Starting phenix.real_space_refine on Tue Sep 15 07:31:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dn3_30779/09_2026/7dn3_30779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dn3_30779/09_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_30779/09_2026/7dn3_30779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dn3_30779/09_2026/7dn3_30779.map" model { file = "/net/cci-nas-00/data/ceres_data/7dn3_30779/09_2026/7dn3_30779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dn3_30779/09_2026/7dn3_30779.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dn3_30779/09_2026/7dn3_30779.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dn3_30779/09_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): 0.20s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 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: 7.62, 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: 3.66 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 307 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN A1902 " pdb="ZN ZN A1902 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 72 " pdb=" ZN A1903 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 25 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 15 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: 1.18 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: 8.55 Time building geometry restraints manager: 4.78 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=" C1' DC Y 10 " pdb=" N1 DC Y 10 " ideal model delta sigma weight residual 1.468 1.538 -0.070 1.40e-02 5.10e+03 2.49e+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 ... (remaining 37612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 49211 3.36 - 6.72: 1547 6.72 - 10.09: 156 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: 22148 35.52 - 71.04: 776 71.04 - 106.56: 29 106.56 - 142.08: 0 142.08 - 177.59: 1 Dihedral angle restraints: 22954 sinusoidal: 9811 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 22951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 5501 0.194 - 0.389: 232 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 44.790 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 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= 0.700 Angle : 1.518 56.145 50977 Z= 0.916 Chirality : 0.092 0.972 5761 Planarity : 0.008 0.080 6377 Dihedral : 16.990 177.595 14450 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/Z covalent geometry : bond 0.01199 / 0.62 (37617) covalent geometry : angle 1.42857 / 0.91 (50956) hydrogen bonds : bond 0.28966 / 19.27 ( 1155) hydrogen bonds : angle 10.65580 / 7.17 ( 3213) metal coordination : bond 0.43706 / 26.85 ( 20) metal coordination : angle 25.28124 / 14.96 ( 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 : 1.320 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: 0.2582 time to fit residues: 510.7922 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 : 1.396 ------------------------------------------------------------------------------- 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... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS A 163 ASN A 422 GLN A 511 GLN A 662 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN A 872 GLN A1190 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 608 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN C 42 GLN C 48 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS C 127 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 M 66 ASN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.091531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.076968 restraints weight = 185717.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.078940 restraints weight = 107879.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.080308 restraints weight = 71580.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.081244 restraints weight = 52105.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.081918 restraints weight = 40810.994| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 37637 Z= 0.214 Angle : 0.987 40.360 50977 Z= 0.478 Chirality : 0.051 0.269 5761 Planarity : 0.007 0.093 6377 Dihedral : 12.289 167.668 5509 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.72 % Favored : 91.01 % Rotamer: Outliers : 4.50 % Allowed : 19.62 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.05 % 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: -3.81 (0.11), residues: 4437 helix: -2.38 (0.10), residues: 1584 sheet: -2.72 (0.20), residues: 529 loop : -2.59 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 258 TYR 0.021 0.002 TYR B1058 PHE 0.030 0.002 PHE G 18 TRP 0.027 0.003 TRP G 201 HIS 0.014 0.002 HIS O 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (37617) covalent geometry : angle 0.93062 / 0.48 (50956) hydrogen bonds : bond 0.05881 / 3.88 ( 1155) hydrogen bonds : angle 6.28773 / 4.25 ( 3213) metal coordination : bond 0.01895 / 1.22 ( 20) metal coordination : angle 16.20794 / 9.84 ( 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 861 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 682 time to evaluate : 1.470 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: A 30 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: A 147 SER cc_start: 0.8720 (t) cc_final: 0.8424 (p) REVERT: A 281 MET cc_start: 0.8928 (tpp) cc_final: 0.8690 (tpp) REVERT: A 305 MET cc_start: 0.7973 (ppp) cc_final: 0.7264 (ppp) REVERT: A 505 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7933 (ptt) REVERT: A 646 MET cc_start: 0.7975 (tpp) cc_final: 0.7459 (mmp) REVERT: A 680 MET cc_start: 0.8943 (ttm) cc_final: 0.8613 (tpp) REVERT: A 815 ASN cc_start: 0.8160 (m-40) cc_final: 0.7932 (m-40) REVERT: A 852 MET cc_start: 0.8679 (mtp) cc_final: 0.8410 (mtp) REVERT: A 1255 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8370 (tt0) REVERT: B 175 GLU cc_start: 0.7239 (pt0) cc_final: 0.6982 (mt-10) REVERT: B 262 MET cc_start: 0.7359 (mmm) cc_final: 0.7124 (mmm) REVERT: B 317 ILE cc_start: 0.8729 (mm) cc_final: 0.8349 (tp) REVERT: B 434 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7148 (tm-30) REVERT: B 451 MET cc_start: 0.8788 (ttm) cc_final: 0.8549 (ttm) REVERT: B 540 PHE cc_start: 0.8023 (m-10) cc_final: 0.7528 (m-10) REVERT: B 625 LEU cc_start: 0.9337 (mp) cc_final: 0.9123 (mp) REVERT: B 769 CYS cc_start: 0.6237 (m) cc_final: 0.5965 (m) REVERT: B 938 MET cc_start: 0.7420 (mtm) cc_final: 0.7063 (mtp) REVERT: B 1062 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7884 (mpp) REVERT: B 1126 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8545 (mt) REVERT: C 87 MET cc_start: 0.7885 (mmm) cc_final: 0.7353 (mmt) REVERT: C 163 TYR cc_start: 0.6484 (t80) cc_final: 0.5802 (t80) REVERT: C 206 GLN cc_start: 0.8192 (mt0) cc_final: 0.7579 (mt0) REVERT: C 235 LEU cc_start: 0.8918 (mt) cc_final: 0.8619 (mt) REVERT: C 330 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8750 (ttm) REVERT: G 37 LYS cc_start: 0.7763 (mmmm) cc_final: 0.7357 (mmmm) REVERT: G 190 ILE cc_start: 0.6456 (mp) cc_final: 0.6175 (mt) REVERT: I 37 LYS cc_start: 0.8095 (tppp) cc_final: 0.7520 (tptt) REVERT: K 66 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7977 (mt-10) REVERT: L 44 MET cc_start: 0.7677 (mtp) cc_final: 0.7025 (mmm) REVERT: P 232 MET cc_start: 0.5648 (mmp) cc_final: 0.5363 (mmp) REVERT: E 23 ASP cc_start: 0.8055 (m-30) cc_final: 0.7661 (m-30) REVERT: E 74 VAL cc_start: 0.7874 (p) cc_final: 0.7649 (p) REVERT: E 110 MET cc_start: 0.7948 (mtp) cc_final: 0.7067 (ttm) REVERT: F 101 LYS cc_start: 0.7826 (mmtp) cc_final: 0.7574 (mmtt) REVERT: H 24 ARG cc_start: 0.7096 (mtm-85) cc_final: 0.6876 (mtm180) REVERT: O 72 VAL cc_start: 0.7598 (t) cc_final: 0.7232 (p) REVERT: O 404 MET cc_start: 0.7584 (mmm) cc_final: 0.7222 (mmm) REVERT: O 423 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7754 (pp) REVERT: O 448 GLU cc_start: 0.9326 (tp30) cc_final: 0.8379 (pp20) REVERT: Q 54 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8357 (tm-30) REVERT: Q 111 MET cc_start: 0.7043 (mmm) cc_final: 0.6497 (tmm) REVERT: D 22 ASP cc_start: 0.9083 (m-30) cc_final: 0.8815 (m-30) REVERT: D 26 GLN cc_start: 0.9575 (mm-40) cc_final: 0.9011 (pp30) REVERT: D 41 ASN cc_start: 0.8835 (m-40) cc_final: 0.8355 (t0) REVERT: D 42 LEU cc_start: 0.9021 (tm) cc_final: 0.8680 (pt) REVERT: M 17 LEU cc_start: 0.5008 (pt) cc_final: 0.4401 (tt) REVERT: M 45 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9114 (mt) REVERT: M 49 ILE cc_start: 0.6755 (mt) cc_final: 0.6431 (mt) REVERT: M 114 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6985 (m-80) REVERT: M 132 ILE cc_start: 0.7053 (mm) cc_final: 0.6850 (mm) REVERT: M 143 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8525 (m-30) REVERT: M 149 HIS cc_start: 0.8649 (m-70) cc_final: 0.8230 (m90) REVERT: M 202 GLU cc_start: 0.8777 (pt0) cc_final: 0.8534 (pt0) REVERT: N 352 THR cc_start: 0.3017 (OUTLIER) cc_final: 0.1478 (p) REVERT: N 356 PHE cc_start: 0.7582 (m-80) cc_final: 0.7001 (m-10) REVERT: N 363 VAL cc_start: 0.7930 (t) cc_final: 0.7670 (t) REVERT: N 382 LYS cc_start: 0.7913 (tttt) cc_final: 0.7534 (pttm) outliers start: 179 outliers final: 92 residues processed: 803 average time/residue: 0.2250 time to fit residues: 297.5802 Evaluate side-chains 649 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 547 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 369 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 698 ILE Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 890 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1067 VAL 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 363 GLU 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 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 795 LEU 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 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 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 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 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 H residue 122 LEU Chi-restraints excluded: chain H residue 141 VAL 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 57 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 O residue 530 THR 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 64 GLU 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 136 ARG Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 194 GLU 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 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: 4.9990 chunk 289 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 435 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 400 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS A 157 HIS A 158 HIS A 374 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN A 794 GLN A 836 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN A1239 HIS ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS B 280 GLN ** 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** B1100 HIS ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS K 85 GLN K 101 ASN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 35 HIS M 106 GLN N 338 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.080061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065680 restraints weight = 191105.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.067436 restraints weight = 108272.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.068653 restraints weight = 71630.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.069509 restraints weight = 52740.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.070052 restraints weight = 41777.741| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 37637 Z= 0.306 Angle : 0.998 58.455 50977 Z= 0.487 Chirality : 0.051 0.325 5761 Planarity : 0.007 0.114 6377 Dihedral : 11.690 178.742 5438 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.44 % Favored : 90.33 % Rotamer: Outliers : 5.21 % Allowed : 20.70 % Favored : 74.09 % 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: -3.13 (0.11), residues: 4437 helix: -1.47 (0.12), residues: 1589 sheet: -2.39 (0.21), residues: 501 loop : -2.47 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 533 TYR 0.027 0.002 TYR J 21 PHE 0.044 0.003 PHE A 462 TRP 0.022 0.002 TRP C 40 HIS 0.020 0.002 HIS M 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.31 (37617) covalent geometry : angle 0.92911 / 0.49 (50956) hydrogen bonds : bond 0.05389 / 3.57 ( 1155) hydrogen bonds : angle 5.85928 / 4.01 ( 3213) metal coordination : bond 0.01932 / 1.08 ( 20) metal coordination : angle 17.99783 / 9.96 ( 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 760 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 553 time to evaluate : 1.365 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: A 30 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: A 144 LYS cc_start: 0.9463 (tppt) cc_final: 0.9081 (tppt) REVERT: A 147 SER cc_start: 0.8743 (t) cc_final: 0.8459 (p) REVERT: A 281 MET cc_start: 0.9068 (tpp) cc_final: 0.8700 (tpp) REVERT: A 307 MET cc_start: 0.8874 (mmm) cc_final: 0.8651 (mmm) REVERT: A 308 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8244 (pt0) REVERT: A 311 ASP cc_start: 0.9073 (m-30) cc_final: 0.8753 (p0) REVERT: A 406 LYS cc_start: 0.9468 (tppt) cc_final: 0.8819 (mmtm) REVERT: A 646 MET cc_start: 0.8664 (tpp) cc_final: 0.8180 (mmp) REVERT: A 654 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9162 (p) REVERT: A 673 GLN cc_start: 0.8554 (pt0) cc_final: 0.8196 (pt0) REVERT: A 680 MET cc_start: 0.9200 (ttm) cc_final: 0.8892 (tpp) REVERT: A 776 SER cc_start: 0.8700 (m) cc_final: 0.8287 (p) REVERT: A 815 ASN cc_start: 0.8541 (m-40) cc_final: 0.8326 (m-40) REVERT: A 953 MET cc_start: 0.7116 (ttm) cc_final: 0.6878 (ttp) REVERT: A 1012 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8698 (tm-30) REVERT: A 1225 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6660 (pp) REVERT: A 1233 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8968 (tmm-80) REVERT: B 186 LYS cc_start: 0.9002 (tmtt) cc_final: 0.8695 (tptp) REVERT: B 243 MET cc_start: 0.8312 (ttm) cc_final: 0.8111 (ttm) REVERT: B 272 CYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8078 (m) REVERT: B 317 ILE cc_start: 0.8856 (mm) cc_final: 0.8529 (tp) REVERT: B 431 MET cc_start: 0.8538 (ppp) cc_final: 0.7968 (ppp) REVERT: B 530 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7255 (tm-30) REVERT: B 679 GLN cc_start: 0.7949 (mt0) cc_final: 0.7339 (mt0) REVERT: B 697 ILE cc_start: 0.9292 (tp) cc_final: 0.8870 (mm) REVERT: B 945 GLU cc_start: 0.8581 (tp30) cc_final: 0.8372 (mm-30) REVERT: B 1126 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9471 (mt) REVERT: C 10 MET cc_start: 0.7565 (mmm) cc_final: 0.7337 (mmm) REVERT: C 81 LEU cc_start: 0.9472 (tp) cc_final: 0.9207 (mp) REVERT: C 87 MET cc_start: 0.8495 (mmm) cc_final: 0.7904 (mmm) REVERT: C 185 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7292 (t80) REVERT: C 279 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8260 (mtp-110) REVERT: C 330 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.8884 (ttm) REVERT: G 37 LYS cc_start: 0.8084 (mmmm) cc_final: 0.7639 (mmmm) REVERT: G 190 ILE cc_start: 0.7468 (mp) cc_final: 0.7057 (mt) REVERT: K 66 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8172 (mt-10) REVERT: K 70 TYR cc_start: 0.8897 (p90) cc_final: 0.8618 (p90) REVERT: K 101 ASN cc_start: 0.9211 (OUTLIER) cc_final: 0.9002 (m-40) REVERT: L 44 MET cc_start: 0.7950 (mtp) cc_final: 0.7672 (mtp) REVERT: L 48 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8266 (ttm-80) REVERT: P 232 MET cc_start: 0.6023 (mmp) cc_final: 0.5218 (mmp) REVERT: E 23 ASP cc_start: 0.8594 (m-30) cc_final: 0.8187 (m-30) REVERT: E 110 MET cc_start: 0.8173 (mtp) cc_final: 0.7261 (ttm) REVERT: E 129 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: F 80 MET cc_start: 0.8646 (mmp) cc_final: 0.8409 (mmp) REVERT: F 83 LEU cc_start: 0.9354 (pt) cc_final: 0.8978 (pp) REVERT: F 96 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8224 (mm-30) REVERT: H 24 ARG cc_start: 0.7982 (mtm-85) cc_final: 0.7601 (mtm180) REVERT: H 37 MET cc_start: 0.8501 (mmm) cc_final: 0.8154 (mmm) REVERT: H 136 GLU cc_start: 0.6834 (mp0) cc_final: 0.6485 (mp0) REVERT: J 17 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8146 (mmtm) REVERT: O 118 MET cc_start: 0.7311 (tmm) cc_final: 0.7033 (tmm) REVERT: O 404 MET cc_start: 0.8054 (mmm) cc_final: 0.7687 (mmm) REVERT: O 423 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7781 (pp) REVERT: O 448 GLU cc_start: 0.9483 (tp30) cc_final: 0.9060 (tp30) REVERT: O 513 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7194 (mt-10) REVERT: O 532 LYS cc_start: 0.7429 (mmmt) cc_final: 0.7147 (mmtt) REVERT: Q 54 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8202 (tm-30) REVERT: Q 111 MET cc_start: 0.7447 (mmm) cc_final: 0.6700 (tmm) REVERT: D 26 GLN cc_start: 0.9598 (mm-40) cc_final: 0.9087 (pp30) REVERT: D 42 LEU cc_start: 0.9304 (tm) cc_final: 0.9035 (pt) REVERT: M 17 LEU cc_start: 0.5047 (pt) cc_final: 0.4369 (tt) REVERT: M 45 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9242 (mt) REVERT: M 54 GLN cc_start: 0.8613 (tp40) cc_final: 0.8089 (tp-100) REVERT: M 114 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: M 143 ASP cc_start: 0.9020 (t0) cc_final: 0.8759 (m-30) REVERT: M 149 HIS cc_start: 0.8816 (m-70) cc_final: 0.8409 (m90) REVERT: M 202 GLU cc_start: 0.8920 (pt0) cc_final: 0.8534 (pt0) REVERT: N 339 LEU cc_start: 0.8926 (mm) cc_final: 0.8640 (tt) REVERT: N 356 PHE cc_start: 0.7814 (m-80) cc_final: 0.7401 (m-10) REVERT: N 363 VAL cc_start: 0.8335 (t) cc_final: 0.7767 (t) outliers start: 207 outliers final: 105 residues processed: 705 average time/residue: 0.2329 time to fit residues: 269.5617 Evaluate side-chains 581 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 459 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 257 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 308 GLU 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 505 MET Chi-restraints excluded: chain A residue 568 ILE 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 818 LEU Chi-restraints excluded: chain A residue 878 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 1160 VAL Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1233 ARG Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 245 VAL 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 583 VAL 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 635 VAL Chi-restraints excluded: chain B residue 641 CYS 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 110 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 208 ILE 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 22 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 101 ASN 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 L residue 48 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain P residue 201 ASN Chi-restraints excluded: chain P residue 203 MET 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 E residue 106 VAL Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain O residue 365 ILE 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 445 ASN Chi-restraints excluded: chain O residue 497 GLN Chi-restraints excluded: chain O residue 530 THR Chi-restraints excluded: chain Q residue 81 ARG 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 64 GLU 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 15 VAL 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 365 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 269 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 212 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 298 optimal weight: 7.9990 chunk 379 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 433 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 ASN B 642 ASN B 679 GLN ** B 692 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 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 HIS C 172 HIS C 181 GLN G 23 ASN P 297 HIS P 306 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN O 402 ASN O 407 GLN O 415 HIS ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3763 r_free = 0.3763 target = 0.078741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.064481 restraints weight = 187976.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.066232 restraints weight = 105398.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.067438 restraints weight = 69320.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.068283 restraints weight = 50913.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068874 restraints weight = 40321.522| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 37637 Z= 0.184 Angle : 0.857 58.054 50977 Z= 0.398 Chirality : 0.048 0.313 5761 Planarity : 0.005 0.090 6377 Dihedral : 11.390 176.999 5426 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.43 % Favored : 91.37 % Rotamer: Outliers : 4.18 % Allowed : 22.56 % Favored : 73.26 % 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: -2.62 (0.12), residues: 4437 helix: -0.82 (0.12), residues: 1584 sheet: -2.34 (0.21), residues: 520 loop : -2.28 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG P 284 TYR 0.041 0.002 TYR A1186 PHE 0.030 0.002 PHE M 28 TRP 0.019 0.002 TRP G 201 HIS 0.019 0.001 HIS D 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (37617) covalent geometry : angle 0.78365 / 0.40 (50956) hydrogen bonds : bond 0.04370 / 2.86 ( 1155) hydrogen bonds : angle 5.45329 / 3.74 ( 3213) metal coordination : bond 0.01253 / 0.66 ( 20) metal coordination : angle 17.07478 / 9.65 ( 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 689 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 523 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8832 (OUTLIER) cc_final: 0.8350 (pm20) REVERT: A 60 MET cc_start: 0.9272 (mmm) cc_final: 0.9027 (mtp) REVERT: A 240 MET cc_start: 0.8722 (mtp) cc_final: 0.8507 (mtm) REVERT: A 281 MET cc_start: 0.9034 (tpp) cc_final: 0.8679 (tpp) REVERT: A 308 GLU cc_start: 0.8713 (pt0) cc_final: 0.8472 (pt0) REVERT: A 406 LYS cc_start: 0.9467 (tppt) cc_final: 0.8797 (mmtm) REVERT: A 443 GLU cc_start: 0.8259 (pt0) cc_final: 0.8038 (pp20) REVERT: A 640 ILE cc_start: 0.9460 (mt) cc_final: 0.9238 (mp) REVERT: A 654 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9091 (p) REVERT: A 673 GLN cc_start: 0.8538 (pt0) cc_final: 0.8120 (pt0) REVERT: A 776 SER cc_start: 0.8689 (m) cc_final: 0.8334 (p) REVERT: A 815 ASN cc_start: 0.8671 (m-40) cc_final: 0.8435 (m-40) REVERT: A 915 LYS cc_start: 0.7529 (pttp) cc_final: 0.7221 (tptp) REVERT: A 1012 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8785 (tm-30) REVERT: A 1226 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8731 (mt) REVERT: A 1275 MET cc_start: 0.8945 (ttt) cc_final: 0.8695 (ttt) REVERT: B 107 MET cc_start: 0.8687 (mtm) cc_final: 0.8432 (mtp) REVERT: B 233 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8227 (t0) REVERT: B 243 MET cc_start: 0.8239 (ttm) cc_final: 0.8028 (ttm) REVERT: B 320 HIS cc_start: 0.6702 (m170) cc_final: 0.6233 (m170) REVERT: B 431 MET cc_start: 0.8457 (ppp) cc_final: 0.7952 (ppp) REVERT: B 451 MET cc_start: 0.8953 (ttm) cc_final: 0.8677 (ttm) REVERT: B 525 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7767 (pt) REVERT: B 530 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7145 (tm-30) REVERT: B 580 ASP cc_start: 0.8500 (t70) cc_final: 0.8202 (t0) REVERT: B 697 ILE cc_start: 0.9317 (tp) cc_final: 0.9077 (mp) REVERT: C 81 LEU cc_start: 0.9543 (tp) cc_final: 0.9254 (mp) REVERT: C 87 MET cc_start: 0.8572 (mmm) cc_final: 0.8195 (mmm) REVERT: C 185 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7353 (t80) REVERT: C 235 LEU cc_start: 0.9303 (mt) cc_final: 0.8921 (mt) REVERT: C 279 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8346 (mtp-110) REVERT: C 330 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.8659 (ttm) REVERT: G 37 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7742 (mmmm) REVERT: G 56 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: G 190 ILE cc_start: 0.7140 (mp) cc_final: 0.6788 (mp) REVERT: I 12 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7141 (pp) REVERT: K 48 ASP cc_start: 0.8983 (p0) cc_final: 0.8737 (p0) REVERT: K 66 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8157 (mt-10) REVERT: K 70 TYR cc_start: 0.8889 (p90) cc_final: 0.8625 (p90) REVERT: L 44 MET cc_start: 0.8073 (mtp) cc_final: 0.7448 (mmm) REVERT: L 48 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8231 (ttm-80) REVERT: E 110 MET cc_start: 0.8228 (mtp) cc_final: 0.7355 (ttm) REVERT: F 96 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8730 (mm-30) REVERT: F 101 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8343 (mmtt) REVERT: H 24 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7773 (mtm180) REVERT: J 17 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8253 (mmtp) REVERT: J 31 GLU cc_start: 0.9106 (mp0) cc_final: 0.8823 (mp0) REVERT: O 404 MET cc_start: 0.8270 (mmm) cc_final: 0.7850 (mmm) REVERT: O 423 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7637 (pp) REVERT: O 448 GLU cc_start: 0.9491 (tp30) cc_final: 0.9066 (tp30) REVERT: O 513 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7221 (mt-10) REVERT: Q 54 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8181 (tm-30) REVERT: Q 57 MET cc_start: 0.9027 (mpp) cc_final: 0.8796 (mpp) REVERT: Q 111 MET cc_start: 0.7336 (mmm) cc_final: 0.6783 (tmm) REVERT: D 5 ASP cc_start: 0.9070 (t0) cc_final: 0.8832 (t0) REVERT: D 22 ASP cc_start: 0.9152 (m-30) cc_final: 0.8904 (m-30) REVERT: D 26 GLN cc_start: 0.9583 (mm-40) cc_final: 0.9077 (pp30) REVERT: D 42 LEU cc_start: 0.9259 (tm) cc_final: 0.8975 (pt) REVERT: M 17 LEU cc_start: 0.5255 (pt) cc_final: 0.4604 (tt) REVERT: M 45 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9272 (pp) REVERT: M 114 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.6899 (m-80) REVERT: M 143 ASP cc_start: 0.8937 (t0) cc_final: 0.8720 (m-30) REVERT: M 149 HIS cc_start: 0.8837 (m-70) cc_final: 0.8393 (m90) REVERT: M 202 GLU cc_start: 0.8978 (pt0) cc_final: 0.8560 (pt0) REVERT: N 339 LEU cc_start: 0.8954 (mm) cc_final: 0.8705 (tt) REVERT: N 356 PHE cc_start: 0.7799 (m-80) cc_final: 0.7235 (m-80) REVERT: N 363 VAL cc_start: 0.8420 (t) cc_final: 0.7977 (t) outliers start: 166 outliers final: 88 residues processed: 644 average time/residue: 0.2250 time to fit residues: 241.0099 Evaluate side-chains 582 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 479 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 165 THR Chi-restraints excluded: chain A residue 382 VAL 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 560 ASP Chi-restraints excluded: chain A residue 568 ILE 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 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 1226 LEU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1317 MET 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 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 545 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 991 SER Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 170 THR 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 7 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 56 ASP Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 48 ARG 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 257 GLU 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 290 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 122 LEU 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 365 ILE Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain O residue 423 LEU Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 531 MET Chi-restraints excluded: chain Q residue 26 LYS 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 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 114 TYR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 205 TRP 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 365 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 376 optimal weight: 5.9990 chunk 436 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 388 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 350 optimal weight: 0.9980 chunk 445 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 HIS ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 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 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN ** C 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN O 60 HIS ** O 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 415 HIS ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.079041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.064792 restraints weight = 186972.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.066557 restraints weight = 104097.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.067766 restraints weight = 68129.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.068620 restraints weight = 49852.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.069213 restraints weight = 39378.516| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 37637 Z= 0.144 Angle : 0.815 51.657 50977 Z= 0.377 Chirality : 0.046 0.235 5761 Planarity : 0.005 0.096 6377 Dihedral : 11.108 176.054 5419 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.88 % Favored : 90.92 % Rotamer: Outliers : 3.90 % Allowed : 22.91 % Favored : 73.19 % 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: -2.35 (0.12), residues: 4437 helix: -0.49 (0.13), residues: 1593 sheet: -2.27 (0.21), residues: 533 loop : -2.19 (0.12), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 81 TYR 0.022 0.001 TYR A1186 PHE 0.029 0.002 PHE I 4 TRP 0.016 0.002 TRP C 40 HIS 0.016 0.001 HIS O 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (37617) covalent geometry : angle 0.75442 / 0.38 (50956) hydrogen bonds : bond 0.04009 / 2.63 ( 1155) hydrogen bonds : angle 5.22251 / 3.62 ( 3213) metal coordination : bond 0.00925 / 0.50 ( 20) metal coordination : angle 15.25454 / 8.76 ( 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 664 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 509 time to evaluate : 1.758 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: A 30 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: A 281 MET cc_start: 0.9044 (tpp) cc_final: 0.8675 (tpp) REVERT: A 406 LYS cc_start: 0.9449 (tppt) cc_final: 0.8776 (mmtm) REVERT: A 440 MET cc_start: 0.8604 (mmm) cc_final: 0.7964 (mmm) REVERT: A 654 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.8956 (p) REVERT: A 673 GLN cc_start: 0.8573 (pt0) cc_final: 0.8093 (pt0) REVERT: A 776 SER cc_start: 0.8664 (m) cc_final: 0.8298 (p) REVERT: A 815 ASN cc_start: 0.8690 (m-40) cc_final: 0.8452 (m-40) REVERT: A 875 LEU cc_start: 0.9543 (mt) cc_final: 0.9331 (mp) REVERT: A 1012 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8788 (tm-30) REVERT: A 1275 MET cc_start: 0.8933 (ttt) cc_final: 0.8611 (ttt) REVERT: A 1280 MET cc_start: 0.8742 (mmt) cc_final: 0.8534 (mmm) REVERT: B 186 LYS cc_start: 0.8941 (tmtt) cc_final: 0.8699 (tptp) REVERT: B 233 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8300 (t0) REVERT: B 243 MET cc_start: 0.8262 (ttm) cc_final: 0.8049 (ttm) REVERT: B 272 CYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8027 (m) REVERT: B 341 ARG cc_start: 0.8682 (mmt90) cc_final: 0.8294 (mmt-90) REVERT: B 431 MET cc_start: 0.8464 (ppp) cc_final: 0.7978 (ppp) REVERT: B 451 MET cc_start: 0.8946 (ttm) cc_final: 0.8581 (ttm) REVERT: B 506 MET cc_start: 0.7882 (mpp) cc_final: 0.7427 (pmm) REVERT: B 525 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8220 (pt) REVERT: B 530 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7130 (tm-30) REVERT: B 580 ASP cc_start: 0.8514 (t70) cc_final: 0.8162 (t0) REVERT: B 600 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7211 (ptmm) REVERT: B 697 ILE cc_start: 0.9350 (tp) cc_final: 0.9111 (mp) REVERT: B 879 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7062 (t80) REVERT: C 87 MET cc_start: 0.8584 (mmm) cc_final: 0.8284 (mmm) REVERT: C 185 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7343 (t80) REVERT: C 235 LEU cc_start: 0.9310 (mt) cc_final: 0.8919 (mt) REVERT: C 279 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8302 (mtp-110) REVERT: C 330 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.8659 (ttm) REVERT: G 37 LYS cc_start: 0.7901 (mmmm) cc_final: 0.7286 (mmmm) REVERT: G 129 TRP cc_start: 0.7805 (m-10) cc_final: 0.7553 (m100) REVERT: K 48 ASP cc_start: 0.9068 (p0) cc_final: 0.8858 (p0) REVERT: K 66 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8154 (mt-10) REVERT: K 70 TYR cc_start: 0.8934 (p90) cc_final: 0.8671 (p90) REVERT: K 79 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9094 (ttpp) REVERT: L 48 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8188 (ttm-80) REVERT: P 232 MET cc_start: 0.5745 (mmp) cc_final: 0.5448 (mmp) REVERT: E 110 MET cc_start: 0.8192 (mtp) cc_final: 0.7307 (ttm) REVERT: F 80 MET cc_start: 0.8707 (mmp) cc_final: 0.8328 (mmp) REVERT: H 8 ASP cc_start: 0.6486 (OUTLIER) cc_final: 0.6180 (m-30) REVERT: H 18 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8417 (mp0) REVERT: H 24 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7740 (mtm180) REVERT: H 37 MET cc_start: 0.8515 (mmm) cc_final: 0.8112 (mmm) REVERT: H 136 GLU cc_start: 0.7002 (mp0) cc_final: 0.6482 (mp0) REVERT: J 17 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8419 (mmtm) REVERT: J 31 GLU cc_start: 0.9073 (mp0) cc_final: 0.8748 (mp0) REVERT: O 404 MET cc_start: 0.8357 (mmm) cc_final: 0.7954 (mmm) REVERT: O 409 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7822 (mt) REVERT: O 423 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7585 (pp) REVERT: O 427 ASN cc_start: 0.8236 (t0) cc_final: 0.7504 (t0) REVERT: O 448 GLU cc_start: 0.9475 (tp30) cc_final: 0.9074 (tp30) REVERT: O 513 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7181 (mt-10) REVERT: Q 23 LYS cc_start: 0.8644 (tptt) cc_final: 0.8441 (tptt) REVERT: Q 54 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8246 (tm-30) REVERT: Q 57 MET cc_start: 0.8961 (mpp) cc_final: 0.8725 (mpp) REVERT: Q 111 MET cc_start: 0.7246 (mmm) cc_final: 0.6640 (tmm) REVERT: D 5 ASP cc_start: 0.9050 (t0) cc_final: 0.8759 (t0) REVERT: D 22 ASP cc_start: 0.9147 (m-30) cc_final: 0.8883 (m-30) REVERT: D 26 GLN cc_start: 0.9598 (mm-40) cc_final: 0.9109 (pp30) REVERT: D 42 LEU cc_start: 0.9234 (tm) cc_final: 0.8997 (pt) REVERT: M 17 LEU cc_start: 0.5081 (pt) cc_final: 0.4542 (tt) REVERT: M 45 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9245 (pp) REVERT: M 114 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6976 (m-80) REVERT: M 149 HIS cc_start: 0.8822 (m-70) cc_final: 0.8358 (m90) REVERT: M 202 GLU cc_start: 0.8968 (pt0) cc_final: 0.8546 (pt0) REVERT: N 336 ARG cc_start: 0.8827 (ttp80) cc_final: 0.8259 (ttp80) REVERT: N 356 PHE cc_start: 0.7737 (m-80) cc_final: 0.7205 (m-80) REVERT: N 380 LYS cc_start: 0.7139 (mptt) cc_final: 0.6543 (mptt) outliers start: 155 outliers final: 88 residues processed: 624 average time/residue: 0.2238 time to fit residues: 232.6193 Evaluate side-chains 572 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 466 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 THR 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 530 VAL 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 805 SER Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 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 1251 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain B residue 27 TRP 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 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 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 857 THR Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 929 MET 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 1053 ASP Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 166 HIS 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 315 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 22 LEU 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 56 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 48 ARG 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 257 GLU 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 283 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 122 LEU 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 57 LEU Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 409 ILE Chi-restraints excluded: chain O residue 423 LEU Chi-restraints excluded: chain Q residue 26 LYS 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 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 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 330 LEU Chi-restraints excluded: chain N residue 365 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 50 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 420 optimal weight: 0.5980 chunk 307 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 274 optimal weight: 6.9990 chunk 347 optimal weight: 9.9990 chunk 289 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A1190 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN E 71 GLN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.077663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.063553 restraints weight = 188641.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.065266 restraints weight = 105081.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066444 restraints weight = 69084.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.067264 restraints weight = 50804.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.067848 restraints weight = 40346.641| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.6605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37637 Z= 0.149 Angle : 0.788 47.563 50977 Z= 0.367 Chirality : 0.046 0.347 5761 Planarity : 0.005 0.102 6377 Dihedral : 10.921 175.237 5417 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.68 % Favored : 91.10 % Rotamer: Outliers : 4.02 % Allowed : 22.91 % Favored : 73.06 % 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: -2.08 (0.12), residues: 4437 helix: -0.17 (0.13), residues: 1574 sheet: -2.14 (0.21), residues: 533 loop : -2.09 (0.12), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 533 TYR 0.027 0.001 TYR B 445 PHE 0.025 0.001 PHE B 559 TRP 0.020 0.002 TRP M 205 HIS 0.007 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (37617) covalent geometry : angle 0.73681 / 0.37 (50956) hydrogen bonds : bond 0.03814 / 2.48 ( 1155) hydrogen bonds : angle 5.10688 / 3.54 ( 3213) metal coordination : bond 0.00939 / 0.51 ( 20) metal coordination : angle 13.84830 / 8.09 ( 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 658 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 498 time to evaluate : 1.363 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: A 30 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8423 (pm20) REVERT: A 281 MET cc_start: 0.9048 (tpp) cc_final: 0.8681 (tpp) REVERT: A 406 LYS cc_start: 0.9450 (tppt) cc_final: 0.8776 (mmtm) REVERT: A 604 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9091 (tt) REVERT: A 673 GLN cc_start: 0.8581 (pt0) cc_final: 0.8095 (pt0) REVERT: A 776 SER cc_start: 0.8849 (m) cc_final: 0.8528 (p) REVERT: A 815 ASN cc_start: 0.8720 (m-40) cc_final: 0.8459 (m-40) REVERT: A 908 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8132 (m-30) REVERT: A 1012 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8809 (tm-30) REVERT: A 1106 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8255 (pp20) REVERT: A 1275 MET cc_start: 0.8948 (ttt) cc_final: 0.8630 (ttt) REVERT: A 1280 MET cc_start: 0.8758 (mmt) cc_final: 0.8555 (mmm) REVERT: A 1299 GLU cc_start: 0.8601 (pm20) cc_final: 0.8137 (pm20) REVERT: B 233 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8307 (t0) REVERT: B 243 MET cc_start: 0.8285 (ttm) cc_final: 0.8075 (ttm) REVERT: B 272 CYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8054 (m) REVERT: B 341 ARG cc_start: 0.8687 (mmt90) cc_final: 0.8290 (mmt-90) REVERT: B 431 MET cc_start: 0.8417 (ppp) cc_final: 0.8021 (ppp) REVERT: B 451 MET cc_start: 0.8986 (ttm) cc_final: 0.8627 (ttm) REVERT: B 506 MET cc_start: 0.7970 (mpp) cc_final: 0.7590 (pmm) REVERT: B 525 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8277 (pt) REVERT: B 527 CYS cc_start: 0.6768 (m) cc_final: 0.4996 (m) REVERT: B 530 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7213 (tm-30) REVERT: B 580 ASP cc_start: 0.8590 (t70) cc_final: 0.8227 (t0) REVERT: B 600 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7250 (ptmm) REVERT: B 697 ILE cc_start: 0.9382 (tp) cc_final: 0.9160 (mp) REVERT: B 879 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7062 (t80) REVERT: B 1009 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: C 87 MET cc_start: 0.8669 (mmm) cc_final: 0.8404 (mmm) REVERT: C 185 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7315 (t80) REVERT: C 235 LEU cc_start: 0.9337 (mt) cc_final: 0.8930 (mt) REVERT: C 279 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8387 (mtp-110) REVERT: C 330 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.8645 (ttm) REVERT: G 28 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8121 (mt-10) REVERT: G 100 SER cc_start: 0.7332 (OUTLIER) cc_final: 0.6928 (t) REVERT: I 32 HIS cc_start: 0.6819 (m90) cc_final: 0.6556 (m90) REVERT: K 70 TYR cc_start: 0.8902 (p90) cc_final: 0.8649 (p90) REVERT: K 79 LYS cc_start: 0.9532 (OUTLIER) cc_final: 0.9065 (ttpp) REVERT: L 48 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8227 (ttm-80) REVERT: P 232 MET cc_start: 0.5680 (mmp) cc_final: 0.5396 (mmp) REVERT: F 80 MET cc_start: 0.8766 (mmp) cc_final: 0.8498 (mmp) REVERT: F 86 GLU cc_start: 0.8771 (mp0) cc_final: 0.8429 (mp0) REVERT: F 96 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8585 (mm-30) REVERT: H 8 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6218 (m-30) REVERT: H 18 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8389 (mp0) REVERT: H 24 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7885 (mtm180) REVERT: H 33 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8148 (mm-30) REVERT: H 136 GLU cc_start: 0.6952 (mp0) cc_final: 0.6252 (mp0) REVERT: J 17 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8589 (mttp) REVERT: J 31 GLU cc_start: 0.9104 (mp0) cc_final: 0.8771 (mp0) REVERT: O 404 MET cc_start: 0.8493 (mmm) cc_final: 0.8051 (mmm) REVERT: O 409 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7824 (mt) REVERT: O 427 ASN cc_start: 0.8358 (t0) cc_final: 0.7624 (t0) REVERT: O 448 GLU cc_start: 0.9451 (tp30) cc_final: 0.9080 (tp30) REVERT: O 513 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7239 (mt-10) REVERT: Q 54 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8065 (tm-30) REVERT: Q 110 MET cc_start: 0.6831 (tmm) cc_final: 0.6513 (tmm) REVERT: Q 111 MET cc_start: 0.7390 (mmm) cc_final: 0.6744 (tmm) REVERT: D 5 ASP cc_start: 0.8988 (t0) cc_final: 0.8754 (t0) REVERT: D 22 ASP cc_start: 0.9173 (m-30) cc_final: 0.8895 (m-30) REVERT: D 26 GLN cc_start: 0.9593 (mm-40) cc_final: 0.9121 (pp30) REVERT: M 17 LEU cc_start: 0.5148 (pt) cc_final: 0.4615 (tt) REVERT: M 45 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9289 (pp) REVERT: M 114 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.6734 (m-10) REVERT: M 143 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8515 (m-30) REVERT: M 149 HIS cc_start: 0.8844 (m-70) cc_final: 0.8467 (m90) REVERT: N 336 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8192 (ttp80) REVERT: N 356 PHE cc_start: 0.7780 (m-80) cc_final: 0.7260 (m-80) REVERT: N 380 LYS cc_start: 0.7255 (mptt) cc_final: 0.6673 (mptt) REVERT: N 382 LYS cc_start: 0.8591 (tttm) cc_final: 0.8367 (tppp) outliers start: 160 outliers final: 98 residues processed: 614 average time/residue: 0.2233 time to fit residues: 228.5592 Evaluate side-chains 582 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 462 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 165 THR Chi-restraints excluded: chain A residue 257 VAL 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 560 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 884 SER 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 1251 THR Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain B residue 27 TRP 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 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 592 LEU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 787 PHE Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 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 1009 TYR 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 315 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 22 LEU 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 100 SER Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 48 ARG 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 257 GLU 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 P residue 283 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 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 E residue 106 VAL 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 122 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 109 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 409 ILE 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 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 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 330 LEU Chi-restraints excluded: chain N residue 365 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 245 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.0870 chunk 77 optimal weight: 10.0000 chunk 357 optimal weight: 0.1980 chunk 228 optimal weight: 8.9990 chunk 168 optimal weight: 0.4980 chunk 355 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 408 optimal weight: 2.9990 chunk 393 optimal weight: 7.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 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 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 HIS H 44 ASN ** O 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 146 ASN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 GLN D 85 GLN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.077815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.063728 restraints weight = 188115.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065447 restraints weight = 104545.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066632 restraints weight = 68470.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.067467 restraints weight = 50146.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.068042 restraints weight = 39721.894| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.6840 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= 0.133 Angle : 0.775 41.827 50977 Z= 0.363 Chirality : 0.045 0.384 5761 Planarity : 0.005 0.101 6377 Dihedral : 10.807 174.417 5416 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.70 % Favored : 91.10 % Rotamer: Outliers : 3.77 % Allowed : 23.24 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.12), residues: 4437 helix: -0.02 (0.13), residues: 1579 sheet: -1.96 (0.22), residues: 522 loop : -2.02 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 533 TYR 0.024 0.001 TYR J 21 PHE 0.019 0.001 PHE B 662 TRP 0.033 0.002 TRP B 804 HIS 0.008 0.001 HIS D 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (37617) covalent geometry : angle 0.73350 / 0.36 (50956) hydrogen bonds : bond 0.03618 / 2.37 ( 1155) hydrogen bonds : angle 4.99247 / 3.46 ( 3213) metal coordination : bond 0.00711 / 0.41 ( 20) metal coordination : angle 12.38456 / 7.34 ( 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 639 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 489 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: A 52 LEU cc_start: 0.7560 (tp) cc_final: 0.7359 (pp) REVERT: A 53 TYR cc_start: 0.4679 (OUTLIER) cc_final: 0.3556 (t80) REVERT: A 97 TYR cc_start: 0.8178 (m-80) cc_final: 0.7740 (m-80) REVERT: A 281 MET cc_start: 0.9035 (tpp) cc_final: 0.8666 (tpp) REVERT: A 351 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7140 (mpt90) REVERT: A 406 LYS cc_start: 0.9411 (tppt) cc_final: 0.8748 (mmtm) REVERT: A 673 GLN cc_start: 0.8578 (pt0) cc_final: 0.8242 (mt0) REVERT: A 776 SER cc_start: 0.8867 (m) cc_final: 0.8562 (p) REVERT: A 815 ASN cc_start: 0.8741 (m-40) cc_final: 0.8465 (m-40) REVERT: A 875 LEU cc_start: 0.9560 (mt) cc_final: 0.9314 (mp) REVERT: A 908 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: A 1012 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8808 (tm-30) REVERT: A 1106 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8228 (pp20) REVERT: A 1275 MET cc_start: 0.8937 (ttt) cc_final: 0.8600 (ttm) REVERT: A 1280 MET cc_start: 0.8788 (mmt) cc_final: 0.8570 (mmm) REVERT: A 1299 GLU cc_start: 0.8652 (pm20) cc_final: 0.8177 (pm20) REVERT: B 233 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8350 (t0) REVERT: B 372 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8200 (pp) REVERT: B 431 MET cc_start: 0.8288 (ppp) cc_final: 0.7924 (ppp) REVERT: B 451 MET cc_start: 0.8976 (ttm) cc_final: 0.8612 (ttm) REVERT: B 525 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8369 (pt) REVERT: B 530 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7248 (tm-30) REVERT: B 580 ASP cc_start: 0.8599 (t70) cc_final: 0.8293 (t0) REVERT: B 600 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7367 (ptmm) REVERT: B 634 ASP cc_start: 0.8617 (p0) cc_final: 0.8248 (p0) REVERT: B 697 ILE cc_start: 0.9375 (tp) cc_final: 0.9166 (mp) REVERT: B 879 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.6989 (t80) REVERT: C 56 MET cc_start: 0.8464 (tmm) cc_final: 0.8065 (tmm) REVERT: C 74 ASN cc_start: 0.8928 (t0) cc_final: 0.8419 (t0) REVERT: C 185 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7320 (t80) REVERT: C 235 LEU cc_start: 0.9332 (mt) cc_final: 0.8914 (mt) REVERT: C 279 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8372 (mtp-110) REVERT: C 330 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8775 (ttm) REVERT: G 28 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8108 (mt-10) REVERT: G 100 SER cc_start: 0.7502 (OUTLIER) cc_final: 0.7099 (t) REVERT: I 4 PHE cc_start: 0.4459 (m-80) cc_final: 0.4154 (m-80) REVERT: I 32 HIS cc_start: 0.6809 (m90) cc_final: 0.6441 (m-70) REVERT: K 70 TYR cc_start: 0.8919 (p90) cc_final: 0.8678 (p90) REVERT: K 79 LYS cc_start: 0.9533 (OUTLIER) cc_final: 0.9114 (ttpp) REVERT: L 44 MET cc_start: 0.7968 (mtp) cc_final: 0.7634 (mmm) REVERT: L 48 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8170 (ttm-80) REVERT: L 51 ARG cc_start: 0.8932 (mmm-85) cc_final: 0.8491 (mtp85) REVERT: P 232 MET cc_start: 0.5968 (mmp) cc_final: 0.5719 (mmp) REVERT: H 8 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6310 (m-30) REVERT: H 18 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8376 (mp0) REVERT: H 24 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7898 (mtm180) REVERT: H 33 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8283 (mm-30) REVERT: H 37 MET cc_start: 0.8524 (mmm) cc_final: 0.7984 (mmm) REVERT: H 136 GLU cc_start: 0.7002 (mp0) cc_final: 0.6337 (mp0) REVERT: J 17 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8638 (mttp) REVERT: J 31 GLU cc_start: 0.9081 (mp0) cc_final: 0.8720 (mp0) REVERT: O 404 MET cc_start: 0.8484 (mmm) cc_final: 0.8038 (mmm) REVERT: O 409 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7756 (mt) REVERT: O 427 ASN cc_start: 0.8318 (t0) cc_final: 0.7585 (t0) REVERT: O 448 GLU cc_start: 0.9450 (tp30) cc_final: 0.9084 (tp30) REVERT: O 513 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7173 (mt-10) REVERT: Q 54 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8040 (tm-30) REVERT: Q 111 MET cc_start: 0.7294 (mmm) cc_final: 0.6722 (tmm) REVERT: D 5 ASP cc_start: 0.8963 (t0) cc_final: 0.8702 (t0) REVERT: D 22 ASP cc_start: 0.9158 (m-30) cc_final: 0.8871 (m-30) REVERT: D 26 GLN cc_start: 0.9612 (mm-40) cc_final: 0.9158 (pp30) REVERT: D 100 MET cc_start: 0.6733 (mmt) cc_final: 0.6298 (mmp) REVERT: M 17 LEU cc_start: 0.5220 (pt) cc_final: 0.4691 (tt) REVERT: M 45 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9320 (pp) REVERT: M 114 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7028 (m-10) REVERT: M 149 HIS cc_start: 0.8863 (m-70) cc_final: 0.8517 (m-70) REVERT: M 202 GLU cc_start: 0.9003 (pt0) cc_final: 0.8205 (mp0) REVERT: N 336 ARG cc_start: 0.8943 (ttp80) cc_final: 0.8348 (ttp80) REVERT: N 356 PHE cc_start: 0.7766 (m-80) cc_final: 0.7229 (m-80) REVERT: N 382 LYS cc_start: 0.8543 (tttm) cc_final: 0.8260 (tptm) outliers start: 150 outliers final: 91 residues processed: 604 average time/residue: 0.2234 time to fit residues: 224.9261 Evaluate side-chains 575 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 463 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 257 VAL Chi-restraints excluded: chain A residue 351 ARG 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 494 THR 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 805 SER Chi-restraints excluded: chain A residue 884 SER 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 1251 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain B residue 27 TRP 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 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 600 LYS Chi-restraints excluded: chain B residue 787 PHE Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 857 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 1113 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 21 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 212 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 100 SER 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 79 LYS Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 48 ARG 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 257 GLU 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 7 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 106 VAL 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 H residue 122 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 365 ILE 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 409 ILE Chi-restraints excluded: chain O residue 415 HIS Chi-restraints excluded: chain O residue 425 THR 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 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 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 330 LEU Chi-restraints excluded: chain N residue 341 LEU 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: 0.9990 chunk 92 optimal weight: 0.0170 chunk 118 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 199 optimal weight: 7.9990 chunk 377 optimal weight: 7.9990 chunk 404 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 406 optimal weight: 8.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** B 692 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 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN H 44 ASN ** O 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 497 GLN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.077141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.063114 restraints weight = 187361.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.064822 restraints weight = 103952.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.065989 restraints weight = 68187.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.066809 restraints weight = 50033.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.067329 restraints weight = 39691.467| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37637 Z= 0.135 Angle : 0.784 39.783 50977 Z= 0.365 Chirality : 0.046 0.320 5761 Planarity : 0.005 0.101 6377 Dihedral : 10.730 173.394 5416 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.59 % Favored : 91.23 % Rotamer: Outliers : 3.50 % Allowed : 23.77 % Favored : 72.74 % 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: -1.79 (0.12), residues: 4437 helix: 0.08 (0.13), residues: 1583 sheet: -1.90 (0.22), residues: 526 loop : -1.95 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG E 101 TYR 0.023 0.001 TYR B 445 PHE 0.018 0.001 PHE B 662 TRP 0.023 0.002 TRP B 804 HIS 0.005 0.001 HIS D 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (37617) covalent geometry : angle 0.74645 / 0.36 (50956) hydrogen bonds : bond 0.03539 / 2.32 ( 1155) hydrogen bonds : angle 4.92802 / 3.42 ( 3213) metal coordination : bond 0.00717 / 0.40 ( 20) metal coordination : angle 11.83184 / 7.05 ( 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 624 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 485 time to evaluate : 1.793 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: A 30 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: A 281 MET cc_start: 0.9056 (tpp) cc_final: 0.8629 (tpp) REVERT: A 307 MET cc_start: 0.8653 (mmp) cc_final: 0.7560 (tmm) REVERT: A 351 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7157 (mpt90) REVERT: A 406 LYS cc_start: 0.9415 (tppt) cc_final: 0.8761 (mmtm) REVERT: A 673 GLN cc_start: 0.8598 (pt0) cc_final: 0.8276 (mt0) REVERT: A 776 SER cc_start: 0.8754 (m) cc_final: 0.8360 (p) REVERT: A 815 ASN cc_start: 0.8722 (m-40) cc_final: 0.8421 (m-40) REVERT: A 908 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: A 1012 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8864 (tm-30) REVERT: A 1061 MET cc_start: 0.5869 (pmm) cc_final: 0.5585 (pmm) REVERT: A 1106 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8244 (pp20) REVERT: A 1236 MET cc_start: 0.8475 (ptm) cc_final: 0.8225 (ptm) REVERT: A 1275 MET cc_start: 0.8955 (ttt) cc_final: 0.8611 (ttm) REVERT: A 1280 MET cc_start: 0.8777 (mmt) cc_final: 0.8557 (mmm) REVERT: A 1299 GLU cc_start: 0.8649 (pm20) cc_final: 0.8328 (pm20) REVERT: B 233 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8316 (t0) REVERT: B 431 MET cc_start: 0.8304 (ppp) cc_final: 0.7946 (ppp) REVERT: B 451 MET cc_start: 0.8986 (ttm) cc_final: 0.8630 (ttm) REVERT: B 525 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8462 (pt) REVERT: B 527 CYS cc_start: 0.7381 (m) cc_final: 0.6870 (m) REVERT: B 530 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7252 (tm-30) REVERT: B 580 ASP cc_start: 0.8533 (t70) cc_final: 0.8244 (t0) REVERT: B 600 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7450 (ptmm) REVERT: B 634 ASP cc_start: 0.8631 (p0) cc_final: 0.8118 (p0) REVERT: B 859 LYS cc_start: 0.8434 (mmmt) cc_final: 0.8137 (mmmt) REVERT: B 879 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7025 (t80) REVERT: B 927 ILE cc_start: 0.9414 (pt) cc_final: 0.9038 (pt) REVERT: B 1009 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: B 1053 ASP cc_start: 0.8853 (m-30) cc_final: 0.8544 (p0) REVERT: C 56 MET cc_start: 0.8573 (tmm) cc_final: 0.8137 (tmm) REVERT: C 74 ASN cc_start: 0.8922 (t0) cc_final: 0.8710 (t0) REVERT: C 185 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7327 (t80) REVERT: C 235 LEU cc_start: 0.9378 (mt) cc_final: 0.8987 (mt) REVERT: C 279 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8369 (mtp-110) REVERT: C 330 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8818 (ttm) REVERT: G 28 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8139 (mt-10) REVERT: I 4 PHE cc_start: 0.4703 (m-80) cc_final: 0.4385 (m-80) REVERT: I 32 HIS cc_start: 0.6735 (m90) cc_final: 0.6464 (m90) REVERT: K 70 TYR cc_start: 0.8983 (p90) cc_final: 0.8756 (p90) REVERT: K 79 LYS cc_start: 0.9541 (OUTLIER) cc_final: 0.9126 (ttpp) REVERT: L 44 MET cc_start: 0.8060 (mtp) cc_final: 0.7647 (tpp) REVERT: L 48 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8238 (ttm-80) REVERT: L 51 ARG cc_start: 0.8920 (mmm-85) cc_final: 0.8460 (mtp85) REVERT: P 232 MET cc_start: 0.5834 (mmp) cc_final: 0.5571 (mmp) REVERT: E 110 MET cc_start: 0.7600 (mtp) cc_final: 0.7157 (ttm) REVERT: F 57 MET cc_start: 0.9299 (tmm) cc_final: 0.9077 (tmm) REVERT: F 80 MET cc_start: 0.8814 (mmp) cc_final: 0.8460 (mmp) REVERT: F 83 LEU cc_start: 0.9383 (pt) cc_final: 0.9119 (pp) REVERT: H 8 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6382 (m-30) REVERT: H 18 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8390 (mp0) REVERT: H 24 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7851 (mtm180) REVERT: H 33 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8209 (mm-30) REVERT: H 37 MET cc_start: 0.8409 (mmm) cc_final: 0.7832 (mmm) REVERT: H 136 GLU cc_start: 0.6982 (mp0) cc_final: 0.6290 (mp0) REVERT: J 31 GLU cc_start: 0.9075 (mp0) cc_final: 0.8717 (mp0) REVERT: O 398 MET cc_start: 0.9235 (mmm) cc_final: 0.9006 (mmm) REVERT: O 404 MET cc_start: 0.8475 (mmm) cc_final: 0.8208 (mmm) REVERT: O 423 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7827 (pp) REVERT: O 427 ASN cc_start: 0.8329 (t0) cc_final: 0.7563 (t0) REVERT: O 448 GLU cc_start: 0.9486 (tp30) cc_final: 0.9127 (tp30) REVERT: O 513 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7023 (mt-10) REVERT: Q 54 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8012 (tm-30) REVERT: Q 111 MET cc_start: 0.7373 (mmm) cc_final: 0.6827 (tmm) REVERT: D 5 ASP cc_start: 0.8991 (t0) cc_final: 0.8738 (t0) REVERT: D 22 ASP cc_start: 0.9163 (m-30) cc_final: 0.8845 (m-30) REVERT: D 26 GLN cc_start: 0.9646 (mm-40) cc_final: 0.9186 (pp30) REVERT: D 100 MET cc_start: 0.6807 (mmt) cc_final: 0.6399 (mmp) REVERT: M 17 LEU cc_start: 0.5326 (pt) cc_final: 0.4820 (tt) REVERT: M 45 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9321 (pp) REVERT: M 114 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.6956 (m-10) REVERT: M 149 HIS cc_start: 0.8853 (m-70) cc_final: 0.8531 (m-70) REVERT: M 202 GLU cc_start: 0.9030 (pt0) cc_final: 0.8186 (mp0) REVERT: N 350 MET cc_start: 0.7194 (ppp) cc_final: 0.6905 (ppp) REVERT: N 356 PHE cc_start: 0.7766 (m-80) cc_final: 0.7311 (m-80) outliers start: 139 outliers final: 96 residues processed: 585 average time/residue: 0.2315 time to fit residues: 224.4028 Evaluate side-chains 567 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 452 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 129 LEU Chi-restraints excluded: chain A residue 137 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 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 771 LEU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 884 SER 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 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 1106 GLU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain B residue 27 TRP 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 344 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 600 LYS Chi-restraints excluded: chain B residue 787 PHE Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 929 MET 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 1009 TYR Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 21 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 212 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 44 LEU 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 152 VAL Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 48 ARG 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 257 GLU 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 307 CYS 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 F residue 58 THR Chi-restraints excluded: chain F residue 79 VAL 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 H residue 122 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 365 ILE 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 423 LEU Chi-restraints excluded: chain O residue 425 THR Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain Q residue 30 VAL 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 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 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 341 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 192 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 349 optimal weight: 4.9990 chunk 402 optimal weight: 2.9990 chunk 350 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN E 71 GLN O 68 HIS O 339 HIS O 457 ASN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS D 61 GLN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.073743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.059925 restraints weight = 191788.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.061564 restraints weight = 105998.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.062683 restraints weight = 69622.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.063479 restraints weight = 51188.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.064020 restraints weight = 40744.317| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.7555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37637 Z= 0.197 Angle : 0.833 44.801 50977 Z= 0.393 Chirality : 0.047 0.345 5761 Planarity : 0.005 0.098 6377 Dihedral : 10.727 173.643 5414 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.99 % Favored : 90.85 % Rotamer: Outliers : 3.52 % Allowed : 24.02 % Favored : 72.46 % 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: 0.13 (0.13), residues: 1579 sheet: -1.84 (0.22), residues: 542 loop : -1.98 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG O 295 TYR 0.024 0.002 TYR J 21 PHE 0.017 0.002 PHE B 662 TRP 0.021 0.002 TRP M 205 HIS 0.010 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (37617) covalent geometry : angle 0.79141 / 0.39 (50956) hydrogen bonds : bond 0.03815 / 2.52 ( 1155) hydrogen bonds : angle 5.01549 / 3.48 ( 3213) metal coordination : bond 0.01198 / 0.65 ( 20) metal coordination : angle 12.79884 / 7.47 ( 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 591 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 451 time to evaluate : 1.539 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 53 TYR cc_start: 0.4957 (OUTLIER) cc_final: 0.3828 (t80) REVERT: A 281 MET cc_start: 0.9048 (tpp) cc_final: 0.8666 (tpp) REVERT: A 307 MET cc_start: 0.8736 (mmp) cc_final: 0.8478 (mmp) REVERT: A 351 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7308 (mpt90) REVERT: A 406 LYS cc_start: 0.9459 (tppt) cc_final: 0.8784 (mmtm) REVERT: A 673 GLN cc_start: 0.8733 (pt0) cc_final: 0.8412 (mt0) REVERT: A 776 SER cc_start: 0.8891 (m) cc_final: 0.8575 (p) REVERT: A 815 ASN cc_start: 0.8787 (m-40) cc_final: 0.8474 (m-40) REVERT: A 871 MET cc_start: 0.8961 (tmm) cc_final: 0.8556 (tmm) REVERT: A 875 LEU cc_start: 0.9520 (mt) cc_final: 0.9316 (mp) REVERT: A 908 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7846 (m-30) REVERT: A 1012 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8840 (tm-30) REVERT: A 1061 MET cc_start: 0.6218 (pmm) cc_final: 0.5955 (pmm) REVERT: A 1106 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8366 (pp20) REVERT: A 1236 MET cc_start: 0.8474 (ptm) cc_final: 0.8151 (ptm) REVERT: A 1275 MET cc_start: 0.9013 (ttt) cc_final: 0.8741 (ttm) REVERT: A 1299 GLU cc_start: 0.8735 (pm20) cc_final: 0.8433 (pm20) REVERT: B 233 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8449 (t0) REVERT: B 243 MET cc_start: 0.8282 (ttm) cc_final: 0.7861 (ttm) REVERT: B 278 PHE cc_start: 0.8532 (m-80) cc_final: 0.8206 (m-80) REVERT: B 281 MET cc_start: 0.8337 (ptp) cc_final: 0.7725 (ptp) REVERT: B 341 ARG cc_start: 0.8851 (mmt90) cc_final: 0.8566 (mpt180) REVERT: B 431 MET cc_start: 0.8212 (ppp) cc_final: 0.7948 (ppp) REVERT: B 451 MET cc_start: 0.9024 (ttm) cc_final: 0.8655 (ttm) REVERT: B 525 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8475 (pt) REVERT: B 527 CYS cc_start: 0.7516 (m) cc_final: 0.6704 (m) REVERT: B 530 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7346 (tm-30) REVERT: B 580 ASP cc_start: 0.8526 (t70) cc_final: 0.8158 (t0) REVERT: B 600 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7641 (ptmm) REVERT: B 634 ASP cc_start: 0.8705 (p0) cc_final: 0.8301 (p0) REVERT: B 879 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7119 (t80) REVERT: B 1009 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: C 56 MET cc_start: 0.8817 (tmm) cc_final: 0.8300 (tmm) REVERT: C 185 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7375 (t80) REVERT: C 235 LEU cc_start: 0.9418 (mt) cc_final: 0.8995 (mt) REVERT: C 279 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8517 (mtp-110) REVERT: C 330 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8789 (ttm) REVERT: G 28 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8271 (mt-10) REVERT: G 37 LYS cc_start: 0.7893 (mmmm) cc_final: 0.7609 (mmmt) REVERT: I 4 PHE cc_start: 0.5207 (m-80) cc_final: 0.4908 (m-80) REVERT: K 46 GLU cc_start: 0.9169 (pm20) cc_final: 0.8811 (pm20) REVERT: K 70 TYR cc_start: 0.9062 (p90) cc_final: 0.8708 (p90) REVERT: K 79 LYS cc_start: 0.9560 (OUTLIER) cc_final: 0.8998 (ptpp) REVERT: L 48 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8272 (ttm-80) REVERT: L 51 ARG cc_start: 0.8942 (mmm-85) cc_final: 0.8443 (mtp85) REVERT: P 232 MET cc_start: 0.5899 (mmp) cc_final: 0.5629 (mmp) REVERT: E 110 MET cc_start: 0.7592 (mtp) cc_final: 0.7174 (ttm) REVERT: F 57 MET cc_start: 0.9280 (tmm) cc_final: 0.9016 (tmm) REVERT: F 80 MET cc_start: 0.8982 (mmp) cc_final: 0.8733 (mmp) REVERT: H 24 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.8001 (mtm180) REVERT: H 33 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8204 (mm-30) REVERT: H 37 MET cc_start: 0.8443 (mmm) cc_final: 0.7838 (mmm) REVERT: H 136 GLU cc_start: 0.7057 (mp0) cc_final: 0.6497 (mp0) REVERT: J 31 GLU cc_start: 0.9105 (mp0) cc_final: 0.8736 (mp0) REVERT: O 271 LEU cc_start: 0.8582 (mt) cc_final: 0.8185 (pp) REVERT: O 404 MET cc_start: 0.8527 (mmm) cc_final: 0.8266 (mmm) REVERT: O 427 ASN cc_start: 0.8383 (t0) cc_final: 0.7662 (t0) REVERT: Q 23 LYS cc_start: 0.8745 (tptt) cc_final: 0.8477 (tptt) REVERT: Q 54 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8351 (tm-30) REVERT: Q 61 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8519 (tppt) REVERT: Q 111 MET cc_start: 0.7506 (mmm) cc_final: 0.6769 (tmm) REVERT: D 5 ASP cc_start: 0.8988 (t0) cc_final: 0.8731 (t0) REVERT: D 26 GLN cc_start: 0.9639 (mm-40) cc_final: 0.9194 (pp30) REVERT: D 100 MET cc_start: 0.6827 (mmt) cc_final: 0.6461 (mmp) REVERT: M 17 LEU cc_start: 0.5170 (pt) cc_final: 0.4702 (tt) REVERT: M 45 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9356 (pp) REVERT: M 75 GLU cc_start: 0.8741 (tp30) cc_final: 0.8537 (tp30) REVERT: M 114 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.6750 (m-10) REVERT: M 149 HIS cc_start: 0.8925 (m-70) cc_final: 0.8526 (m-70) REVERT: N 268 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8339 (t80) REVERT: N 350 MET cc_start: 0.7278 (ppp) cc_final: 0.6822 (ppp) REVERT: N 356 PHE cc_start: 0.7677 (m-80) cc_final: 0.7197 (m-80) REVERT: N 382 LYS cc_start: 0.8406 (tppp) cc_final: 0.8073 (tppp) outliers start: 140 outliers final: 96 residues processed: 551 average time/residue: 0.2277 time to fit residues: 207.6988 Evaluate side-chains 542 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 428 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 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 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 805 SER Chi-restraints excluded: chain A residue 884 SER 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 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 1106 GLU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1256 LYS Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 91 PHE 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 344 LEU Chi-restraints excluded: chain B residue 364 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 600 LYS Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 815 CYS 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 1009 TYR Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 21 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 212 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 7 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 54 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain L residue 48 ARG 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 P residue 283 VAL Chi-restraints excluded: chain P residue 295 ASP Chi-restraints excluded: chain P residue 307 CYS 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 F residue 58 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU 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 Q residue 26 LYS Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain D residue 60 HIS 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 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 268 PHE Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 79 optimal weight: 7.9990 chunk 325 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 392 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 51 optimal weight: 0.0030 chunk 109 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A1039 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1118 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN F 72 GLN O 339 HIS Q 114 ASN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 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 = 0.3678 r_free = 0.3678 target = 0.074393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060473 restraints weight = 191360.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.062131 restraints weight = 105248.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.063273 restraints weight = 68901.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.064079 restraints weight = 50653.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.064634 restraints weight = 40263.008| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.7733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 37637 Z= 0.143 Angle : 0.831 42.469 50977 Z= 0.385 Chirality : 0.046 0.332 5761 Planarity : 0.005 0.091 6377 Dihedral : 10.700 173.196 5412 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.50 % Favored : 91.35 % Rotamer: Outliers : 2.77 % Allowed : 25.08 % Favored : 72.16 % 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: -1.71 (0.13), residues: 4437 helix: 0.21 (0.13), residues: 1583 sheet: -1.80 (0.22), residues: 534 loop : -1.98 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 101 TYR 0.033 0.002 TYR D 52 PHE 0.023 0.001 PHE K 96 TRP 0.026 0.002 TRP M 205 HIS 0.020 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (37617) covalent geometry : angle 0.79276 / 0.38 (50956) hydrogen bonds : bond 0.03640 / 2.40 ( 1155) hydrogen bonds : angle 4.91077 / 3.42 ( 3213) metal coordination : bond 0.00927 / 0.60 ( 20) metal coordination : angle 12.30389 / 7.26 ( 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 563 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 453 time to evaluate : 1.496 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: A 30 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8370 (pm20) REVERT: A 53 TYR cc_start: 0.4986 (OUTLIER) cc_final: 0.3599 (t80) REVERT: A 140 ARG cc_start: 0.8979 (ttp80) cc_final: 0.8757 (mtm110) REVERT: A 281 MET cc_start: 0.9023 (tpp) cc_final: 0.8621 (tpp) REVERT: A 307 MET cc_start: 0.8688 (mmp) cc_final: 0.8462 (mmp) REVERT: A 351 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7264 (mpt90) REVERT: A 406 LYS cc_start: 0.9402 (tppt) cc_final: 0.8750 (mmtm) REVERT: A 776 SER cc_start: 0.8723 (m) cc_final: 0.8357 (p) REVERT: A 815 ASN cc_start: 0.8749 (m-40) cc_final: 0.8520 (m-40) REVERT: A 871 MET cc_start: 0.8877 (tmm) cc_final: 0.8555 (tmm) REVERT: A 875 LEU cc_start: 0.9550 (mt) cc_final: 0.9338 (mp) REVERT: A 908 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: A 1012 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8868 (tm-30) REVERT: A 1061 MET cc_start: 0.6200 (pmm) cc_final: 0.5970 (pmm) REVERT: A 1106 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8355 (pp20) REVERT: A 1275 MET cc_start: 0.8983 (ttt) cc_final: 0.8670 (ttm) REVERT: A 1280 MET cc_start: 0.8728 (mmt) cc_final: 0.8467 (mmm) REVERT: A 1299 GLU cc_start: 0.8676 (pm20) cc_final: 0.8366 (pm20) REVERT: B 233 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8400 (t0) REVERT: B 243 MET cc_start: 0.8155 (ttm) cc_final: 0.7740 (ttm) REVERT: B 278 PHE cc_start: 0.8534 (m-10) cc_final: 0.8202 (m-80) REVERT: B 281 MET cc_start: 0.8373 (ptp) cc_final: 0.7755 (ptp) REVERT: B 431 MET cc_start: 0.8255 (ppp) cc_final: 0.7997 (ppp) REVERT: B 451 MET cc_start: 0.8976 (ttm) cc_final: 0.8700 (ttm) REVERT: B 525 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8554 (pt) REVERT: B 527 CYS cc_start: 0.7436 (m) cc_final: 0.6890 (m) REVERT: B 530 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7275 (tm-30) REVERT: B 580 ASP cc_start: 0.8526 (t70) cc_final: 0.7958 (p0) REVERT: B 600 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7577 (ptmm) REVERT: B 634 ASP cc_start: 0.8661 (p0) cc_final: 0.8378 (p0) REVERT: B 879 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7123 (t80) REVERT: B 1053 ASP cc_start: 0.8834 (m-30) cc_final: 0.8544 (p0) REVERT: C 56 MET cc_start: 0.8800 (tmm) cc_final: 0.8293 (tmm) REVERT: C 185 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7318 (t80) REVERT: C 279 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8447 (mtp-110) REVERT: C 330 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8778 (ttm) REVERT: G 28 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8357 (mt-10) REVERT: G 32 LYS cc_start: 0.9050 (mtmm) cc_final: 0.8515 (mmtt) REVERT: G 37 LYS cc_start: 0.7837 (mmmm) cc_final: 0.7594 (mmmt) REVERT: I 4 PHE cc_start: 0.5268 (m-80) cc_final: 0.4995 (m-80) REVERT: K 70 TYR cc_start: 0.8897 (p90) cc_final: 0.8693 (p90) REVERT: K 79 LYS cc_start: 0.9529 (OUTLIER) cc_final: 0.9102 (ttpp) REVERT: L 48 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8243 (ttm-80) REVERT: L 51 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8492 (mtp85) REVERT: P 232 MET cc_start: 0.6003 (mmp) cc_final: 0.5734 (mmp) REVERT: E 110 MET cc_start: 0.7578 (mtp) cc_final: 0.7181 (ttm) REVERT: F 57 MET cc_start: 0.9287 (tmm) cc_final: 0.9036 (tmm) REVERT: H 8 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6715 (m-30) REVERT: H 24 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.8005 (mtm180) REVERT: H 33 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8280 (mm-30) REVERT: H 37 MET cc_start: 0.8459 (mmm) cc_final: 0.7860 (mmm) REVERT: H 136 GLU cc_start: 0.7065 (mp0) cc_final: 0.6529 (mp0) REVERT: J 31 GLU cc_start: 0.9030 (mp0) cc_final: 0.8665 (mp0) REVERT: O 271 LEU cc_start: 0.8517 (mt) cc_final: 0.8144 (pp) REVERT: O 404 MET cc_start: 0.8416 (mmm) cc_final: 0.8004 (mmm) REVERT: O 427 ASN cc_start: 0.8416 (t0) cc_final: 0.7687 (t0) REVERT: O 434 MET cc_start: 0.8689 (ppp) cc_final: 0.8343 (ppp) REVERT: Q 54 GLU cc_start: 0.9281 (mm-30) cc_final: 0.7972 (tm-30) REVERT: Q 61 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8533 (tppt) REVERT: Q 111 MET cc_start: 0.7336 (mmm) cc_final: 0.6698 (tmm) REVERT: Q 114 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7320 (t0) REVERT: D 5 ASP cc_start: 0.8947 (t0) cc_final: 0.8693 (t0) REVERT: D 22 ASP cc_start: 0.9205 (m-30) cc_final: 0.8948 (m-30) REVERT: D 26 GLN cc_start: 0.9642 (mm-40) cc_final: 0.9204 (pp30) REVERT: M 17 LEU cc_start: 0.5234 (pt) cc_final: 0.4750 (tt) REVERT: M 45 LEU cc_start: 0.9592 (tp) cc_final: 0.9349 (pp) REVERT: M 114 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6632 (m-10) REVERT: M 149 HIS cc_start: 0.8887 (m-70) cc_final: 0.8540 (m-70) REVERT: M 202 GLU cc_start: 0.8973 (pt0) cc_final: 0.8130 (mp0) REVERT: N 350 MET cc_start: 0.7357 (ppp) cc_final: 0.6765 (ppp) REVERT: N 356 PHE cc_start: 0.7697 (m-80) cc_final: 0.7265 (m-80) REVERT: N 382 LYS cc_start: 0.8452 (tppp) cc_final: 0.8065 (tppp) outliers start: 110 outliers final: 80 residues processed: 533 average time/residue: 0.2289 time to fit residues: 204.2121 Evaluate side-chains 534 residues out of total 3993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 436 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 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 593 THR Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 805 SER 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 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 1106 GLU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 91 PHE 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 344 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 600 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 787 PHE 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 21 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 212 MET Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain G residue 7 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 56 ASP 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 79 LYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 48 ARG Chi-restraints excluded: chain P residue 201 ASN 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 307 CYS 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 F residue 58 THR Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 79 VAL 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 H residue 122 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain O residue 395 LEU Chi-restraints excluded: chain O residue 425 THR Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 114 ASN 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 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 330 LEU Chi-restraints excluded: chain N residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 222 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 362 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 315 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 388 optimal weight: 5.9990 chunk 229 optimal weight: 0.0040 chunk 337 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 HIS ** 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** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN O 339 HIS ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 ASN ** M 76 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 = 0.3676 r_free = 0.3676 target = 0.074335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060496 restraints weight = 190353.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.062124 restraints weight = 105857.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.063249 restraints weight = 69697.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.064027 restraints weight = 51403.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.064583 restraints weight = 41083.670| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.7747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.278 37637 Z= 0.216 Angle : 0.954 59.200 50977 Z= 0.494 Chirality : 0.047 0.666 5761 Planarity : 0.005 0.092 6377 Dihedral : 10.699 173.189 5412 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.68 % Favored : 91.17 % Rotamer: Outliers : 2.77 % Allowed : 25.15 % Favored : 72.08 % Cbeta Deviations : 0.05 % 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: -1.71 (0.13), residues: 4437 helix: 0.21 (0.13), residues: 1583 sheet: -1.80 (0.22), residues: 534 loop : -1.97 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 101 TYR 0.024 0.001 TYR D 52 PHE 0.029 0.001 PHE O 403 TRP 0.023 0.002 TRP M 205 HIS 0.024 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 (37617) covalent geometry : angle 0.92102 / 0.49 (50956) hydrogen bonds : bond 0.03642 / 2.40 ( 1155) hydrogen bonds : angle 4.91890 / 3.43 ( 3213) metal coordination : bond 0.00858 / 0.54 ( 20) metal coordination : angle 12.29434 / 7.25 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7858.44 seconds wall clock time: 136 minutes 27.27 seconds (8187.27 seconds total)