 MET cc_start: 0.8556 (ptt) cc_final: 0.8309 (ptm) REVERT: B 233 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8316 (t0) REVERT: B 243 MET cc_start: 0.8338 (ttm) cc_final: 0.8130 (ttm) REVERT: B 272 CYS cc_start: 0.9020 (OUTLIER) cc_final: 0.7998 (m) REVERT: B 317 ILE cc_start: 0.8890 (mm) cc_final: 0.8547 (tp) REVERT: B 431 MET cc_start: 0.8627 (ppp) cc_final: 0.8100 (ppp) REVERT: B 525 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7835 (pt) REVERT: B 527 CYS cc_start: 0.7907 (m) cc_final: 0.6950 (m) REVERT: B 530 GLU cc_start: 0.7342 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 559 PHE cc_start: 0.7908 (t80) cc_final: 0.7639 (t80) REVERT: B 1126 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9070 (mt) REVERT: C 10 MET cc_start: 0.7487 (mmm) cc_final: 0.7213 (mmp) REVERT: C 32 ASN cc_start: 0.8105 (m-40) cc_final: 0.7739 (m110) REVERT: C 87 MET cc_start: 0.8477 (mmm) cc_final: 0.8047 (mmm) REVERT: C 279 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8045 (mtp-110) REVERT: C 330 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.8992 (ttm) REVERT: G 56 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: G 190 ILE cc_start: 0.7323 (mp) cc_final: 0.6943 (mt) REVERT: K 30 VAL cc_start: 0.4607 (OUTLIER) cc_final: 0.4407 (t) REVERT: K 48 ASP cc_start: 0.8940 (p0) cc_final: 0.8736 (p0) REVERT: K 66 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8212 (mp0) REVERT: K 70 TYR cc_start: 0.8915 (p90) cc_final: 0.8643 (p90) REVERT: L 44 MET cc_start: 0.8179 (mtp) cc_final: 0.7837 (mtp) REVERT: P 222 GLU cc_start: 0.8497 (tp30) cc_final: 0.7897 (mp0) REVERT: P 232 MET cc_start: 0.5913 (mmp) cc_final: 0.5095 (mmp) REVERT: P 298 GLU cc_start: 0.7014 (tp30) cc_final: 0.6805 (tm-30) REVERT: E 23 ASP cc_start: 0.8720 (m-30) cc_final: 0.8336 (m-30) REVERT: E 94 MET cc_start: 0.8221 (tpt) cc_final: 0.7975 (tpt) REVERT: E 110 MET cc_start: 0.8116 (mtp) cc_final: 0.7253 (ttm) REVERT: F 80 MET cc_start: 0.8769 (mmp) cc_final: 0.8564 (mmp) REVERT: F 83 LEU cc_start: 0.9399 (pt) cc_final: 0.9141 (pp) REVERT: F 101 LYS cc_start: 0.8642 (mmtp) cc_final: 0.8407 (mmtt) REVERT: H 24 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7698 (mtm180) REVERT: H 136 GLU cc_start: 0.6808 (mp0) cc_final: 0.6427 (mp0) REVERT: H 145 MET cc_start: 0.7502 (tmm) cc_final: 0.6878 (tmm) REVERT: J 17 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8152 (mmtm) REVERT: J 31 GLU cc_start: 0.9220 (mp0) cc_final: 0.8910 (mp0) REVERT: O 60 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.8090 (m-70) REVERT: O 404 MET cc_start: 0.8030 (mmm) cc_final: 0.7772 (mmm) REVERT: O 414 ASP cc_start: 0.8110 (m-30) cc_final: 0.7823 (m-30) REVERT: O 423 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7822 (pp) REVERT: O 448 GLU cc_start: 0.9457 (tp30) cc_final: 0.9075 (tp30) REVERT: O 513 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7399 (mt-10) REVERT: O 532 LYS cc_start: 0.7416 (mmmt) cc_final: 0.7176 (mmtt) REVERT: Q 54 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8150 (tm-30) REVERT: Q 111 MET cc_start: 0.7401 (mmm) cc_final: 0.6788 (tmm) REVERT: D 5 ASP cc_start: 0.9092 (t0) cc_final: 0.8866 (t0) REVERT: D 26 GLN cc_start: 0.9594 (mm-40) cc_final: 0.9074 (pp30) REVERT: D 41 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8806 (m-40) REVERT: D 42 LEU cc_start: 0.9264 (tm) cc_final: 0.9017 (pt) REVERT: D 89 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7562 (t-90) REVERT: D 100 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6826 (mmt) REVERT: M 17 LEU cc_start: 0.4991 (pt) cc_final: 0.4281 (tt) REVERT: M 45 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9244 (pp) REVERT: M 54 GLN cc_start: 0.8413 (tt0) cc_final: 0.7825 (tp-100) REVERT: M 114 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.6995 (m-80) REVERT: M 143 ASP cc_start: 0.8948 (t0) cc_final: 0.8718 (m-30) REVERT: M 149 HIS cc_start: 0.8821 (m-70) cc_final: 0.8507 (m-70) REVERT: M 202 GLU cc_start: 0.8986 (pt0) cc_final: 0.8557 (pt0) REVERT: N 268 PHE cc_start: 0.8062 (t80) cc_final: 0.7673 (t80) REVERT: N 350 MET cc_start: 0.7396 (ppp) cc_final: 0.7170 (ppp) REVERT: N 356 PHE cc_start: 0.7760 (m-80) cc_final: 0.7309 (m-10) REVERT: N 363 VAL cc_start: 0.8375 (t) cc_final: 0.7701 (t) outliers start: 202 outliers final: 94 residues processed: 707 average time/residue: 0.2155 time to fit residues: 248.9899 Evaluate side-chains 596 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 484 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 219 TYR Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 395 LEU Chi-restraints excluded: chain O residue 423 LEU Chi-restraints excluded: chain O residue 425 THR Chi-restraints excluded: chain O residue 497 GLN Chi-restraints excluded: chain O residue 530 THR Chi-restraints excluded: chain O residue 531 MET Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 81 ARG Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 365 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 269 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 chunk 379 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 433 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN G 23 ASN P 306 ASN E 35 GLN E 132 GLN F 72 GLN ** O 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 407 GLN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 41 ASN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 HIS ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.077174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.063101 restraints weight = 189289.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.064784 restraints weight = 106111.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.065982 restraints weight = 69925.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.066800 restraints weight = 51279.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.067384 restraints weight = 40715.451| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 37637 Z= 0.197 Angle : 0.828 58.150 50977 Z= 0.387 Chirality : 0.046 0.308 5761 Planarity : 0.005 0.087 6377 Dihedral : 11.402 178.955 5444 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.83 % Favored : 90.96 % Rotamer: Outliers : 4.80 % Allowed : 21.40 % Favored : 73.79 % 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: -2.42 (0.12), residues: 4437 helix: -0.56 (0.13), residues: 1576 sheet: -2.23 (0.21), residues: 548 loop : -2.22 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 581 TYR 0.016 0.002 TYR O 88 PHE 0.023 0.002 PHE B1114 TRP 0.019 0.002 TRP G 201 HIS 0.015 0.001 HIS D 76 Details of bonding type rmsd covalent geometry : bond 0.00447 (37617) covalent geometry : angle 0.75964 (50956) hydrogen bonds : bond 0.04097 ( 1155) hydrogen bonds : angle 5.31046 ( 3213) metal coordination : bond 0.01369 ( 20) metal coordination : angle 16.28985 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 521 time to evaluate : 1.366 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: A 30 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: A 60 MET cc_start: 0.9281 (mmm) cc_final: 0.9072 (mtp) REVERT: A 144 LYS cc_start: 0.9516 (tppt) cc_final: 0.9313 (tptp) REVERT: A 281 MET cc_start: 0.9033 (tpp) cc_final: 0.8628 (tpp) REVERT: A 308 GLU cc_start: 0.8800 (pt0) cc_final: 0.8510 (pt0) REVERT: A 406 LYS cc_start: 0.9484 (tppt) cc_final: 0.8804 (mmtm) REVERT: A 640 ILE cc_start: 0.9446 (mt) cc_final: 0.9227 (mp) REVERT: A 654 THR cc_start: 0.9428 (OUTLIER) cc_final: 0.8977 (p) REVERT: A 815 ASN cc_start: 0.8687 (m-40) cc_final: 0.8371 (m-40) REVERT: A 871 MET cc_start: 0.8863 (tmm) cc_final: 0.8641 (tmm) REVERT: A 915 LYS cc_start: 0.7555 (pttp) cc_final: 0.7280 (tptp) REVERT: A 1012 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8803 (tm-30) REVERT: A 1275 MET cc_start: 0.8909 (ttt) cc_final: 0.8631 (ttt) REVERT: A 1280 MET cc_start: 0.8755 (mmt) cc_final: 0.8516 (mmm) REVERT: B 233 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8289 (t0) REVERT: B 243 MET cc_start: 0.8301 (ttm) cc_final: 0.8079 (ttm) REVERT: B 272 CYS cc_start: 0.9049 (OUTLIER) cc_final: 0.7992 (m) REVERT: B 317 ILE cc_start: 0.8980 (mm) cc_final: 0.8747 (tp) REVERT: B 320 HIS cc_start: 0.6599 (m170) cc_final: 0.6132 (m170) REVERT: B 341 ARG cc_start: 0.8710 (mmt90) cc_final: 0.8347 (mmt-90) REVERT: B 431 MET cc_start: 0.8423 (ppp) cc_final: 0.7917 (ppp) REVERT: B 451 MET cc_start: 0.9047 (ttm) cc_final: 0.8730 (ttm) REVERT: B 506 MET cc_start: 0.7952 (mpp) cc_final: 0.7585 (pmm) REVERT: B 525 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8071 (pt) REVERT: B 527 CYS cc_start: 0.7557 (m) cc_final: 0.6686 (m) REVERT: B 530 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7150 (tm-30) REVERT: B 559 PHE cc_start: 0.8260 (t80) cc_final: 0.8046 (t80) REVERT: B 580 ASP cc_start: 0.8524 (t70) cc_final: 0.8196 (t0) REVERT: B 600 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7365 (ptmm) REVERT: B 634 ASP cc_start: 0.8757 (p0) cc_final: 0.8452 (p0) REVERT: B 879 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7019 (t80) REVERT: B 938 MET cc_start: 0.8342 (ttm) cc_final: 0.7631 (mtp) REVERT: B 1116 GLU cc_start: 0.8965 (pt0) cc_final: 0.8752 (pt0) REVERT: C 32 ASN cc_start: 0.8299 (m-40) cc_final: 0.7905 (m110) REVERT: C 87 MET cc_start: 0.8632 (mmm) cc_final: 0.8311 (mmm) REVERT: C 279 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8363 (mtp-110) REVERT: C 330 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.8657 (ttm) REVERT: G 28 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8048 (mt-10) REVERT: G 56 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: I 32 HIS cc_start: 0.6993 (m90) cc_final: 0.6645 (m-70) REVERT: K 66 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8032 (mp0) REVERT: K 70 TYR cc_start: 0.8986 (p90) cc_final: 0.8739 (p90) REVERT: P 193 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.6624 (tm-30) REVERT: E 94 MET cc_start: 0.8256 (tpt) cc_final: 0.8031 (tpt) REVERT: E 110 MET cc_start: 0.8089 (mtp) cc_final: 0.7207 (ttm) REVERT: F 61 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8325 (mt-10) REVERT: H 24 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7833 (mtm180) REVERT: H 37 MET cc_start: 0.8602 (mmm) cc_final: 0.8040 (mmm) REVERT: J 17 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8463 (mttp) REVERT: J 31 GLU cc_start: 0.9125 (mp0) cc_final: 0.8770 (mp0) REVERT: O 9 CYS cc_start: 0.8636 (m) cc_final: 0.8306 (m) REVERT: O 112 LEU cc_start: 0.8614 (mt) cc_final: 0.8366 (tp) REVERT: O 404 MET cc_start: 0.8294 (mmm) cc_final: 0.7998 (mmm) REVERT: O 423 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7659 (pp) REVERT: O 427 ASN cc_start: 0.8278 (t0) cc_final: 0.7533 (t0) REVERT: O 448 GLU cc_start: 0.9529 (tp30) cc_final: 0.9128 (tp30) REVERT: O 513 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7372 (mt-10) REVERT: Q 54 GLU cc_start: 0.9202 (mm-30) cc_final: 0.7983 (tm-30) REVERT: Q 57 MET cc_start: 0.9078 (mpp) cc_final: 0.8839 (mpp) REVERT: Q 111 MET cc_start: 0.7455 (mmm) cc_final: 0.6769 (tmm) REVERT: D 5 ASP cc_start: 0.9090 (t0) cc_final: 0.8852 (t0) REVERT: D 22 ASP cc_start: 0.9161 (m-30) cc_final: 0.8911 (m-30) REVERT: D 26 GLN cc_start: 0.9588 (mm-40) cc_final: 0.9090 (pp30) REVERT: D 51 LYS cc_start: 0.9602 (tppt) cc_final: 0.9245 (tppt) REVERT: D 55 LYS cc_start: 0.9187 (mmmt) cc_final: 0.8895 (mmmt) REVERT: D 89 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7673 (t-90) REVERT: D 100 MET cc_start: 0.6885 (mmt) cc_final: 0.6614 (mmt) REVERT: M 17 LEU cc_start: 0.5311 (pt) cc_final: 0.4672 (tt) REVERT: M 45 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9297 (pp) REVERT: M 76 GLN cc_start: 0.8755 (pt0) cc_final: 0.8165 (pm20) REVERT: M 114 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: M 149 HIS cc_start: 0.8806 (m-70) cc_final: 0.8359 (m90) REVERT: N 350 MET cc_start: 0.7623 (ppp) cc_final: 0.7209 (ppp) REVERT: N 356 PHE cc_start: 0.7752 (m-80) cc_final: 0.7215 (m-80) outliers start: 191 outliers final: 104 residues processed: 661 average time/residue: 0.2092 time to fit residues: 227.6338 Evaluate side-chains 583 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 463 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 219 TYR Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 259 THR Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 270 TYR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain O residue 395 LEU Chi-restraints excluded: chain O residue 406 LEU Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain O residue 423 LEU Chi-restraints excluded: chain O residue 425 THR Chi-restraints excluded: chain O residue 497 GLN Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain O residue 530 THR Chi-restraints excluded: chain O residue 531 MET Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 87 TYR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 376 optimal weight: 2.9990 chunk 436 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 350 optimal weight: 9.9990 chunk 445 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN B 692 GLN ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN C 59 ASN ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN G 23 ASN P 297 HIS F 72 GLN H 44 ASN ** O 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 457 ASN O 497 GLN ** Q 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN M 106 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.072423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.058562 restraints weight = 192836.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.060176 restraints weight = 107383.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.061272 restraints weight = 70799.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.062049 restraints weight = 52214.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.062581 restraints weight = 41828.308| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.7402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 37637 Z= 0.220 Angle : 0.861 60.689 50977 Z= 0.403 Chirality : 0.047 0.221 5761 Planarity : 0.005 0.089 6377 Dihedral : 11.183 178.648 5440 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.44 % Favored : 90.33 % Rotamer: Outliers : 5.18 % Allowed : 21.53 % Favored : 73.29 % 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: -2.15 (0.12), residues: 4437 helix: -0.27 (0.13), residues: 1589 sheet: -2.18 (0.22), residues: 524 loop : -2.11 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 295 TYR 0.026 0.002 TYR B1003 PHE 0.023 0.002 PHE M 28 TRP 0.027 0.002 TRP B 804 HIS 0.012 0.001 HIS B 806 Details of bonding type rmsd covalent geometry : bond 0.00499 (37617) covalent geometry : angle 0.79619 (50956) hydrogen bonds : bond 0.04106 ( 1155) hydrogen bonds : angle 5.25179 ( 3213) metal coordination : bond 0.01539 ( 20) metal coordination : angle 16.16162 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 466 time to evaluate : 1.305 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 30 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: A 53 TYR cc_start: 0.5069 (OUTLIER) cc_final: 0.3868 (t80) REVERT: A 281 MET cc_start: 0.9020 (tpp) cc_final: 0.8622 (tpp) REVERT: A 308 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8449 (pt0) REVERT: A 351 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7525 (mpt90) REVERT: A 406 LYS cc_start: 0.9480 (tppt) cc_final: 0.8784 (mmtm) REVERT: A 463 ASN cc_start: 0.8887 (t0) cc_final: 0.8658 (t0) REVERT: A 815 ASN cc_start: 0.8757 (m-40) cc_final: 0.8520 (m-40) REVERT: A 871 MET cc_start: 0.8959 (tmm) cc_final: 0.8751 (tmm) REVERT: A 908 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: A 1012 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8824 (tm-30) REVERT: A 1061 MET cc_start: 0.6409 (pmm) cc_final: 0.6180 (pmm) REVERT: A 1106 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8360 (pp20) REVERT: A 1236 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8434 (ptp) REVERT: A 1275 MET cc_start: 0.8947 (ttt) cc_final: 0.8652 (ttt) REVERT: A 1280 MET cc_start: 0.8780 (mmt) cc_final: 0.8436 (mmm) REVERT: B 233 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8293 (t0) REVERT: B 243 MET cc_start: 0.8398 (ttm) cc_final: 0.8124 (ttm) REVERT: B 272 CYS cc_start: 0.9054 (OUTLIER) cc_final: 0.7919 (m) REVERT: B 317 ILE cc_start: 0.9005 (mm) cc_final: 0.8798 (tp) REVERT: B 320 HIS cc_start: 0.6721 (m170) cc_final: 0.6256 (m170) REVERT: B 341 ARG cc_start: 0.8908 (mmt90) cc_final: 0.8607 (mpt180) REVERT: B 431 MET cc_start: 0.8386 (ppp) cc_final: 0.8066 (ppp) REVERT: B 525 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8465 (tp) REVERT: B 527 CYS cc_start: 0.7804 (m) cc_final: 0.7089 (m) REVERT: B 530 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7345 (tm-30) REVERT: B 559 PHE cc_start: 0.8564 (t80) cc_final: 0.8321 (t80) REVERT: B 580 ASP cc_start: 0.8540 (t70) cc_final: 0.8163 (t0) REVERT: B 600 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7702 (ptmm) REVERT: B 634 ASP cc_start: 0.8748 (p0) cc_final: 0.8358 (p0) REVERT: B 697 ILE cc_start: 0.9337 (tp) cc_final: 0.9011 (mp) REVERT: B 819 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: B 879 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7361 (t80) REVERT: B 883 MET cc_start: 0.7947 (mmm) cc_final: 0.7651 (mmm) REVERT: B 1009 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: C 32 ASN cc_start: 0.8626 (m-40) cc_final: 0.8259 (m110) REVERT: C 87 MET cc_start: 0.8786 (mmm) cc_final: 0.8562 (mmm) REVERT: C 279 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8536 (mtp-110) REVERT: C 330 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8622 (ttm) REVERT: G 28 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8334 (mt-10) REVERT: I 12 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6607 (pp) REVERT: K 66 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8157 (mp0) REVERT: K 70 TYR cc_start: 0.9051 (p90) cc_final: 0.8652 (p90) REVERT: K 120 ASP cc_start: 0.9393 (OUTLIER) cc_final: 0.9088 (m-30) REVERT: P 193 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: P 222 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7092 (mp0) REVERT: F 86 GLU cc_start: 0.8922 (mp0) cc_final: 0.8668 (mp0) REVERT: H 8 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6662 (m-30) REVERT: H 24 ARG cc_start: 0.8201 (mtm-85) cc_final: 0.7769 (mtm180) REVERT: H 33 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8173 (mm-30) REVERT: J 31 GLU cc_start: 0.9153 (mp0) cc_final: 0.8767 (mp0) REVERT: O 9 CYS cc_start: 0.8608 (m) cc_final: 0.8385 (m) REVERT: O 368 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9222 (mm) REVERT: O 404 MET cc_start: 0.8475 (mmm) cc_final: 0.8104 (mmm) REVERT: O 427 ASN cc_start: 0.8477 (t0) cc_final: 0.7923 (t0) REVERT: Q 54 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8119 (tm-30) REVERT: Q 61 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8484 (tppt) REVERT: Q 111 MET cc_start: 0.7552 (mmm) cc_final: 0.6834 (tmm) REVERT: Q 114 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7583 (t0) REVERT: D 5 ASP cc_start: 0.9094 (t0) cc_final: 0.8838 (t0) REVERT: D 26 GLN cc_start: 0.9578 (mm-40) cc_final: 0.9143 (pp30) REVERT: D 61 GLN cc_start: 0.6562 (OUTLIER) cc_final: 0.6229 (mm110) REVERT: D 89 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.8200 (t-90) REVERT: D 100 MET cc_start: 0.6938 (mmt) cc_final: 0.6660 (mmt) REVERT: M 17 LEU cc_start: 0.5403 (pt) cc_final: 0.4919 (tt) REVERT: M 45 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9348 (pp) REVERT: M 75 GLU cc_start: 0.8821 (tp30) cc_final: 0.8610 (tp30) REVERT: M 114 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.6955 (m-80) REVERT: M 143 ASP cc_start: 0.9165 (OUTLIER) cc_final: 0.8531 (m-30) REVERT: M 149 HIS cc_start: 0.8904 (m-70) cc_final: 0.8543 (m90) REVERT: N 350 MET cc_start: 0.7782 (ppp) cc_final: 0.7302 (ppp) REVERT: N 356 PHE cc_start: 0.7664 (m-80) cc_final: 0.7190 (m-80) outliers start: 206 outliers final: 108 residues processed: 625 average time/residue: 0.2068 time to fit residues: 214.4742 Evaluate side-chains 553 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 417 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 787 PHE Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1009 TYR Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 259 THR Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 270 TYR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain O residue 395 LEU Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 406 LEU Chi-restraints excluded: chain O residue 425 THR Chi-restraints excluded: chain O residue 446 LEU Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain O residue 530 THR Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 114 ASN Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 62 SER 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 45 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 330 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 50 optimal weight: 10.0000 chunk 321 optimal weight: 1.9990 chunk 420 optimal weight: 20.0000 chunk 307 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 225 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 chunk 274 optimal weight: 0.9980 chunk 347 optimal weight: 4.9990 chunk 289 optimal weight: 0.9980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1121 ASN ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN H 44 ASN ** O 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 146 ASN O 339 HIS ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 457 ASN Q 114 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN ** 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 = 0.3636 r_free = 0.3636 target = 0.072536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.058690 restraints weight = 192387.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.060290 restraints weight = 107368.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.061383 restraints weight = 70987.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.062154 restraints weight = 52447.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062696 restraints weight = 41992.713| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.7706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37637 Z= 0.151 Angle : 0.791 52.431 50977 Z= 0.366 Chirality : 0.045 0.231 5761 Planarity : 0.005 0.093 6377 Dihedral : 11.030 179.577 5434 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.68 % Favored : 91.12 % Rotamer: Outliers : 3.87 % Allowed : 23.01 % Favored : 73.11 % 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: -1.89 (0.12), residues: 4437 helix: 0.02 (0.13), residues: 1573 sheet: -2.03 (0.22), residues: 529 loop : -2.00 (0.13), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 151 TYR 0.022 0.001 TYR B 445 PHE 0.018 0.001 PHE C 185 TRP 0.020 0.002 TRP M 205 HIS 0.009 0.001 HIS I 32 Details of bonding type rmsd covalent geometry : bond 0.00349 (37617) covalent geometry : angle 0.73456 (50956) hydrogen bonds : bond 0.03685 ( 1155) hydrogen bonds : angle 5.04696 ( 3213) metal coordination : bond 0.00877 ( 20) metal coordination : angle 14.47634 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 457 time to evaluate : 1.306 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 30 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8518 (pm20) REVERT: A 53 TYR cc_start: 0.5196 (OUTLIER) cc_final: 0.3789 (t80) REVERT: A 60 MET cc_start: 0.8832 (mtp) cc_final: 0.8208 (mtm) REVERT: A 281 MET cc_start: 0.8971 (tpp) cc_final: 0.8686 (mmm) REVERT: A 308 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: A 351 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7392 (mpt90) REVERT: A 463 ASN cc_start: 0.8847 (t0) cc_final: 0.8547 (t0) REVERT: A 871 MET cc_start: 0.8955 (tmm) cc_final: 0.8726 (tmm) REVERT: A 908 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8043 (m-30) REVERT: A 1012 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8815 (tm-30) REVERT: A 1061 MET cc_start: 0.6411 (pmm) cc_final: 0.6208 (pmm) REVERT: A 1106 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8370 (pp20) REVERT: A 1236 MET cc_start: 0.8964 (ptp) cc_final: 0.8432 (ptp) REVERT: A 1275 MET cc_start: 0.8929 (ttt) cc_final: 0.8611 (ttm) REVERT: B 233 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8332 (t0) REVERT: B 243 MET cc_start: 0.8415 (ttm) cc_final: 0.8129 (ttm) REVERT: B 278 PHE cc_start: 0.8481 (m-80) cc_final: 0.8186 (m-10) REVERT: B 317 ILE cc_start: 0.8984 (mm) cc_final: 0.8773 (tp) REVERT: B 320 HIS cc_start: 0.6594 (m170) cc_final: 0.6118 (m170) REVERT: B 341 ARG cc_start: 0.8911 (mmt90) cc_final: 0.8551 (mpt180) REVERT: B 431 MET cc_start: 0.8311 (ppp) cc_final: 0.8007 (ppp) REVERT: B 506 MET cc_start: 0.8014 (mpp) cc_final: 0.7750 (pmm) REVERT: B 525 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8313 (pt) REVERT: B 527 CYS cc_start: 0.7783 (m) cc_final: 0.6576 (m) REVERT: B 530 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7504 (tm-30) REVERT: B 559 PHE cc_start: 0.8650 (t80) cc_final: 0.8438 (t80) REVERT: B 562 MET cc_start: 0.8781 (mmm) cc_final: 0.8579 (mmm) REVERT: B 580 ASP cc_start: 0.8531 (t70) cc_final: 0.8132 (t0) REVERT: B 600 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7744 (ptmm) REVERT: B 697 ILE cc_start: 0.9330 (tp) cc_final: 0.8988 (mp) REVERT: B 819 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: B 879 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7195 (t80) REVERT: C 32 ASN cc_start: 0.8607 (m-40) cc_final: 0.8309 (m-40) REVERT: C 87 MET cc_start: 0.8807 (mmm) cc_final: 0.8580 (mmm) REVERT: C 279 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8504 (mtp-110) REVERT: C 330 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8733 (ttm) REVERT: G 28 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8353 (mt-10) REVERT: G 36 ASN cc_start: 0.6280 (m-40) cc_final: 0.6026 (m-40) REVERT: K 66 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8147 (mp0) REVERT: K 70 TYR cc_start: 0.8911 (p90) cc_final: 0.8705 (p90) REVERT: K 79 LYS cc_start: 0.9507 (ptmt) cc_final: 0.9137 (ptpp) REVERT: P 193 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: P 196 ARG cc_start: 0.8522 (ptt180) cc_final: 0.7949 (ptt90) REVERT: P 222 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7142 (mp0) REVERT: P 232 MET cc_start: 0.5970 (mmp) cc_final: 0.5672 (mmp) REVERT: F 83 LEU cc_start: 0.9350 (pt) cc_final: 0.9014 (pt) REVERT: H 8 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6902 (m-30) REVERT: H 24 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.7990 (mtm180) REVERT: H 33 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8244 (mm-30) REVERT: H 37 MET cc_start: 0.8522 (mmm) cc_final: 0.7960 (mmm) REVERT: J 31 GLU cc_start: 0.9076 (mp0) cc_final: 0.8689 (mp0) REVERT: O 9 CYS cc_start: 0.8807 (m) cc_final: 0.8551 (m) REVERT: O 368 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9216 (mm) REVERT: O 404 MET cc_start: 0.8545 (mmm) cc_final: 0.8150 (mmm) REVERT: O 427 ASN cc_start: 0.8570 (t0) cc_final: 0.7933 (t0) REVERT: Q 54 GLU cc_start: 0.9289 (mm-30) cc_final: 0.7952 (tm-30) REVERT: Q 61 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8543 (tppt) REVERT: Q 111 MET cc_start: 0.7539 (mmm) cc_final: 0.6862 (tmm) REVERT: Q 114 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7424 (t0) REVERT: D 5 ASP cc_start: 0.9085 (t0) cc_final: 0.8831 (t0) REVERT: D 22 ASP cc_start: 0.9287 (m-30) cc_final: 0.9016 (m-30) REVERT: D 26 GLN cc_start: 0.9605 (mm-40) cc_final: 0.9178 (pp30) REVERT: D 61 GLN cc_start: 0.6326 (OUTLIER) cc_final: 0.6021 (mm110) REVERT: D 100 MET cc_start: 0.6861 (mmt) cc_final: 0.6609 (mmt) REVERT: M 17 LEU cc_start: 0.5402 (pt) cc_final: 0.4925 (tt) REVERT: M 45 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9355 (pp) REVERT: M 49 ILE cc_start: 0.7235 (mp) cc_final: 0.6889 (mp) REVERT: M 114 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: M 149 HIS cc_start: 0.8847 (m-70) cc_final: 0.8558 (m-70) REVERT: M 202 GLU cc_start: 0.8924 (pt0) cc_final: 0.8076 (mp0) REVERT: N 350 MET cc_start: 0.7899 (ppp) cc_final: 0.7367 (ppp) REVERT: N 356 PHE cc_start: 0.7644 (m-80) cc_final: 0.7142 (m-80) REVERT: N 382 LYS cc_start: 0.8600 (ttpp) cc_final: 0.8087 (pttp) outliers start: 154 outliers final: 93 residues processed: 575 average time/residue: 0.2081 time to fit residues: 198.4643 Evaluate side-chains 532 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 418 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1081 SER Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 787 PHE Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain O residue 395 LEU Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 425 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 114 ASN Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 62 SER 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 28 PHE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 344 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 245 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 357 optimal weight: 0.4980 chunk 228 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 355 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 408 optimal weight: 0.0870 chunk 393 optimal weight: 7.9990 overall best weight: 2.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 HIS ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN ** O 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 339 HIS O 457 ASN O 497 GLN ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN ** M 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 ASN M 200 HIS M 207 HIS ** 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 = 0.3616 r_free = 0.3616 target = 0.070991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.057346 restraints weight = 195899.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058852 restraints weight = 111187.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.059891 restraints weight = 74476.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.060625 restraints weight = 55674.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.061137 restraints weight = 44916.416| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.8084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37637 Z= 0.172 Angle : 0.802 52.104 50977 Z= 0.371 Chirality : 0.045 0.231 5761 Planarity : 0.005 0.146 6377 Dihedral : 10.946 179.518 5434 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.26 % Favored : 90.53 % Rotamer: Outliers : 3.90 % Allowed : 23.49 % Favored : 72.61 % 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: -1.77 (0.13), residues: 4437 helix: 0.17 (0.13), residues: 1576 sheet: -2.02 (0.22), residues: 534 loop : -1.96 (0.13), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG Q 113 TYR 0.021 0.001 TYR B 445 PHE 0.018 0.001 PHE B 662 TRP 0.020 0.002 TRP M 205 HIS 0.008 0.001 HIS I 32 Details of bonding type rmsd covalent geometry : bond 0.00399 (37617) covalent geometry : angle 0.74788 (50956) hydrogen bonds : bond 0.03673 ( 1155) hydrogen bonds : angle 5.03699 ( 3213) metal coordination : bond 0.01607 ( 20) metal coordination : angle 14.24963 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 424 time to evaluate : 1.385 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: A 281 MET cc_start: 0.8972 (tpp) cc_final: 0.8687 (tpp) REVERT: A 307 MET cc_start: 0.8674 (mmp) cc_final: 0.8406 (mmp) REVERT: A 308 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8551 (pt0) REVERT: A 351 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7513 (mpt90) REVERT: A 490 GLU cc_start: 0.7674 (mp0) cc_final: 0.7289 (mp0) REVERT: A 871 MET cc_start: 0.8943 (tmm) cc_final: 0.8715 (tmm) REVERT: A 908 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8001 (m-30) REVERT: A 1012 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8877 (tm-30) REVERT: A 1039 GLN cc_start: 0.8530 (mm110) cc_final: 0.8284 (mm-40) REVERT: A 1106 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8420 (pp20) REVERT: A 1275 MET cc_start: 0.8916 (ttt) cc_final: 0.8620 (ttm) REVERT: A 1280 MET cc_start: 0.8734 (mmt) cc_final: 0.8494 (mmm) REVERT: B 233 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.7303 (p0) REVERT: B 243 MET cc_start: 0.8364 (ttm) cc_final: 0.8051 (ttm) REVERT: B 278 PHE cc_start: 0.8544 (m-80) cc_final: 0.8208 (m-80) REVERT: B 320 HIS cc_start: 0.6643 (m170) cc_final: 0.6201 (m170) REVERT: B 341 ARG cc_start: 0.8929 (mmt90) cc_final: 0.8681 (mmt90) REVERT: B 431 MET cc_start: 0.8251 (ppp) cc_final: 0.8033 (ppp) REVERT: B 506 MET cc_start: 0.8161 (mpp) cc_final: 0.7943 (pmm) REVERT: B 525 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8520 (pt) REVERT: B 527 CYS cc_start: 0.7972 (m) cc_final: 0.7269 (m) REVERT: B 530 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7583 (tm-30) REVERT: B 559 PHE cc_start: 0.8774 (t80) cc_final: 0.8564 (t80) REVERT: B 580 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8193 (t0) REVERT: B 600 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7714 (ptmm) REVERT: B 634 ASP cc_start: 0.8556 (p0) cc_final: 0.8226 (p0) REVERT: B 819 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: B 879 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7211 (t80) REVERT: C 87 MET cc_start: 0.8893 (mmm) cc_final: 0.8562 (mmm) REVERT: C 330 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8681 (ttm) REVERT: G 28 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8427 (mt-10) REVERT: G 32 LYS cc_start: 0.9106 (mtmm) cc_final: 0.8595 (mmtt) REVERT: G 36 ASN cc_start: 0.6530 (m-40) cc_final: 0.6231 (m-40) REVERT: G 90 LYS cc_start: 0.8432 (mmtm) cc_final: 0.8155 (mptt) REVERT: K 66 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8126 (mp0) REVERT: K 79 LYS cc_start: 0.9529 (ptmt) cc_final: 0.9179 (ptpp) REVERT: L 51 ARG cc_start: 0.8918 (mmm-85) cc_final: 0.8533 (mtp85) REVERT: P 193 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: P 196 ARG cc_start: 0.8446 (ptt180) cc_final: 0.7975 (ptt90) REVERT: P 203 MET cc_start: 0.7650 (mmp) cc_final: 0.7312 (mmp) REVERT: P 222 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7093 (mp0) REVERT: E 71 GLN cc_start: 0.4286 (OUTLIER) cc_final: 0.2878 (mp10) REVERT: F 57 MET cc_start: 0.9197 (tmm) cc_final: 0.8963 (tmm) REVERT: H 8 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6966 (m-30) REVERT: H 24 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.8042 (mtm180) REVERT: H 33 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8439 (mm-30) REVERT: H 37 MET cc_start: 0.8543 (mmm) cc_final: 0.7905 (mmm) REVERT: H 56 PHE cc_start: 0.8908 (p90) cc_final: 0.8093 (p90) REVERT: J 31 GLU cc_start: 0.9001 (mp0) cc_final: 0.8640 (mp0) REVERT: O 9 CYS cc_start: 0.8937 (m) cc_final: 0.8674 (m) REVERT: O 368 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9234 (mm) REVERT: O 404 MET cc_start: 0.8494 (mmm) cc_final: 0.8116 (mmm) REVERT: O 427 ASN cc_start: 0.8668 (t0) cc_final: 0.8058 (t0) REVERT: Q 54 GLU cc_start: 0.9269 (mm-30) cc_final: 0.7961 (tm-30) REVERT: Q 111 MET cc_start: 0.7503 (mmm) cc_final: 0.6576 (tmm) REVERT: Q 114 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.7226 (t0) REVERT: D 5 ASP cc_start: 0.9030 (t0) cc_final: 0.8788 (t0) REVERT: D 22 ASP cc_start: 0.9308 (m-30) cc_final: 0.9049 (m-30) REVERT: D 26 GLN cc_start: 0.9596 (mm-40) cc_final: 0.9191 (pp30) REVERT: D 100 MET cc_start: 0.6751 (mmt) cc_final: 0.6496 (mmt) REVERT: M 17 LEU cc_start: 0.5430 (pt) cc_final: 0.4916 (tt) REVERT: M 45 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9310 (pp) REVERT: M 114 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.6938 (m-80) REVERT: M 149 HIS cc_start: 0.8904 (m-70) cc_final: 0.8570 (m-70) REVERT: M 202 GLU cc_start: 0.8934 (pt0) cc_final: 0.8025 (mp0) REVERT: N 350 MET cc_start: 0.7603 (ppp) cc_final: 0.6969 (ppp) REVERT: N 356 PHE cc_start: 0.7594 (m-80) cc_final: 0.7081 (m-80) REVERT: N 382 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8129 (pttp) outliers start: 155 outliers final: 99 residues processed: 535 average time/residue: 0.2003 time to fit residues: 179.2028 Evaluate side-chains 530 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 412 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 787 PHE Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 107 CYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 259 THR Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain O residue 395 LEU Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 425 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 114 ASN Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 62 SER 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 42 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 344 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 240 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 377 optimal weight: 9.9990 chunk 404 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 406 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN E 71 GLN E 169 GLN F 72 GLN ** O 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 339 HIS ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 GLN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.071394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.057907 restraints weight = 193314.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.059420 restraints weight = 108363.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.060464 restraints weight = 72015.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.061200 restraints weight = 53648.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.061707 restraints weight = 43165.964| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.8319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37637 Z= 0.139 Angle : 0.782 48.388 50977 Z= 0.360 Chirality : 0.045 0.302 5761 Planarity : 0.005 0.094 6377 Dihedral : 10.846 178.443 5434 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.79 % Favored : 91.01 % Rotamer: Outliers : 3.60 % Allowed : 23.74 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.13), residues: 4437 helix: 0.27 (0.13), residues: 1584 sheet: -1.95 (0.22), residues: 528 loop : -1.91 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 101 TYR 0.034 0.001 TYR K 70 PHE 0.019 0.001 PHE B 934 TRP 0.024 0.002 TRP M 205 HIS 0.005 0.001 HIS I 32 Details of bonding type rmsd covalent geometry : bond 0.00324 (37617) covalent geometry : angle 0.73393 (50956) hydrogen bonds : bond 0.03508 ( 1155) hydrogen bonds : angle 4.91494 ( 3213) metal coordination : bond 0.00825 ( 20) metal coordination : angle 13.34787 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 440 time to evaluate : 1.261 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 30 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: A 52 LEU cc_start: 0.7669 (tp) cc_final: 0.7451 (pp) REVERT: A 53 TYR cc_start: 0.5410 (OUTLIER) cc_final: 0.3842 (t80) REVERT: A 243 GLU cc_start: 0.9060 (mp0) cc_final: 0.8801 (mp0) REVERT: A 281 MET cc_start: 0.9006 (tpp) cc_final: 0.8406 (ptt) REVERT: A 307 MET cc_start: 0.8637 (mmp) cc_final: 0.8406 (mmp) REVERT: A 308 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: A 490 GLU cc_start: 0.7604 (mp0) cc_final: 0.7200 (mp0) REVERT: A 523 MET cc_start: 0.9073 (pmm) cc_final: 0.8872 (pmm) REVERT: A 871 MET cc_start: 0.8968 (tmm) cc_final: 0.8722 (tmm) REVERT: A 1012 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8929 (tm-30) REVERT: A 1106 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8486 (pp20) REVERT: A 1275 MET cc_start: 0.8880 (ttt) cc_final: 0.8595 (ttm) REVERT: A 1280 MET cc_start: 0.8704 (mmt) cc_final: 0.8429 (mmm) REVERT: B 131 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8759 (tt) REVERT: B 233 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.7193 (p0) REVERT: B 243 MET cc_start: 0.8338 (ttm) cc_final: 0.8044 (ttm) REVERT: B 254 MET cc_start: 0.8927 (mmt) cc_final: 0.8578 (mmt) REVERT: B 278 PHE cc_start: 0.8561 (m-80) cc_final: 0.8191 (m-80) REVERT: B 281 MET cc_start: 0.8849 (ptp) cc_final: 0.8086 (ptp) REVERT: B 341 ARG cc_start: 0.8885 (mmt90) cc_final: 0.8628 (mmt90) REVERT: B 431 MET cc_start: 0.8267 (ppp) cc_final: 0.8049 (ppp) REVERT: B 525 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8567 (pt) REVERT: B 526 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8421 (mm) REVERT: B 527 CYS cc_start: 0.7960 (m) cc_final: 0.6961 (m) REVERT: B 530 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7565 (tm-30) REVERT: B 580 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8142 (t0) REVERT: B 600 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7613 (ptmm) REVERT: B 634 ASP cc_start: 0.8598 (p0) cc_final: 0.8274 (p0) REVERT: B 819 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: B 879 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7184 (t80) REVERT: C 10 MET cc_start: 0.7176 (mmp) cc_final: 0.6962 (mmp) REVERT: C 87 MET cc_start: 0.8920 (mmm) cc_final: 0.8600 (mmm) REVERT: C 330 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8700 (ttm) REVERT: G 28 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8389 (mt-10) REVERT: G 32 LYS cc_start: 0.9080 (mtmm) cc_final: 0.8570 (mmtt) REVERT: K 66 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8130 (mp0) REVERT: K 79 LYS cc_start: 0.9511 (ptmt) cc_final: 0.9172 (ptpp) REVERT: L 51 ARG cc_start: 0.8948 (mmm-85) cc_final: 0.8497 (mtp85) REVERT: P 193 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7199 (mt-10) REVERT: P 196 ARG cc_start: 0.8453 (ptt180) cc_final: 0.7976 (ptt90) REVERT: P 232 MET cc_start: 0.5941 (mmp) cc_final: 0.5636 (mmp) REVERT: F 57 MET cc_start: 0.9212 (tmm) cc_final: 0.8955 (tmm) REVERT: F 80 MET cc_start: 0.8875 (mmp) cc_final: 0.8637 (mmp) REVERT: H 8 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.6959 (m-30) REVERT: H 24 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.8088 (mtm180) REVERT: H 33 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8481 (mm-30) REVERT: H 56 PHE cc_start: 0.8853 (p90) cc_final: 0.8115 (p90) REVERT: H 136 GLU cc_start: 0.7212 (mp0) cc_final: 0.6489 (mp0) REVERT: J 6 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8134 (mmt90) REVERT: J 31 GLU cc_start: 0.8970 (mp0) cc_final: 0.8561 (mp0) REVERT: O 9 CYS cc_start: 0.9017 (m) cc_final: 0.8742 (m) REVERT: O 271 LEU cc_start: 0.8175 (mt) cc_final: 0.7498 (tt) REVERT: O 368 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9222 (mm) REVERT: O 404 MET cc_start: 0.8484 (mmm) cc_final: 0.8122 (mmm) REVERT: O 427 ASN cc_start: 0.8611 (t0) cc_final: 0.7853 (t0) REVERT: Q 54 GLU cc_start: 0.9235 (mm-30) cc_final: 0.7849 (tm-30) REVERT: Q 62 GLN cc_start: 0.8517 (pp30) cc_final: 0.7764 (mm-40) REVERT: Q 111 MET cc_start: 0.7485 (mmm) cc_final: 0.6662 (tmm) REVERT: D 5 ASP cc_start: 0.8978 (t0) cc_final: 0.8719 (t0) REVERT: D 22 ASP cc_start: 0.9296 (m-30) cc_final: 0.9024 (m-30) REVERT: D 26 GLN cc_start: 0.9621 (mm-40) cc_final: 0.9213 (pp30) REVERT: D 60 HIS cc_start: 0.3984 (OUTLIER) cc_final: 0.3449 (m90) REVERT: D 100 MET cc_start: 0.6730 (mmt) cc_final: 0.6465 (mmt) REVERT: M 17 LEU cc_start: 0.5424 (pt) cc_final: 0.4910 (tt) REVERT: M 45 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9316 (pp) REVERT: M 75 GLU cc_start: 0.8747 (tp30) cc_final: 0.8542 (tp30) REVERT: M 114 TYR cc_start: 0.7641 (m-80) cc_final: 0.6910 (m-80) REVERT: M 149 HIS cc_start: 0.8860 (m-70) cc_final: 0.8506 (m-70) REVERT: M 202 GLU cc_start: 0.8942 (pt0) cc_final: 0.8036 (mp0) REVERT: N 350 MET cc_start: 0.7862 (ppp) cc_final: 0.6893 (ppp) REVERT: N 356 PHE cc_start: 0.7572 (m-80) cc_final: 0.7054 (m-80) REVERT: N 382 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8074 (pttm) outliers start: 143 outliers final: 103 residues processed: 550 average time/residue: 0.2074 time to fit residues: 191.6952 Evaluate side-chains 538 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 415 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1106 GLU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 787 PHE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 259 THR Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 12 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 82 VAL Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain O residue 395 LEU Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 406 LEU Chi-restraints excluded: chain O residue 425 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 62 SER 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 42 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 192 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 281 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 349 optimal weight: 4.9990 chunk 402 optimal weight: 0.3980 chunk 350 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 158 HIS ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A1364 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN F 72 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS O 261 GLN O 339 HIS ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.069325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056047 restraints weight = 196758.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.057533 restraints weight = 110135.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.058537 restraints weight = 73113.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.059261 restraints weight = 54431.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.059707 restraints weight = 43780.433| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.8751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37637 Z= 0.181 Angle : 0.816 50.284 50977 Z= 0.379 Chirality : 0.046 0.235 5761 Planarity : 0.005 0.095 6377 Dihedral : 10.799 177.706 5432 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.17 % Favored : 90.65 % Rotamer: Outliers : 3.45 % Allowed : 24.30 % Favored : 72.26 % 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: -1.63 (0.13), residues: 4437 helix: 0.31 (0.13), residues: 1581 sheet: -1.90 (0.22), residues: 523 loop : -1.91 (0.13), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 140 TYR 0.031 0.002 TYR K 70 PHE 0.018 0.001 PHE C 185 TRP 0.023 0.002 TRP M 205 HIS 0.006 0.001 HIS K 45 Details of bonding type rmsd covalent geometry : bond 0.00421 (37617) covalent geometry : angle 0.76561 (50956) hydrogen bonds : bond 0.03682 ( 1155) hydrogen bonds : angle 4.97563 ( 3213) metal coordination : bond 0.01112 ( 20) metal coordination : angle 13.98779 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 428 time to evaluate : 1.468 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 52 LEU cc_start: 0.7778 (tp) cc_final: 0.7480 (pp) REVERT: A 53 TYR cc_start: 0.5582 (OUTLIER) cc_final: 0.3973 (t80) REVERT: A 243 GLU cc_start: 0.9053 (mp0) cc_final: 0.8813 (mp0) REVERT: A 308 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8481 (pt0) REVERT: A 406 LYS cc_start: 0.9372 (tppt) cc_final: 0.8680 (mmtm) REVERT: A 490 GLU cc_start: 0.7551 (mp0) cc_final: 0.7134 (mp0) REVERT: A 523 MET cc_start: 0.9097 (pmm) cc_final: 0.8870 (pmm) REVERT: A 860 ASP cc_start: 0.8927 (m-30) cc_final: 0.8430 (m-30) REVERT: A 871 MET cc_start: 0.9007 (tmm) cc_final: 0.8737 (tmm) REVERT: A 912 MET cc_start: 0.8778 (tpp) cc_final: 0.8417 (tpt) REVERT: A 1012 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8934 (tm-30) REVERT: A 1027 MET cc_start: 0.8898 (tpt) cc_final: 0.8672 (tpp) REVERT: A 1039 GLN cc_start: 0.8480 (mm110) cc_final: 0.8255 (mm-40) REVERT: A 1236 MET cc_start: 0.8845 (ptp) cc_final: 0.8405 (ptp) REVERT: A 1275 MET cc_start: 0.8918 (ttt) cc_final: 0.8640 (ttm) REVERT: A 1351 ILE cc_start: 0.9392 (tp) cc_final: 0.9115 (pt) REVERT: A 1376 PRO cc_start: 0.7404 (Cg_endo) cc_final: 0.7189 (Cg_exo) REVERT: B 131 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8773 (tt) REVERT: B 233 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.7300 (p0) REVERT: B 243 MET cc_start: 0.8446 (ttm) cc_final: 0.8171 (ttm) REVERT: B 254 MET cc_start: 0.8974 (mmt) cc_final: 0.8763 (mmt) REVERT: B 278 PHE cc_start: 0.8613 (m-80) cc_final: 0.8319 (m-80) REVERT: B 281 MET cc_start: 0.9000 (ptp) cc_final: 0.8234 (ptp) REVERT: B 527 CYS cc_start: 0.8006 (m) cc_final: 0.6994 (m) REVERT: B 580 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8264 (t0) REVERT: B 600 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7751 (ptmm) REVERT: B 634 ASP cc_start: 0.8497 (p0) cc_final: 0.8279 (p0) REVERT: B 819 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: B 879 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7275 (t80) REVERT: C 87 MET cc_start: 0.8968 (mmm) cc_final: 0.8618 (mmm) REVERT: C 330 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8657 (ttm) REVERT: G 28 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8447 (mt-10) REVERT: G 32 LYS cc_start: 0.9140 (mtmm) cc_final: 0.8504 (mmtt) REVERT: G 36 ASN cc_start: 0.6957 (m-40) cc_final: 0.6741 (m-40) REVERT: G 37 LYS cc_start: 0.8492 (mmmm) cc_final: 0.8178 (mmmm) REVERT: K 46 GLU cc_start: 0.9237 (pm20) cc_final: 0.9034 (pm20) REVERT: K 66 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8162 (mp0) REVERT: K 79 LYS cc_start: 0.9468 (ptmt) cc_final: 0.9160 (ptpp) REVERT: L 51 ARG cc_start: 0.8944 (mmm-85) cc_final: 0.8503 (mtp85) REVERT: P 193 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: P 196 ARG cc_start: 0.8504 (ptt180) cc_final: 0.8082 (ptt90) REVERT: H 8 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7073 (m-30) REVERT: H 24 ARG cc_start: 0.8438 (mtm-85) cc_final: 0.8147 (mtm180) REVERT: H 33 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8520 (mm-30) REVERT: H 37 MET cc_start: 0.8349 (mmm) cc_final: 0.7836 (mmm) REVERT: H 56 PHE cc_start: 0.8965 (p90) cc_final: 0.8246 (p90) REVERT: H 136 GLU cc_start: 0.7225 (mp0) cc_final: 0.6545 (mp0) REVERT: J 6 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8385 (mmt90) REVERT: O 9 CYS cc_start: 0.9054 (m) cc_final: 0.8805 (m) REVERT: O 271 LEU cc_start: 0.8545 (mt) cc_final: 0.7879 (tt) REVERT: O 368 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9188 (mm) REVERT: O 385 MET cc_start: 0.8669 (mpp) cc_final: 0.6699 (tpt) REVERT: O 404 MET cc_start: 0.8423 (mmm) cc_final: 0.7938 (mmm) REVERT: Q 62 GLN cc_start: 0.8639 (pp30) cc_final: 0.8024 (mm-40) REVERT: Q 111 MET cc_start: 0.7585 (mmm) cc_final: 0.6906 (tmm) REVERT: D 5 ASP cc_start: 0.8964 (t0) cc_final: 0.8711 (t0) REVERT: D 22 ASP cc_start: 0.9329 (m-30) cc_final: 0.9098 (m-30) REVERT: D 26 GLN cc_start: 0.9621 (mm-40) cc_final: 0.9226 (pp30) REVERT: D 60 HIS cc_start: 0.3979 (OUTLIER) cc_final: 0.3523 (m90) REVERT: D 100 MET cc_start: 0.6874 (mmt) cc_final: 0.6649 (mmt) REVERT: M 17 LEU cc_start: 0.5356 (pt) cc_final: 0.4740 (tt) REVERT: M 114 TYR cc_start: 0.7809 (m-80) cc_final: 0.7058 (m-80) REVERT: M 149 HIS cc_start: 0.8836 (m-70) cc_final: 0.8484 (m-70) REVERT: N 350 MET cc_start: 0.7849 (ppp) cc_final: 0.6900 (ppp) REVERT: N 356 PHE cc_start: 0.7615 (m-80) cc_final: 0.7095 (m-80) REVERT: N 382 LYS cc_start: 0.8742 (ttpp) cc_final: 0.8102 (pttm) outliers start: 137 outliers final: 95 residues processed: 534 average time/residue: 0.2096 time to fit residues: 187.5328 Evaluate side-chains 510 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 400 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 259 THR Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 12 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 82 VAL Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain O residue 395 LEU Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 425 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 62 SER 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 42 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 79 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 392 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 HIS ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS M 207 HIS ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.067653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054509 restraints weight = 197495.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.055943 restraints weight = 110625.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.056945 restraints weight = 73672.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.057649 restraints weight = 54775.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.058127 restraints weight = 44223.490| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.9202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 37637 Z= 0.208 Angle : 0.852 51.851 50977 Z= 0.395 Chirality : 0.046 0.205 5761 Planarity : 0.005 0.098 6377 Dihedral : 10.835 177.356 5432 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.08 % Favored : 90.71 % Rotamer: Outliers : 3.14 % Allowed : 24.90 % Favored : 71.96 % 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: -1.63 (0.13), residues: 4437 helix: 0.33 (0.13), residues: 1560 sheet: -1.95 (0.22), residues: 519 loop : -1.91 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1024 TYR 0.033 0.002 TYR K 70 PHE 0.022 0.002 PHE G 18 TRP 0.021 0.002 TRP M 205 HIS 0.006 0.001 HIS M 130 Details of bonding type rmsd covalent geometry : bond 0.00477 (37617) covalent geometry : angle 0.79902 (50956) hydrogen bonds : bond 0.03770 ( 1155) hydrogen bonds : angle 5.07790 ( 3213) metal coordination : bond 0.01252 ( 20) metal coordination : angle 14.62270 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 405 time to evaluate : 1.447 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: A 30 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8455 (pm20) REVERT: A 52 LEU cc_start: 0.7788 (tp) cc_final: 0.7449 (pp) REVERT: A 53 TYR cc_start: 0.5710 (OUTLIER) cc_final: 0.4062 (t80) REVERT: A 243 GLU cc_start: 0.9114 (mp0) cc_final: 0.8878 (mp0) REVERT: A 351 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7530 (mpt90) REVERT: A 406 LYS cc_start: 0.9377 (tppt) cc_final: 0.8717 (mmtm) REVERT: A 490 GLU cc_start: 0.7484 (mp0) cc_final: 0.7018 (mp0) REVERT: A 523 MET cc_start: 0.9020 (pmm) cc_final: 0.8810 (pmm) REVERT: A 588 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8221 (mm) REVERT: A 650 MET cc_start: 0.9168 (mmm) cc_final: 0.8813 (mmm) REVERT: A 860 ASP cc_start: 0.8905 (m-30) cc_final: 0.8413 (m-30) REVERT: A 871 MET cc_start: 0.9092 (tmm) cc_final: 0.8868 (tmm) REVERT: A 1012 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8947 (tm-30) REVERT: A 1023 MET cc_start: 0.9243 (mmm) cc_final: 0.8874 (mmt) REVERT: A 1236 MET cc_start: 0.8817 (ptp) cc_final: 0.8413 (ptp) REVERT: A 1376 PRO cc_start: 0.7611 (Cg_endo) cc_final: 0.7402 (Cg_exo) REVERT: B 233 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.7351 (p0) REVERT: B 243 MET cc_start: 0.8468 (ttm) cc_final: 0.8177 (ttm) REVERT: B 278 PHE cc_start: 0.8616 (m-80) cc_final: 0.8362 (m-80) REVERT: B 281 MET cc_start: 0.9088 (ptp) cc_final: 0.8337 (ptp) REVERT: B 527 CYS cc_start: 0.7896 (m) cc_final: 0.6703 (m) REVERT: B 580 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8355 (t0) REVERT: B 600 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7829 (ptmm) REVERT: B 634 ASP cc_start: 0.8576 (p0) cc_final: 0.8265 (p0) REVERT: B 819 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: B 879 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7331 (t80) REVERT: C 87 MET cc_start: 0.8968 (mmm) cc_final: 0.8624 (mmm) REVERT: C 330 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8685 (ttm) REVERT: G 28 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8488 (mt-10) REVERT: G 32 LYS cc_start: 0.9175 (mtmm) cc_final: 0.8553 (mmtt) REVERT: K 66 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8150 (mp0) REVERT: K 79 LYS cc_start: 0.9523 (ptmt) cc_final: 0.9179 (ptpp) REVERT: L 51 ARG cc_start: 0.8963 (mmm-85) cc_final: 0.8648 (mmm-85) REVERT: P 193 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: P 196 ARG cc_start: 0.8482 (ptt180) cc_final: 0.8103 (ptt90) REVERT: P 232 MET cc_start: 0.5911 (mmp) cc_final: 0.5611 (mmp) REVERT: H 8 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7222 (m-30) REVERT: H 24 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8154 (mtm180) REVERT: H 33 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8549 (mm-30) REVERT: H 136 GLU cc_start: 0.7219 (mp0) cc_final: 0.6423 (mp0) REVERT: O 9 CYS cc_start: 0.9164 (m) cc_final: 0.8922 (m) REVERT: O 368 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9193 (mm) REVERT: O 404 MET cc_start: 0.8382 (mmm) cc_final: 0.7861 (mmm) REVERT: Q 62 GLN cc_start: 0.8707 (pp30) cc_final: 0.8117 (mm-40) REVERT: Q 111 MET cc_start: 0.7696 (mmm) cc_final: 0.6940 (tmm) REVERT: D 5 ASP cc_start: 0.8948 (t0) cc_final: 0.8724 (t0) REVERT: D 26 GLN cc_start: 0.9613 (mm-40) cc_final: 0.9213 (pp30) REVERT: D 61 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.5888 (mm110) REVERT: D 100 MET cc_start: 0.6882 (mmt) cc_final: 0.6636 (mmt) REVERT: M 17 LEU cc_start: 0.5246 (pt) cc_final: 0.4692 (tt) REVERT: M 114 TYR cc_start: 0.7694 (m-80) cc_final: 0.7401 (m-80) REVERT: M 149 HIS cc_start: 0.8912 (m-70) cc_final: 0.8559 (m-70) REVERT: M 202 GLU cc_start: 0.9162 (pt0) cc_final: 0.8655 (mp0) REVERT: N 350 MET cc_start: 0.7847 (ppp) cc_final: 0.6849 (ppp) REVERT: N 356 PHE cc_start: 0.7671 (m-80) cc_final: 0.7168 (m-80) REVERT: N 382 LYS cc_start: 0.8834 (ttpp) cc_final: 0.8169 (pttm) outliers start: 125 outliers final: 93 residues processed: 504 average time/residue: 0.1994 time to fit residues: 167.7471 Evaluate side-chains 495 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 387 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 306 TYR Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 266 HIS Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 293 PHE Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain O residue 395 LEU Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 425 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 195 PHE Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 375 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 222 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 297 optimal weight: 9.9990 chunk 362 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 315 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1121 ASN ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 HIS ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.067703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.054609 restraints weight = 196565.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056049 restraints weight = 110104.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.057042 restraints weight = 73159.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.057735 restraints weight = 54435.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058222 restraints weight = 43886.774| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.9218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.196 37637 Z= 0.225 Angle : 0.922 59.199 50977 Z= 0.450 Chirality : 0.046 0.299 5761 Planarity : 0.005 0.099 6377 Dihedral : 10.827 177.340 5431 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.22 % Favored : 90.58 % Rotamer: Outliers : 2.94 % Allowed : 25.70 % Favored : 71.35 % 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: -1.64 (0.13), residues: 4437 helix: 0.33 (0.13), residues: 1560 sheet: -1.98 (0.22), residues: 519 loop : -1.91 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 101 TYR 0.029 0.002 TYR K 70 PHE 0.058 0.002 PHE C 185 TRP 0.019 0.002 TRP M 205 HIS 0.012 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00531 (37617) covalent geometry : angle 0.87347 (50956) hydrogen bonds : bond 0.03753 ( 1155) hydrogen bonds : angle 5.07355 ( 3213) metal coordination : bond 0.01205 ( 20) metal coordination : angle 14.60644 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7221.71 seconds wall clock time: 125 minutes 31.60 seconds (7531.60 seconds total)