Starting phenix.real_space_refine on Sun Aug 9 15:28:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sv6_55239/08_2026/9sv6_55239.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sv6_55239/08_2026/9sv6_55239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sv6_55239/08_2026/9sv6_55239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sv6_55239/08_2026/9sv6_55239.map" model { file = "/net/cci-nas-00/data/ceres_data/9sv6_55239/08_2026/9sv6_55239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sv6_55239/08_2026/9sv6_55239.cif" } resolution = 1.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 K 1 8.98 5 Zn 8 6.06 5 P 100 5.49 5 Mg 2 5.21 5 S 185 5.16 5 C 20928 2.51 5 N 5871 2.21 5 O 7938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35033 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10942 Classifications: {'peptide': 1390} Link IDs: {'PCIS': 2, 'PTRANS': 60, 'TRANS': 1327} Chain breaks: 6 Chain: "B" Number of atoms: 9173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 9173 Classifications: {'peptide': 1152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1101} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1311 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 712 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 901 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 907 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "U" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 554 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' K': 1, ' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: "C" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 530 Classifications: {'water': 530} Link IDs: {None: 529} Chain: "B" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 380 Classifications: {'water': 380} Link IDs: {None: 379} Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "K" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "L" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "T" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 40.896 83.406 89.602 1.00 29.46 S ATOM 479 SG CYS A 70 41.961 86.564 87.768 1.00 31.68 S ATOM 532 SG CYS A 77 44.280 83.472 88.080 1.00 26.45 S ATOM 762 SG CYS A 107 63.513 81.084 131.623 1.00 59.23 S ATOM 786 SG CYS A 110 62.208 84.561 131.832 1.00 59.96 S ATOM 1091 SG CYS A 148 65.550 83.645 133.464 1.00 58.57 S ATOM 1105 SG CYS A 167 62.270 82.317 134.978 1.00 74.46 S ATOM 19621 SG CYS B1163 50.331 95.794 98.190 1.00 20.58 S ATOM 19639 SG CYS B1166 51.575 92.575 99.723 1.00 22.33 S ATOM 19764 SG CYS B1182 47.883 93.200 98.743 1.00 29.42 S ATOM 19783 SG CYS B1185 49.440 94.910 101.843 1.00 28.59 S ATOM 20771 SG CYS C 86 56.126 66.475 23.138 1.00 53.66 S ATOM 20788 SG CYS C 88 53.961 65.017 25.910 1.00 51.65 S ATOM 20821 SG CYS C 92 54.389 63.345 22.455 1.00 37.71 S ATOM 20844 SG CYS C 95 57.219 63.389 25.165 1.00 34.77 S ATOM 28447 SG CYS I 7 98.107 25.345 133.210 1.00118.78 S ATOM 28472 SG CYS I 10 94.419 25.933 132.926 1.00121.87 S ATOM 28638 SG CYS I 29 96.541 28.582 134.583 1.00127.20 S ATOM 28662 SG CYS I 32 95.968 25.208 136.318 1.00125.50 S ATOM 28989 SG CYS I 75 123.656 27.005 96.973 1.00 87.97 S ATOM 29011 SG CYS I 78 124.489 23.387 95.883 1.00 97.82 S ATOM 29227 SG CYS I 103 121.156 24.904 95.011 1.00 81.06 S ATOM 29247 SG CYS I 106 122.053 23.979 98.638 1.00 88.84 S ATOM 29349 SG CYS J 7 82.590 49.668 38.473 1.00 8.11 S ATOM 29372 SG CYS J 10 83.602 51.260 35.174 1.00 10.25 S ATOM 29652 SG CYS J 45 86.280 50.474 37.891 1.00 16.01 S ATOM 29658 SG CYS J 46 84.629 47.943 35.541 1.00 15.75 S ATOM 30781 SG CYS L 31 45.716 33.085 56.034 1.00 50.58 S ATOM 30801 SG CYS L 34 45.160 30.369 53.471 1.00 62.98 S ATOM 30905 SG CYS L 48 42.195 31.911 55.346 1.00 62.25 S ATOM 30928 SG CYS L 51 44.696 29.585 57.086 1.00 64.73 S Residues with excluded nonbonded symmetry interactions: 25 residue: pdb=" O HOH A1996 " occ=0.77 residue: pdb=" O HOH A2036 " occ=0.42 residue: pdb=" O HOH A2072 " occ=0.39 residue: pdb=" O HOH A2172 " occ=0.56 residue: pdb=" O HOH A2177 " occ=0.52 residue: pdb=" O HOH A2183 " occ=0.64 residue: pdb=" O HOH A2285 " occ=0.42 residue: pdb=" O HOH A2334 " occ=0.69 residue: pdb=" O HOH B1481 " occ=0.56 residue: pdb=" O HOH B1483 " occ=0.64 residue: pdb=" O HOH B1566 " occ=0.50 residue: pdb=" O HOH B1618 " occ=0.64 ... (remaining 13 not shown) Time building chain proxies: 7.40, per 1000 atoms: 0.21 Number of scatterers: 35033 At special positions: 0 Unit cell: (149.12, 158.44, 178.944, 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 8 29.99 K 1 19.00 S 185 16.00 P 100 15.00 Mg 2 11.99 O 7938 8.00 N 5871 7.00 C 20928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS U 25 " - pdb=" SG CYS U 28 " distance=2.02 Simple disulfide: pdb=" SG CYS U 49 " - pdb=" SG CYS U 52 " distance=2.03 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: 3.10 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 70 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 167 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 45 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7484 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 49 sheets defined 40.1% alpha, 20.0% beta 40 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 5.35 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.679A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 removed outlier: 3.643A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.588A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.772A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.702A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 846 removed outlier: 3.765A pdb=" N THR A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.691A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.829A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.900A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 removed outlier: 3.617A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1083 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1084 through 1087 Processing helix chain 'A' and resid 1091 through 1107 removed outlier: 4.359A pdb=" N VAL A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Proline residue: A1099 - end of helix Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1143 through 1146 No H-bonds generated for 'chain 'A' and resid 1143 through 1146' Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 4.580A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.507A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1271 removed outlier: 3.747A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 4.026A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1453 Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.585A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 66 removed outlier: 4.021A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 156 through 160 removed outlier: 3.513A pdb=" N ASP B 159 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.708A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.593A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.639A pdb=" N GLU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.653A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.980A pdb=" N GLU B 711 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.525A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 808 through 813 removed outlier: 3.565A pdb=" N LEU B 812 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1014 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.811A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.617A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.751A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 268 removed outlier: 3.921A pdb=" N ASP C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 135 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.664A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 5 through 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 55 through 58 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.508A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.645A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.554A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.594A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.035A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.614A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.188A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.020A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.804A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.653A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.733A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.845A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.720A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.755A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 3.792A pdb=" N ARG A1274 " --> pdb=" O THR A1141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.313A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.602A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.602A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.008A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.008A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.848A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC8, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.413A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.870A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.870A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.316A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.505A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.418A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'E' and resid 47 through 48 removed outlier: 5.133A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE7, first strand: chain 'G' and resid 86 through 87 removed outlier: 5.662A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR G 90 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.612A pdb=" N THR G 120 " --> pdb=" O GLN G 131 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.547A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF2, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.620A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.679A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 16 through 17 removed outlier: 3.510A pdb=" N GLN U 17 " --> pdb=" O LEU U 38 " (cutoff:3.500A) 1454 hydrogen bonds defined for protein. 3960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 13.88 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5539 1.32 - 1.44: 9124 1.44 - 1.57: 19322 1.57 - 1.69: 196 1.69 - 1.82: 293 Bond restraints: 34474 Sorted by residual: bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.192 0.182 1.00e-02 1.00e+04 3.32e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.216 0.154 1.20e-02 6.94e+03 1.64e+02 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.03e+02 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.340 0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C5 ATP A1801 " pdb=" N7 ATP A1801 " ideal model delta sigma weight residual 1.387 1.455 -0.068 1.00e-02 1.00e+04 4.69e+01 ... (remaining 34469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 46791 3.31 - 6.63: 164 6.63 - 9.94: 8 9.94 - 13.25: 1 13.25 - 16.57: 2 Bond angle restraints: 46966 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 123.30 16.57 1.00e+00 1.00e+00 2.74e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.17 -13.45 1.00e+00 1.00e+00 1.81e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 124.59 12.24 1.00e+00 1.00e+00 1.50e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 119.72 8.97 1.00e+00 1.00e+00 8.05e+01 angle pdb=" O4' DC N 48 " pdb=" C1' DC N 48 " pdb=" N1 DC N 48 " ideal model delta sigma weight residual 108.00 112.50 -4.50 7.00e-01 2.04e+00 4.13e+01 ... (remaining 46961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.92: 19991 31.92 - 63.84: 761 63.84 - 95.77: 88 95.77 - 127.69: 2 127.69 - 159.61: 3 Dihedral angle restraints: 20845 sinusoidal: 9291 harmonic: 11554 Sorted by residual: dihedral pdb=" CB CYS U 49 " pdb=" SG CYS U 49 " pdb=" SG CYS U 52 " pdb=" CB CYS U 52 " ideal model delta sinusoidal sigma weight residual 93.00 139.09 -46.09 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CA VAL E 90 " pdb=" C VAL E 90 " pdb=" N LYS E 91 " pdb=" CA LYS E 91 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ILE C 38 " pdb=" C ILE C 38 " pdb=" N ALA C 39 " pdb=" CA ALA C 39 " ideal model delta harmonic sigma weight residual -180.00 -157.00 -23.00 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 20842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4075 0.050 - 0.100: 949 0.100 - 0.150: 254 0.150 - 0.201: 6 0.201 - 0.251: 2 Chirality restraints: 5286 Sorted by residual: chirality pdb=" CA SER B 764 " pdb=" N SER B 764 " pdb=" C SER B 764 " pdb=" CB SER B 764 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB THR J 52 " pdb=" CA THR J 52 " pdb=" OG1 THR J 52 " pdb=" CG2 THR J 52 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3' ATP A1801 " pdb=" C2' ATP A1801 " pdb=" C4' ATP A1801 " pdb=" O3' ATP A1801 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 5283 not shown) Planarity restraints: 5733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 444 " -0.023 2.00e-02 2.50e+03 2.22e-02 8.60e+00 pdb=" CG PHE A 444 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 444 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 444 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 444 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 444 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 444 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 494 " 0.022 2.00e-02 2.50e+03 2.28e-02 7.82e+00 pdb=" CG HIS B 494 " -0.049 2.00e-02 2.50e+03 pdb=" ND1 HIS B 494 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS B 494 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS B 494 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 494 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 48 " 0.023 2.00e-02 2.50e+03 1.24e-02 3.44e+00 pdb=" N1 DC N 48 " -0.028 2.00e-02 2.50e+03 pdb=" C2 DC N 48 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DC N 48 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DC N 48 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DC N 48 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC N 48 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC N 48 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC N 48 " -0.004 2.00e-02 2.50e+03 ... (remaining 5730 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.61: 658 2.61 - 3.24: 35121 3.24 - 3.87: 76772 3.87 - 4.51: 102443 4.51 - 5.14: 157427 Nonbonded interactions: 372421 Sorted by model distance: nonbonded pdb=" O2G ATP A1801 " pdb="MG MG A1802 " model vdw 1.976 2.170 nonbonded pdb=" O LYS A1205 " pdb=" NH2 ARG A1274 " model vdw 2.137 3.120 nonbonded pdb=" OE1 GLU B 945 " pdb=" O HOH B1401 " model vdw 2.196 3.040 nonbonded pdb=" O ARG A 677 " pdb=" OG1 THR A 680 " model vdw 2.198 3.040 nonbonded pdb=" O VAL C 235 " pdb=" O HOH C 501 " model vdw 2.201 3.040 ... (remaining 372416 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=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 47.110 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.004 0.182 34508 Z= 0.279 Angle : 0.635 16.567 47015 Z= 0.410 Chirality : 0.046 0.251 5286 Planarity : 0.004 0.065 5733 Dihedral : 15.796 159.612 13355 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.30 % Rotamer: Outliers : 0.20 % Allowed : 0.09 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.65 (0.13), residues: 3927 helix: 1.17 (0.14), residues: 1342 sheet: 0.35 (0.20), residues: 641 loop : 0.05 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 336 TYR 0.019 0.002 TYR B 486 PHE 0.051 0.002 PHE A 444 TRP 0.022 0.002 TRP C 170 HIS 0.024 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.28 (34474) covalent geometry : angle 0.62634 / 0.41 (46966) SS BOND : bond 0.01029 / 0.64 ( 2) SS BOND : angle 1.06603 / 0.49 ( 4) hydrogen bonds : bond 0.16504 / 10.95 ( 1512) hydrogen bonds : angle 6.62277 / 4.74 ( 4166) metal coordination : bond 0.00460 / 0.26 ( 32) metal coordination : angle 3.34997 / 2.28 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 669 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8702 (m-80) cc_final: 0.8447 (m-80) REVERT: A 39 GLU cc_start: 0.7055 (mp0) cc_final: 0.6824 (mp0) REVERT: A 177 ASP cc_start: 0.6966 (t0) cc_final: 0.6597 (t0) REVERT: A 291 GLU cc_start: 0.7265 (tt0) cc_final: 0.6973 (pp20) REVERT: A 293 GLU cc_start: 0.7761 (tt0) cc_final: 0.6889 (tp30) REVERT: A 691 LEU cc_start: 0.8656 (tp) cc_final: 0.8159 (tm) REVERT: A 695 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7807 (mptm) REVERT: A 771 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8053 (mm-30) REVERT: A 900 ASP cc_start: 0.7315 (t0) cc_final: 0.7107 (t0) REVERT: A 915 SER cc_start: 0.7366 (p) cc_final: 0.7147 (t) REVERT: A 934 LYS cc_start: 0.8408 (tttm) cc_final: 0.8028 (mttp) REVERT: A 938 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8173 (tttt) REVERT: A 1005 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7760 (mp0) REVERT: A 1048 ASN cc_start: 0.8658 (m-40) cc_final: 0.8301 (t0) REVERT: A 1112 LYS cc_start: 0.7718 (mptt) cc_final: 0.7395 (mtmm) REVERT: A 1134 ILE cc_start: 0.8117 (mm) cc_final: 0.7827 (mm) REVERT: A 1285 MET cc_start: 0.7776 (mmt) cc_final: 0.7570 (tpp) REVERT: A 1297 GLU cc_start: 0.8196 (pm20) cc_final: 0.7728 (pm20) REVERT: A 1317 MET cc_start: 0.8318 (ptt) cc_final: 0.8104 (ptp) REVERT: A 1363 VAL cc_start: 0.9078 (t) cc_final: 0.8838 (p) REVERT: A 1391 ARG cc_start: 0.8344 (mmt90) cc_final: 0.7939 (mmt180) REVERT: B 103 ASN cc_start: 0.7617 (p0) cc_final: 0.7359 (m-40) REVERT: B 115 GLN cc_start: 0.8531 (pp30) cc_final: 0.7960 (tp40) REVERT: B 193 LYS cc_start: 0.8643 (mmtp) cc_final: 0.8348 (mmtt) REVERT: B 451 LYS cc_start: 0.8353 (mtmt) cc_final: 0.8077 (mttt) REVERT: B 552 MET cc_start: 0.7943 (mmm) cc_final: 0.7444 (tpp) REVERT: B 608 ASP cc_start: 0.8005 (m-30) cc_final: 0.7797 (m-30) REVERT: B 789 MET cc_start: 0.8645 (mmm) cc_final: 0.8429 (mmm) REVERT: B 908 GLU cc_start: 0.7155 (mp0) cc_final: 0.6595 (mm-30) REVERT: B 948 ILE cc_start: 0.8847 (mp) cc_final: 0.8582 (tt) REVERT: B 999 MET cc_start: 0.9139 (mmt) cc_final: 0.8812 (mmt) REVERT: B 1057 LYS cc_start: 0.8735 (mttt) cc_final: 0.8404 (mmtm) REVERT: C 78 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7530 (mp0) REVERT: C 106 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7035 (pm20) REVERT: D 123 LEU cc_start: 0.4225 (mt) cc_final: 0.3915 (tp) REVERT: E 43 LYS cc_start: 0.7339 (mtmt) cc_final: 0.7073 (mtpm) REVERT: E 69 ILE cc_start: 0.7979 (mm) cc_final: 0.7761 (mm) REVERT: E 93 MET cc_start: 0.6839 (tpp) cc_final: 0.6606 (tpp) REVERT: E 172 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8433 (mt-10) REVERT: E 192 ARG cc_start: 0.8258 (ttt180) cc_final: 0.8004 (ttm-80) REVERT: E 201 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8569 (mmtm) REVERT: F 78 GLN cc_start: 0.8031 (mt0) cc_final: 0.7796 (mt0) REVERT: G 22 MET cc_start: 0.8122 (ttp) cc_final: 0.7436 (ttp) REVERT: G 73 LYS cc_start: 0.7606 (mmtp) cc_final: 0.7379 (mmtt) REVERT: G 80 LYS cc_start: 0.4932 (tptt) cc_final: 0.4537 (ttpp) REVERT: G 107 LYS cc_start: 0.4077 (ttmm) cc_final: 0.3781 (mmtt) REVERT: H 7 ASP cc_start: 0.7784 (t0) cc_final: 0.7492 (t0) REVERT: H 129 TYR cc_start: 0.6797 (p90) cc_final: 0.6478 (p90) REVERT: K 17 SER cc_start: 0.8683 (m) cc_final: 0.8456 (t) REVERT: K 20 LYS cc_start: 0.8663 (tttp) cc_final: 0.7699 (mppt) REVERT: K 52 ASN cc_start: 0.9160 (m-40) cc_final: 0.8954 (m-40) REVERT: K 54 ARG cc_start: 0.8435 (mtm180) cc_final: 0.8225 (mmt-90) REVERT: K 79 GLU cc_start: 0.7701 (tt0) cc_final: 0.7021 (mp0) REVERT: K 84 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8380 (mtmm) REVERT: K 110 ASN cc_start: 0.9021 (m-40) cc_final: 0.8775 (m110) REVERT: L 28 LYS cc_start: 0.7818 (mptt) cc_final: 0.7486 (mmtt) REVERT: L 36 SER cc_start: 0.8405 (m) cc_final: 0.8141 (t) REVERT: L 54 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7871 (mtp85) outliers start: 7 outliers final: 0 residues processed: 674 average time/residue: 0.9011 time to fit residues: 707.7546 Evaluate side-chains 461 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 68 GLN A 118 HIS A 427 GLN A 965 GLN A1082 ASN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN B 494 HIS B 572 HIS B 592 ASN B 610 ASN B 686 ASN C 195 GLN E 8 ASN E 63 ASN E 99 HIS G 10 ASN G 71 ASN G 122 ASN J 23 ASN K 89 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.197577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125908 restraints weight = 24129.639| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.31 r_work: 0.3238 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 34508 Z= 0.152 Angle : 0.614 13.779 47015 Z= 0.336 Chirality : 0.046 0.266 5286 Planarity : 0.005 0.062 5733 Dihedral : 16.515 160.353 5429 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.67 % Favored : 97.28 % Rotamer: Outliers : 1.00 % Allowed : 6.11 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.67 (0.13), residues: 3927 helix: 1.24 (0.14), residues: 1384 sheet: 0.42 (0.20), residues: 612 loop : -0.04 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 476 TYR 0.020 0.002 TYR B 486 PHE 0.032 0.002 PHE A 444 TRP 0.015 0.002 TRP B 31 HIS 0.019 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (34474) covalent geometry : angle 0.60445 / 0.34 (46966) SS BOND : bond 0.00586 / 0.37 ( 2) SS BOND : angle 1.22050 / 0.61 ( 4) hydrogen bonds : bond 0.05428 / 3.64 ( 1512) hydrogen bonds : angle 5.27426 / 3.78 ( 4166) metal coordination : bond 0.00533 / 0.30 ( 32) metal coordination : angle 3.50489 / 2.38 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 474 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8688 (m-80) cc_final: 0.8455 (m-80) REVERT: A 39 GLU cc_start: 0.7155 (mp0) cc_final: 0.6869 (mp0) REVERT: A 74 MET cc_start: 0.8279 (mtt) cc_final: 0.7938 (mmm) REVERT: A 277 GLU cc_start: 0.7655 (tt0) cc_final: 0.7359 (mt-10) REVERT: A 291 GLU cc_start: 0.7249 (tt0) cc_final: 0.6948 (pp20) REVERT: A 293 GLU cc_start: 0.7772 (tt0) cc_final: 0.6872 (tp30) REVERT: A 470 LEU cc_start: 0.8577 (pp) cc_final: 0.8308 (mm) REVERT: A 644 LYS cc_start: 0.8346 (mppt) cc_final: 0.8115 (mmtm) REVERT: A 678 GLU cc_start: 0.7348 (tt0) cc_final: 0.7057 (mt-10) REVERT: A 691 LEU cc_start: 0.8638 (tp) cc_final: 0.8107 (tm) REVERT: A 695 LYS cc_start: 0.7940 (mmtm) cc_final: 0.7721 (mptm) REVERT: A 771 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8028 (mm-30) REVERT: A 900 ASP cc_start: 0.7391 (t0) cc_final: 0.7137 (t0) REVERT: A 915 SER cc_start: 0.7404 (p) cc_final: 0.7193 (t) REVERT: A 934 LYS cc_start: 0.8365 (tttm) cc_final: 0.7988 (mttp) REVERT: A 938 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8214 (tttp) REVERT: A 1005 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7708 (mp0) REVERT: A 1112 LYS cc_start: 0.7891 (mptt) cc_final: 0.7532 (mtmm) REVERT: A 1285 MET cc_start: 0.7842 (mmt) cc_final: 0.7605 (tpp) REVERT: A 1287 TYR cc_start: 0.7993 (m-80) cc_final: 0.7740 (m-10) REVERT: A 1297 GLU cc_start: 0.8320 (pm20) cc_final: 0.7769 (pm20) REVERT: A 1300 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7680 (ttpp) REVERT: A 1363 VAL cc_start: 0.9057 (t) cc_final: 0.8814 (p) REVERT: B 103 ASN cc_start: 0.7668 (p0) cc_final: 0.7317 (m-40) REVERT: B 115 GLN cc_start: 0.8563 (pp30) cc_final: 0.7976 (tp40) REVERT: B 133 LYS cc_start: 0.6932 (mtpt) cc_final: 0.6503 (ttpp) REVERT: B 193 LYS cc_start: 0.8697 (mmtp) cc_final: 0.8320 (mmtt) REVERT: B 422 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7953 (mttm) REVERT: B 451 LYS cc_start: 0.8234 (mtmt) cc_final: 0.8015 (mttt) REVERT: B 531 GLN cc_start: 0.7692 (tt0) cc_final: 0.7251 (tm-30) REVERT: B 552 MET cc_start: 0.7932 (mmm) cc_final: 0.7408 (tpp) REVERT: B 860 MET cc_start: 0.8828 (tmm) cc_final: 0.8598 (tmm) REVERT: B 908 GLU cc_start: 0.7103 (mp0) cc_final: 0.6533 (mm-30) REVERT: B 948 ILE cc_start: 0.8872 (mp) cc_final: 0.8655 (tt) REVERT: B 999 MET cc_start: 0.9141 (mmt) cc_final: 0.8805 (mmt) REVERT: B 1057 LYS cc_start: 0.8746 (mttt) cc_final: 0.8444 (mmtm) REVERT: C 78 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7496 (mp0) REVERT: C 106 GLU cc_start: 0.7637 (mt-10) cc_final: 0.6996 (pm20) REVERT: D 123 LEU cc_start: 0.4196 (mt) cc_final: 0.3900 (tp) REVERT: E 50 MET cc_start: 0.5152 (pp-130) cc_final: 0.4926 (pp-130) REVERT: E 57 MET cc_start: 0.6913 (mtp) cc_final: 0.6676 (ptt) REVERT: E 69 ILE cc_start: 0.7823 (mm) cc_final: 0.7579 (mm) REVERT: E 93 MET cc_start: 0.6953 (tpp) cc_final: 0.6753 (tpp) REVERT: E 172 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8376 (mt-10) REVERT: E 192 ARG cc_start: 0.8117 (ttt180) cc_final: 0.7870 (ttm-80) REVERT: E 201 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8527 (mmtt) REVERT: F 78 GLN cc_start: 0.7987 (mt0) cc_final: 0.7735 (mt0) REVERT: G 22 MET cc_start: 0.8023 (ttp) cc_final: 0.7493 (ttp) REVERT: G 107 LYS cc_start: 0.4040 (ttmm) cc_final: 0.3622 (mmtt) REVERT: H 7 ASP cc_start: 0.7666 (t0) cc_final: 0.7431 (t0) REVERT: H 11 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7970 (tp-100) REVERT: I 87 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6274 (mp10) REVERT: J 48 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7953 (ppt170) REVERT: K 17 SER cc_start: 0.8650 (m) cc_final: 0.8411 (t) REVERT: K 20 LYS cc_start: 0.8563 (tttp) cc_final: 0.7492 (mppt) REVERT: K 52 ASN cc_start: 0.9099 (m-40) cc_final: 0.8893 (m-40) REVERT: K 79 GLU cc_start: 0.7663 (tt0) cc_final: 0.6996 (mp0) REVERT: K 84 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8333 (mtmm) REVERT: K 110 ASN cc_start: 0.8930 (m-40) cc_final: 0.8677 (m110) REVERT: L 28 LYS cc_start: 0.7771 (mptt) cc_final: 0.7331 (mmtt) REVERT: L 36 SER cc_start: 0.8380 (m) cc_final: 0.7979 (t) REVERT: L 54 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7720 (mtp85) outliers start: 35 outliers final: 17 residues processed: 491 average time/residue: 0.9340 time to fit residues: 532.5648 Evaluate side-chains 467 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 445 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1300 LYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 31 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 236 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 289 optimal weight: 20.0000 chunk 256 optimal weight: 0.4980 chunk 286 optimal weight: 8.9990 chunk 335 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 366 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 209 ASN A 213 HIS A 427 GLN A 965 GLN A 994 GLN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 ASN C 24 ASN G 10 ASN G 71 ASN G 122 ASN J 23 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.196632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124827 restraints weight = 24028.846| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.38 r_work: 0.3212 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 34508 Z= 0.156 Angle : 0.606 14.349 47015 Z= 0.331 Chirality : 0.046 0.276 5286 Planarity : 0.005 0.065 5733 Dihedral : 16.497 159.271 5429 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.67 % Favored : 97.28 % Rotamer: Outliers : 1.60 % Allowed : 7.08 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.69 (0.13), residues: 3927 helix: 1.31 (0.14), residues: 1387 sheet: 0.38 (0.20), residues: 617 loop : -0.06 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 77 TYR 0.020 0.002 TYR B 486 PHE 0.031 0.002 PHE A 219 TRP 0.016 0.002 TRP C 192 HIS 0.014 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (34474) covalent geometry : angle 0.59628 / 0.33 (46966) SS BOND : bond 0.00463 / 0.29 ( 2) SS BOND : angle 0.96452 / 0.48 ( 4) hydrogen bonds : bond 0.05267 / 3.54 ( 1512) hydrogen bonds : angle 5.08124 / 3.64 ( 4166) metal coordination : bond 0.00538 / 0.31 ( 32) metal coordination : angle 3.54107 / 2.43 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 463 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8638 (m-80) cc_final: 0.8340 (m-80) REVERT: A 39 GLU cc_start: 0.7224 (mp0) cc_final: 0.6858 (mp0) REVERT: A 141 LEU cc_start: 0.8289 (mt) cc_final: 0.8054 (mp) REVERT: A 277 GLU cc_start: 0.7573 (tt0) cc_final: 0.7288 (mt-10) REVERT: A 291 GLU cc_start: 0.7232 (tt0) cc_final: 0.6846 (pp20) REVERT: A 293 GLU cc_start: 0.7750 (tt0) cc_final: 0.6813 (tp30) REVERT: A 383 TYR cc_start: 0.8346 (m-80) cc_final: 0.8116 (m-80) REVERT: A 470 LEU cc_start: 0.8583 (pp) cc_final: 0.8265 (mm) REVERT: A 678 GLU cc_start: 0.7347 (tt0) cc_final: 0.7051 (mt-10) REVERT: A 691 LEU cc_start: 0.8606 (tp) cc_final: 0.8053 (tm) REVERT: A 695 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7548 (mptm) REVERT: A 771 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7857 (mm-30) REVERT: A 822 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: A 900 ASP cc_start: 0.7406 (t0) cc_final: 0.7130 (t0) REVERT: A 915 SER cc_start: 0.7397 (p) cc_final: 0.7144 (t) REVERT: A 934 LYS cc_start: 0.8329 (tttm) cc_final: 0.7910 (mttp) REVERT: A 938 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8174 (tttp) REVERT: A 984 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7550 (tttt) REVERT: A 1005 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7642 (mp0) REVERT: A 1112 LYS cc_start: 0.7785 (mptt) cc_final: 0.7397 (mtmm) REVERT: A 1285 MET cc_start: 0.7863 (mmt) cc_final: 0.7657 (tpp) REVERT: A 1297 GLU cc_start: 0.8311 (pm20) cc_final: 0.7762 (pm20) REVERT: A 1300 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7818 (ttpp) REVERT: A 1363 VAL cc_start: 0.9048 (t) cc_final: 0.8787 (p) REVERT: B 103 ASN cc_start: 0.7661 (p0) cc_final: 0.7262 (m-40) REVERT: B 115 GLN cc_start: 0.8581 (pp30) cc_final: 0.8011 (tp40) REVERT: B 133 LYS cc_start: 0.6946 (mtpt) cc_final: 0.6386 (ttpp) REVERT: B 193 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8286 (mmtt) REVERT: B 241 ARG cc_start: 0.6913 (mtm180) cc_final: 0.6675 (mtm180) REVERT: B 432 MET cc_start: 0.6655 (ttp) cc_final: 0.6194 (mtp) REVERT: B 451 LYS cc_start: 0.8233 (mtmt) cc_final: 0.8014 (mttt) REVERT: B 531 GLN cc_start: 0.7687 (tt0) cc_final: 0.7238 (tm-30) REVERT: B 552 MET cc_start: 0.7930 (mmm) cc_final: 0.7404 (tpp) REVERT: B 619 ILE cc_start: 0.8127 (mm) cc_final: 0.7886 (mm) REVERT: B 860 MET cc_start: 0.8839 (tmm) cc_final: 0.8631 (tmm) REVERT: B 886 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7294 (mttm) REVERT: B 908 GLU cc_start: 0.7071 (mp0) cc_final: 0.6470 (mm-30) REVERT: B 948 ILE cc_start: 0.8889 (mp) cc_final: 0.8643 (tt) REVERT: B 999 MET cc_start: 0.9176 (mmt) cc_final: 0.8893 (mmt) REVERT: B 1010 LEU cc_start: 0.8854 (mt) cc_final: 0.8645 (mt) REVERT: B 1057 LYS cc_start: 0.8742 (mttt) cc_final: 0.8424 (mmtm) REVERT: B 1181 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: C 15 LYS cc_start: 0.7408 (ptmm) cc_final: 0.7101 (ttpt) REVERT: C 78 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7372 (mp0) REVERT: D 123 LEU cc_start: 0.4064 (mt) cc_final: 0.3830 (tp) REVERT: E 43 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6995 (mtpm) REVERT: E 69 ILE cc_start: 0.7799 (mm) cc_final: 0.7561 (mm) REVERT: E 93 MET cc_start: 0.6938 (tpp) cc_final: 0.6709 (tpp) REVERT: E 172 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8371 (mt-10) REVERT: E 192 ARG cc_start: 0.8127 (ttt180) cc_final: 0.7839 (ttm-80) REVERT: E 201 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8476 (mmtm) REVERT: F 76 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8474 (tttm) REVERT: F 78 GLN cc_start: 0.7965 (mt0) cc_final: 0.7707 (mt0) REVERT: G 22 MET cc_start: 0.8001 (ttp) cc_final: 0.7447 (ttp) REVERT: G 107 LYS cc_start: 0.3927 (ttmm) cc_final: 0.3541 (mmtt) REVERT: H 7 ASP cc_start: 0.7706 (t0) cc_final: 0.7447 (t0) REVERT: I 70 ARG cc_start: 0.7653 (mpt180) cc_final: 0.7350 (mpt180) REVERT: I 87 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6234 (mp10) REVERT: J 19 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7751 (pm20) REVERT: K 17 SER cc_start: 0.8655 (m) cc_final: 0.8374 (t) REVERT: K 20 LYS cc_start: 0.8543 (tttp) cc_final: 0.7410 (mppt) REVERT: K 36 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8457 (mm-30) REVERT: K 79 GLU cc_start: 0.7693 (tt0) cc_final: 0.6924 (mp0) REVERT: K 84 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8256 (mtmm) REVERT: L 28 LYS cc_start: 0.7785 (mptt) cc_final: 0.7129 (mtmp) REVERT: L 36 SER cc_start: 0.8394 (m) cc_final: 0.7959 (t) REVERT: L 54 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7705 (mtp85) REVERT: U 25 CYS cc_start: 0.0648 (OUTLIER) cc_final: 0.0421 (m) REVERT: U 28 CYS cc_start: 0.1334 (OUTLIER) cc_final: 0.0921 (t) outliers start: 56 outliers final: 24 residues processed: 493 average time/residue: 0.8834 time to fit residues: 506.3208 Evaluate side-chains 485 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 452 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1300 LYS Chi-restraints excluded: chain A residue 1449 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 886 LYS Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain U residue 25 CYS Chi-restraints excluded: chain U residue 28 CYS Chi-restraints excluded: chain U residue 78 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 371 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 321 optimal weight: 0.3980 chunk 200 optimal weight: 8.9990 chunk 245 optimal weight: 0.6980 chunk 80 optimal weight: 0.1980 chunk 134 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 396 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 GLN A 965 GLN A 975 HIS A1048 ASN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 ASN B1178 ASN G 71 ASN K 110 ASN ** L 53 HIS ** 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 = 0.4237 r_free = 0.4237 target = 0.198402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127512 restraints weight = 24123.341| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.32 r_work: 0.3257 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 34508 Z= 0.118 Angle : 0.542 13.605 47015 Z= 0.296 Chirality : 0.044 0.279 5286 Planarity : 0.004 0.046 5733 Dihedral : 16.417 159.297 5429 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 1.28 % Allowed : 8.56 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.85 (0.13), residues: 3927 helix: 1.55 (0.14), residues: 1378 sheet: 0.39 (0.21), residues: 616 loop : -0.02 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 77 TYR 0.017 0.001 TYR B 486 PHE 0.028 0.001 PHE A 219 TRP 0.014 0.001 TRP C 192 HIS 0.010 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (34474) covalent geometry : angle 0.53304 / 0.30 (46966) SS BOND : bond 0.00433 / 0.27 ( 2) SS BOND : angle 0.98943 / 0.49 ( 4) hydrogen bonds : bond 0.04324 / 2.89 ( 1512) hydrogen bonds : angle 4.76705 / 3.43 ( 4166) metal coordination : bond 0.00401 / 0.24 ( 32) metal coordination : angle 3.22296 / 2.22 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 470 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8661 (m-80) cc_final: 0.8426 (m-80) REVERT: A 39 GLU cc_start: 0.7238 (mp0) cc_final: 0.6917 (mp0) REVERT: A 74 MET cc_start: 0.8222 (mtt) cc_final: 0.7970 (mmm) REVERT: A 141 LEU cc_start: 0.8333 (mt) cc_final: 0.8100 (mp) REVERT: A 277 GLU cc_start: 0.7525 (tt0) cc_final: 0.7230 (mt-10) REVERT: A 291 GLU cc_start: 0.7184 (tt0) cc_final: 0.6812 (pp20) REVERT: A 293 GLU cc_start: 0.7691 (tt0) cc_final: 0.6776 (tp30) REVERT: A 383 TYR cc_start: 0.8364 (m-80) cc_final: 0.8005 (m-80) REVERT: A 470 LEU cc_start: 0.8516 (pp) cc_final: 0.8216 (mm) REVERT: A 678 GLU cc_start: 0.7301 (tt0) cc_final: 0.7066 (mt-10) REVERT: A 695 LYS cc_start: 0.7853 (mmtm) cc_final: 0.7553 (mptm) REVERT: A 771 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7862 (mm-30) REVERT: A 822 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: A 900 ASP cc_start: 0.7425 (t0) cc_final: 0.7143 (t0) REVERT: A 915 SER cc_start: 0.7519 (p) cc_final: 0.7223 (t) REVERT: A 934 LYS cc_start: 0.8349 (tttm) cc_final: 0.7961 (mttp) REVERT: A 938 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8219 (tttp) REVERT: A 1005 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7665 (mp0) REVERT: A 1112 LYS cc_start: 0.7890 (mptt) cc_final: 0.7518 (mtmm) REVERT: A 1297 GLU cc_start: 0.8292 (pm20) cc_final: 0.7732 (pm20) REVERT: A 1300 LYS cc_start: 0.8280 (ttpp) cc_final: 0.8071 (ttmt) REVERT: A 1363 VAL cc_start: 0.9028 (t) cc_final: 0.8772 (p) REVERT: B 115 GLN cc_start: 0.8580 (pp30) cc_final: 0.8149 (tp40) REVERT: B 133 LYS cc_start: 0.7027 (mtpt) cc_final: 0.6408 (ttpp) REVERT: B 193 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8291 (mmtt) REVERT: B 241 ARG cc_start: 0.7027 (mtm180) cc_final: 0.6746 (mtp85) REVERT: B 393 LYS cc_start: 0.7356 (mtpt) cc_final: 0.6876 (mmtt) REVERT: B 422 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7921 (mttp) REVERT: B 432 MET cc_start: 0.6828 (ttp) cc_final: 0.6474 (mtp) REVERT: B 451 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7472 (tmtt) REVERT: B 510 LYS cc_start: 0.7786 (tmtt) cc_final: 0.7495 (tptt) REVERT: B 531 GLN cc_start: 0.7651 (tt0) cc_final: 0.7190 (tm-30) REVERT: B 552 MET cc_start: 0.7906 (mmm) cc_final: 0.7359 (tpp) REVERT: B 619 ILE cc_start: 0.8127 (mm) cc_final: 0.7876 (mm) REVERT: B 778 MET cc_start: 0.8766 (mtt) cc_final: 0.8404 (ttm) REVERT: B 860 MET cc_start: 0.8784 (tmm) cc_final: 0.8488 (tmm) REVERT: B 908 GLU cc_start: 0.7087 (mp0) cc_final: 0.6483 (mm-30) REVERT: B 948 ILE cc_start: 0.8858 (mp) cc_final: 0.8650 (tt) REVERT: B 1057 LYS cc_start: 0.8709 (mttt) cc_final: 0.8448 (mmtm) REVERT: B 1181 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: C 15 LYS cc_start: 0.7391 (ptmm) cc_final: 0.7107 (tttm) REVERT: C 78 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7446 (mp0) REVERT: E 43 LYS cc_start: 0.7278 (mtmt) cc_final: 0.7007 (mtpm) REVERT: E 69 ILE cc_start: 0.7868 (mm) cc_final: 0.7606 (mm) REVERT: E 93 MET cc_start: 0.6960 (tpp) cc_final: 0.6732 (tpp) REVERT: E 172 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8379 (mt-10) REVERT: E 192 ARG cc_start: 0.8053 (ttt180) cc_final: 0.7811 (ttm-80) REVERT: E 201 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8490 (mmtm) REVERT: F 78 GLN cc_start: 0.7962 (mt0) cc_final: 0.7730 (mt0) REVERT: G 22 MET cc_start: 0.7995 (ttp) cc_final: 0.7579 (ttp) REVERT: G 83 LYS cc_start: 0.3358 (tttt) cc_final: 0.3061 (mptt) REVERT: G 107 LYS cc_start: 0.3948 (ttmm) cc_final: 0.3577 (mmtt) REVERT: H 7 ASP cc_start: 0.7746 (t0) cc_final: 0.7500 (t0) REVERT: I 70 ARG cc_start: 0.7692 (mpt180) cc_final: 0.7395 (mpt180) REVERT: I 87 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6315 (mp10) REVERT: J 49 MET cc_start: 0.8854 (mmm) cc_final: 0.8563 (mmm) REVERT: K 79 GLU cc_start: 0.7705 (tt0) cc_final: 0.6975 (mp0) REVERT: K 84 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8289 (mtmm) REVERT: K 110 ASN cc_start: 0.8763 (m-40) cc_final: 0.8556 (m110) REVERT: L 28 LYS cc_start: 0.7761 (mptt) cc_final: 0.7127 (mtmp) REVERT: L 36 SER cc_start: 0.8422 (m) cc_final: 0.8008 (t) REVERT: L 54 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7694 (mtp85) REVERT: U 28 CYS cc_start: 0.1532 (OUTLIER) cc_final: 0.1045 (t) outliers start: 45 outliers final: 16 residues processed: 493 average time/residue: 0.9328 time to fit residues: 534.8231 Evaluate side-chains 470 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 449 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain U residue 28 CYS Chi-restraints excluded: chain U residue 78 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 189 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 234 optimal weight: 0.5980 chunk 352 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 381 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 317 optimal weight: 0.0170 chunk 187 optimal weight: 3.9990 overall best weight: 1.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 GLN A 706 HIS A 965 GLN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 ASN B1178 ASN E 63 ASN G 71 ASN ** L 53 HIS ** 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 = 0.4218 r_free = 0.4218 target = 0.196488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124663 restraints weight = 23960.306| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.34 r_work: 0.3218 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 34508 Z= 0.156 Angle : 0.595 14.533 47015 Z= 0.324 Chirality : 0.045 0.276 5286 Planarity : 0.005 0.067 5733 Dihedral : 16.461 159.668 5429 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 1.46 % Allowed : 8.64 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.80 (0.13), residues: 3927 helix: 1.47 (0.14), residues: 1381 sheet: 0.38 (0.21), residues: 616 loop : -0.01 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 77 TYR 0.020 0.002 TYR B 486 PHE 0.030 0.002 PHE A 219 TRP 0.015 0.002 TRP B 31 HIS 0.009 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (34474) covalent geometry : angle 0.58482 / 0.32 (46966) SS BOND : bond 0.00621 / 0.39 ( 2) SS BOND : angle 2.10983 / 0.83 ( 4) hydrogen bonds : bond 0.05025 / 3.37 ( 1512) hydrogen bonds : angle 4.87940 / 3.50 ( 4166) metal coordination : bond 0.00547 / 0.32 ( 32) metal coordination : angle 3.53205 / 2.43 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 454 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7329 (mp0) cc_final: 0.6968 (mp0) REVERT: A 141 LEU cc_start: 0.8345 (mt) cc_final: 0.8106 (mp) REVERT: A 277 GLU cc_start: 0.7552 (tt0) cc_final: 0.7242 (mt-10) REVERT: A 291 GLU cc_start: 0.7209 (tt0) cc_final: 0.6810 (pp20) REVERT: A 293 GLU cc_start: 0.7742 (tt0) cc_final: 0.6821 (tp30) REVERT: A 383 TYR cc_start: 0.8370 (m-80) cc_final: 0.8047 (m-80) REVERT: A 678 GLU cc_start: 0.7337 (tt0) cc_final: 0.7071 (mt-10) REVERT: A 695 LYS cc_start: 0.7891 (mmtm) cc_final: 0.7595 (mptm) REVERT: A 771 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7876 (mm-30) REVERT: A 822 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: A 900 ASP cc_start: 0.7402 (t0) cc_final: 0.7136 (t0) REVERT: A 915 SER cc_start: 0.7520 (p) cc_final: 0.7206 (t) REVERT: A 934 LYS cc_start: 0.8360 (tttm) cc_final: 0.7940 (mttp) REVERT: A 938 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8215 (tttp) REVERT: A 1005 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7685 (mp0) REVERT: A 1112 LYS cc_start: 0.7814 (mptt) cc_final: 0.7420 (mtmm) REVERT: A 1138 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7692 (mt) REVERT: A 1297 GLU cc_start: 0.8283 (pm20) cc_final: 0.7730 (pm20) REVERT: A 1300 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7876 (mttm) REVERT: A 1317 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8177 (ttp) REVERT: A 1363 VAL cc_start: 0.9050 (t) cc_final: 0.8798 (p) REVERT: A 1391 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7808 (mmt-90) REVERT: B 115 GLN cc_start: 0.8586 (pp30) cc_final: 0.8054 (tp40) REVERT: B 133 LYS cc_start: 0.7036 (mtpt) cc_final: 0.6460 (ttpp) REVERT: B 193 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8246 (mmtt) REVERT: B 241 ARG cc_start: 0.7022 (mtm180) cc_final: 0.6753 (mtp85) REVERT: B 393 LYS cc_start: 0.7464 (mtpt) cc_final: 0.6962 (mptt) REVERT: B 422 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7908 (mttm) REVERT: B 432 MET cc_start: 0.6735 (ttp) cc_final: 0.6423 (mtp) REVERT: B 510 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7569 (tptt) REVERT: B 531 GLN cc_start: 0.7750 (tt0) cc_final: 0.7292 (tm-30) REVERT: B 552 MET cc_start: 0.7974 (mmm) cc_final: 0.7483 (tpp) REVERT: B 619 ILE cc_start: 0.8180 (mm) cc_final: 0.7916 (mm) REVERT: B 908 GLU cc_start: 0.7090 (mp0) cc_final: 0.6533 (mm-30) REVERT: B 948 ILE cc_start: 0.8876 (mp) cc_final: 0.8648 (tt) REVERT: B 1057 LYS cc_start: 0.8707 (mttt) cc_final: 0.8422 (mmtm) REVERT: B 1181 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: C 15 LYS cc_start: 0.7450 (ptmm) cc_final: 0.7138 (tttm) REVERT: C 78 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7447 (mp0) REVERT: E 43 LYS cc_start: 0.7271 (mtmt) cc_final: 0.7003 (mtpm) REVERT: E 69 ILE cc_start: 0.7878 (mm) cc_final: 0.7606 (mm) REVERT: E 93 MET cc_start: 0.7012 (tpp) cc_final: 0.6752 (tpp) REVERT: E 172 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8378 (mt-10) REVERT: E 192 ARG cc_start: 0.8085 (ttt180) cc_final: 0.7874 (ttm-80) REVERT: E 201 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8512 (mmtt) REVERT: F 78 GLN cc_start: 0.7958 (mt0) cc_final: 0.7711 (mt0) REVERT: G 22 MET cc_start: 0.7990 (ttp) cc_final: 0.7586 (ttp) REVERT: G 83 LYS cc_start: 0.3441 (tttt) cc_final: 0.3124 (mptt) REVERT: G 107 LYS cc_start: 0.3918 (ttmm) cc_final: 0.3615 (mmtt) REVERT: H 7 ASP cc_start: 0.7762 (t0) cc_final: 0.7529 (t0) REVERT: I 70 ARG cc_start: 0.7678 (mpt180) cc_final: 0.7373 (mpt180) REVERT: I 87 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.6224 (mp10) REVERT: K 79 GLU cc_start: 0.7706 (tt0) cc_final: 0.6971 (mp0) REVERT: K 84 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8312 (mtmm) REVERT: L 28 LYS cc_start: 0.7794 (mptt) cc_final: 0.7190 (mtmp) REVERT: L 36 SER cc_start: 0.8411 (m) cc_final: 0.7978 (t) REVERT: L 54 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7692 (mtp85) outliers start: 51 outliers final: 20 residues processed: 480 average time/residue: 0.9449 time to fit residues: 526.2606 Evaluate side-chains 477 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 448 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1300 LYS Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1391 ARG Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain U residue 78 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 205 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 170 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 312 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 372 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 18 GLN A 64 ASN A 390 GLN A 706 HIS A 965 GLN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 ASN B1178 ASN E 63 ASN G 71 ASN K 110 ASN L 53 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.194960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122337 restraints weight = 23692.578| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.32 r_work: 0.3186 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 34508 Z= 0.228 Angle : 0.701 15.385 47015 Z= 0.380 Chirality : 0.050 0.323 5286 Planarity : 0.006 0.100 5733 Dihedral : 16.562 160.669 5429 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 1.40 % Allowed : 9.27 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.59 (0.13), residues: 3927 helix: 1.19 (0.14), residues: 1385 sheet: 0.31 (0.20), residues: 615 loop : -0.07 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 344 TYR 0.022 0.003 TYR B 486 PHE 0.033 0.003 PHE A 219 TRP 0.020 0.003 TRP B 31 HIS 0.012 0.002 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (34474) covalent geometry : angle 0.68923 / 0.38 (46966) SS BOND : bond 0.00354 / 0.22 ( 2) SS BOND : angle 2.56852 / 1.07 ( 4) hydrogen bonds : bond 0.05986 / 4.03 ( 1512) hydrogen bonds : angle 5.14131 / 3.69 ( 4166) metal coordination : bond 0.00794 / 0.47 ( 32) metal coordination : angle 4.05576 / 2.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 454 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.7823 (t0) cc_final: 0.7557 (p0) REVERT: A 108 MET cc_start: 0.8083 (mmm) cc_final: 0.7523 (mmm) REVERT: A 141 LEU cc_start: 0.8365 (mt) cc_final: 0.8119 (mp) REVERT: A 277 GLU cc_start: 0.7588 (tt0) cc_final: 0.7366 (mt-10) REVERT: A 291 GLU cc_start: 0.7263 (tt0) cc_final: 0.6907 (pp20) REVERT: A 470 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8296 (pt) REVERT: A 678 GLU cc_start: 0.7341 (tt0) cc_final: 0.7057 (mt-10) REVERT: A 695 LYS cc_start: 0.7913 (mmtm) cc_final: 0.7647 (mptm) REVERT: A 771 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8035 (mm-30) REVERT: A 900 ASP cc_start: 0.7471 (t0) cc_final: 0.7223 (t0) REVERT: A 915 SER cc_start: 0.7531 (p) cc_final: 0.7197 (t) REVERT: A 934 LYS cc_start: 0.8398 (tttm) cc_final: 0.7933 (mttp) REVERT: A 938 LYS cc_start: 0.8452 (ttmt) cc_final: 0.8207 (tttp) REVERT: A 1005 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7680 (mp0) REVERT: A 1112 LYS cc_start: 0.7836 (mptt) cc_final: 0.7443 (mtmm) REVERT: A 1138 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7707 (mt) REVERT: A 1297 GLU cc_start: 0.8300 (pm20) cc_final: 0.7792 (pm20) REVERT: A 1300 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7880 (mttm) REVERT: A 1363 VAL cc_start: 0.9078 (t) cc_final: 0.8841 (p) REVERT: A 1391 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8046 (mmt-90) REVERT: B 103 ASN cc_start: 0.7676 (p0) cc_final: 0.7269 (m-40) REVERT: B 115 GLN cc_start: 0.8679 (pp30) cc_final: 0.8153 (tp40) REVERT: B 133 LYS cc_start: 0.7029 (mtpt) cc_final: 0.6391 (ttpp) REVERT: B 193 LYS cc_start: 0.8647 (mmtp) cc_final: 0.8241 (mmtt) REVERT: B 241 ARG cc_start: 0.7022 (mtm180) cc_final: 0.6788 (mtp85) REVERT: B 393 LYS cc_start: 0.7486 (mtpt) cc_final: 0.6999 (mptt) REVERT: B 432 MET cc_start: 0.6730 (ttp) cc_final: 0.6378 (mtp) REVERT: B 510 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7595 (tptt) REVERT: B 531 GLN cc_start: 0.7746 (tt0) cc_final: 0.7296 (tm-30) REVERT: B 552 MET cc_start: 0.8010 (mmm) cc_final: 0.7601 (tpt) REVERT: B 619 ILE cc_start: 0.8197 (mm) cc_final: 0.7983 (mm) REVERT: B 908 GLU cc_start: 0.7148 (mp0) cc_final: 0.6817 (mt-10) REVERT: B 948 ILE cc_start: 0.8896 (mp) cc_final: 0.8623 (tt) REVERT: B 1057 LYS cc_start: 0.8747 (mttt) cc_final: 0.8423 (mmtm) REVERT: B 1181 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: B 1190 ASP cc_start: 0.8143 (t0) cc_final: 0.7906 (t70) REVERT: C 78 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7472 (mp0) REVERT: E 69 ILE cc_start: 0.7879 (mm) cc_final: 0.7619 (mm) REVERT: E 93 MET cc_start: 0.6957 (tpp) cc_final: 0.6634 (tpp) REVERT: E 172 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8403 (mt-10) REVERT: E 192 ARG cc_start: 0.8203 (ttt180) cc_final: 0.7969 (ttm-80) REVERT: E 201 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8530 (mmtt) REVERT: F 78 GLN cc_start: 0.7978 (mt0) cc_final: 0.7730 (mt0) REVERT: G 22 MET cc_start: 0.7983 (ttp) cc_final: 0.7570 (ttp) REVERT: G 83 LYS cc_start: 0.3655 (tttt) cc_final: 0.3278 (mptt) REVERT: G 107 LYS cc_start: 0.3856 (ttmm) cc_final: 0.3543 (mmtt) REVERT: H 7 ASP cc_start: 0.7814 (t0) cc_final: 0.7554 (t0) REVERT: I 70 ARG cc_start: 0.7667 (mpt180) cc_final: 0.7364 (mpt180) REVERT: I 73 ARG cc_start: 0.6350 (mtt180) cc_final: 0.6081 (mtm180) REVERT: I 87 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6229 (mp10) REVERT: I 93 LYS cc_start: 0.6366 (mppt) cc_final: 0.5902 (mptp) REVERT: L 28 LYS cc_start: 0.7868 (mptt) cc_final: 0.7216 (mtmp) REVERT: L 36 SER cc_start: 0.8393 (m) cc_final: 0.7842 (t) REVERT: L 54 ARG cc_start: 0.8125 (mtt-85) cc_final: 0.7714 (mtp85) outliers start: 49 outliers final: 25 residues processed: 480 average time/residue: 0.8923 time to fit residues: 496.1374 Evaluate side-chains 473 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 441 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1300 LYS Chi-restraints excluded: chain A residue 1391 ARG Chi-restraints excluded: chain A residue 1449 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 444 MET Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 80 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 126 optimal weight: 2.9990 chunk 139 optimal weight: 0.0030 chunk 219 optimal weight: 0.6980 chunk 12 optimal weight: 0.0040 chunk 356 optimal weight: 0.3980 chunk 103 optimal weight: 6.9990 chunk 337 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 52 optimal weight: 0.0870 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 390 GLN A 965 GLN A1048 ASN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 ASN B1093 GLN E 63 ASN G 71 ASN K 110 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.199384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128005 restraints weight = 24364.862| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.48 r_work: 0.3296 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34508 Z= 0.111 Angle : 0.532 12.175 47015 Z= 0.291 Chirality : 0.043 0.289 5286 Planarity : 0.004 0.043 5733 Dihedral : 16.401 160.875 5429 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.53 % Rotamer: Outliers : 0.97 % Allowed : 10.24 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.88 (0.14), residues: 3927 helix: 1.60 (0.14), residues: 1373 sheet: 0.33 (0.20), residues: 629 loop : 0.01 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 320 TYR 0.017 0.001 TYR E 112 PHE 0.027 0.001 PHE A 219 TRP 0.017 0.001 TRP C 192 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (34474) covalent geometry : angle 0.52339 / 0.29 (46966) SS BOND : bond 0.00952 / 0.59 ( 2) SS BOND : angle 2.63763 / 1.18 ( 4) hydrogen bonds : bond 0.03895 / 2.60 ( 1512) hydrogen bonds : angle 4.60123 / 3.31 ( 4166) metal coordination : bond 0.00434 / 0.26 ( 32) metal coordination : angle 3.01586 / 2.08 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 462 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8083 (tt0) cc_final: 0.7865 (tt0) REVERT: A 39 GLU cc_start: 0.7355 (mp0) cc_final: 0.6981 (mp0) REVERT: A 108 MET cc_start: 0.8007 (mmm) cc_final: 0.7587 (mmm) REVERT: A 141 LEU cc_start: 0.8348 (mt) cc_final: 0.8116 (mp) REVERT: A 200 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6662 (ttm170) REVERT: A 277 GLU cc_start: 0.7529 (tt0) cc_final: 0.7271 (mt-10) REVERT: A 291 GLU cc_start: 0.7188 (tt0) cc_final: 0.6775 (pp20) REVERT: A 383 TYR cc_start: 0.8263 (m-80) cc_final: 0.7987 (m-80) REVERT: A 427 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7513 (mt0) REVERT: A 771 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7865 (mm-30) REVERT: A 822 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: A 900 ASP cc_start: 0.7431 (t0) cc_final: 0.7123 (t0) REVERT: A 915 SER cc_start: 0.7574 (p) cc_final: 0.7259 (t) REVERT: A 934 LYS cc_start: 0.8326 (tttm) cc_final: 0.7954 (mttp) REVERT: A 938 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8231 (tttp) REVERT: A 1005 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7717 (mp0) REVERT: A 1112 LYS cc_start: 0.7887 (mptt) cc_final: 0.7514 (mtmm) REVERT: A 1297 GLU cc_start: 0.8258 (pm20) cc_final: 0.7694 (pm20) REVERT: A 1300 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8070 (ttmt) REVERT: B 115 GLN cc_start: 0.8637 (pp30) cc_final: 0.8115 (tp40) REVERT: B 133 LYS cc_start: 0.7011 (mtpt) cc_final: 0.6392 (ttpp) REVERT: B 193 LYS cc_start: 0.8600 (mmtp) cc_final: 0.8206 (mmtt) REVERT: B 199 MET cc_start: 0.8368 (mtt) cc_final: 0.8153 (mtp) REVERT: B 393 LYS cc_start: 0.7234 (mtpt) cc_final: 0.6736 (mptt) REVERT: B 422 LYS cc_start: 0.8206 (mmtp) cc_final: 0.7876 (mttm) REVERT: B 432 MET cc_start: 0.6619 (ttp) cc_final: 0.6369 (mtp) REVERT: B 510 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7481 (tptt) REVERT: B 531 GLN cc_start: 0.7670 (tt0) cc_final: 0.7231 (tm-30) REVERT: B 552 MET cc_start: 0.7980 (mmm) cc_final: 0.7437 (tpp) REVERT: B 619 ILE cc_start: 0.8122 (mm) cc_final: 0.7901 (mm) REVERT: B 778 MET cc_start: 0.8760 (mtt) cc_final: 0.8529 (ttm) REVERT: B 908 GLU cc_start: 0.7054 (mp0) cc_final: 0.6525 (mm-30) REVERT: B 1057 LYS cc_start: 0.8696 (mttt) cc_final: 0.8432 (mmtm) REVERT: B 1181 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: C 15 LYS cc_start: 0.7340 (ptmm) cc_final: 0.7087 (tttm) REVERT: C 78 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7453 (mp0) REVERT: D 122 GLU cc_start: 0.1782 (OUTLIER) cc_final: 0.1123 (tp30) REVERT: D 206 GLU cc_start: 0.3620 (OUTLIER) cc_final: 0.3267 (tt0) REVERT: E 43 LYS cc_start: 0.7259 (mtmt) cc_final: 0.6990 (mtpm) REVERT: E 93 MET cc_start: 0.7030 (tpp) cc_final: 0.6753 (tpp) REVERT: E 121 MET cc_start: 0.6922 (mmm) cc_final: 0.6682 (mmm) REVERT: E 172 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8365 (mt-10) REVERT: E 192 ARG cc_start: 0.8117 (ttt180) cc_final: 0.7892 (ttm-80) REVERT: E 201 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8506 (mmtt) REVERT: F 78 GLN cc_start: 0.7877 (mt0) cc_final: 0.7632 (mt0) REVERT: G 22 MET cc_start: 0.7984 (ttp) cc_final: 0.7510 (ttp) REVERT: G 83 LYS cc_start: 0.3491 (tttt) cc_final: 0.3133 (mptt) REVERT: G 107 LYS cc_start: 0.3840 (ttmm) cc_final: 0.3493 (mmtt) REVERT: H 7 ASP cc_start: 0.7728 (t0) cc_final: 0.7482 (t0) REVERT: I 87 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6319 (mp10) REVERT: I 93 LYS cc_start: 0.6333 (mppt) cc_final: 0.5917 (ptmt) REVERT: K 20 LYS cc_start: 0.8355 (tmmt) cc_final: 0.8025 (ttmt) REVERT: L 28 LYS cc_start: 0.7786 (mptt) cc_final: 0.7180 (mtmp) REVERT: L 36 SER cc_start: 0.8412 (m) cc_final: 0.8009 (t) REVERT: L 54 ARG cc_start: 0.8068 (mtt-85) cc_final: 0.7704 (mtp85) outliers start: 34 outliers final: 12 residues processed: 479 average time/residue: 0.8903 time to fit residues: 493.5204 Evaluate side-chains 469 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 448 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1300 LYS Chi-restraints excluded: chain A residue 1449 SER Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain U residue 78 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 315 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 331 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 343 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 318 optimal weight: 0.8980 chunk 196 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 390 GLN A 965 GLN A1128 GLN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 ASN B1178 ASN G 71 ASN K 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.196102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127382 restraints weight = 23791.509| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.21 r_work: 0.3204 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 34508 Z= 0.157 Angle : 0.599 14.953 47015 Z= 0.326 Chirality : 0.046 0.279 5286 Planarity : 0.005 0.068 5733 Dihedral : 16.456 161.344 5429 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.67 % Favored : 97.28 % Rotamer: Outliers : 1.00 % Allowed : 10.47 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.86 (0.13), residues: 3927 helix: 1.53 (0.14), residues: 1375 sheet: 0.37 (0.20), residues: 623 loop : 0.02 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 77 TYR 0.021 0.002 TYR B 486 PHE 0.030 0.002 PHE A 219 TRP 0.015 0.002 TRP C 192 HIS 0.009 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (34474) covalent geometry : angle 0.58862 / 0.32 (46966) SS BOND : bond 0.00258 / 0.16 ( 2) SS BOND : angle 2.79884 / 1.24 ( 4) hydrogen bonds : bond 0.04975 / 3.35 ( 1512) hydrogen bonds : angle 4.81149 / 3.46 ( 4166) metal coordination : bond 0.00519 / 0.31 ( 32) metal coordination : angle 3.53122 / 2.43 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 450 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8103 (tt0) cc_final: 0.7877 (tt0) REVERT: A 108 MET cc_start: 0.8099 (mmm) cc_final: 0.7715 (mmm) REVERT: A 141 LEU cc_start: 0.8341 (mt) cc_final: 0.8104 (mp) REVERT: A 277 GLU cc_start: 0.7542 (tt0) cc_final: 0.7244 (mt-10) REVERT: A 291 GLU cc_start: 0.7240 (tt0) cc_final: 0.6845 (pp20) REVERT: A 320 ARG cc_start: 0.7121 (ttp80) cc_final: 0.6841 (ttp80) REVERT: A 383 TYR cc_start: 0.8296 (m-80) cc_final: 0.8064 (m-80) REVERT: A 470 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8313 (pt) REVERT: A 771 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7833 (mm-30) REVERT: A 822 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: A 900 ASP cc_start: 0.7441 (t0) cc_final: 0.7203 (t0) REVERT: A 915 SER cc_start: 0.7544 (p) cc_final: 0.7200 (t) REVERT: A 934 LYS cc_start: 0.8341 (tttm) cc_final: 0.7892 (mttp) REVERT: A 938 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8179 (tttp) REVERT: A 1005 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7613 (mp0) REVERT: A 1048 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8297 (t0) REVERT: A 1112 LYS cc_start: 0.7909 (mptt) cc_final: 0.7481 (mtmm) REVERT: A 1297 GLU cc_start: 0.8275 (pm20) cc_final: 0.7705 (pm20) REVERT: A 1300 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7960 (ttpp) REVERT: A 1363 VAL cc_start: 0.9044 (t) cc_final: 0.8765 (p) REVERT: A 1391 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7701 (mmt-90) REVERT: B 115 GLN cc_start: 0.8622 (pp30) cc_final: 0.8029 (tp40) REVERT: B 133 LYS cc_start: 0.7059 (mtpt) cc_final: 0.6472 (ttpp) REVERT: B 193 LYS cc_start: 0.8592 (mmtp) cc_final: 0.8159 (mmtt) REVERT: B 325 GLN cc_start: 0.6202 (OUTLIER) cc_final: 0.5689 (mt0) REVERT: B 393 LYS cc_start: 0.7247 (mtpt) cc_final: 0.6741 (mptt) REVERT: B 422 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7958 (mttp) REVERT: B 432 MET cc_start: 0.6677 (ttp) cc_final: 0.6377 (mtp) REVERT: B 510 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7425 (tptt) REVERT: B 531 GLN cc_start: 0.7679 (tt0) cc_final: 0.7183 (tm-30) REVERT: B 552 MET cc_start: 0.7970 (mmm) cc_final: 0.7494 (tpp) REVERT: B 619 ILE cc_start: 0.8136 (mm) cc_final: 0.7920 (mm) REVERT: B 1057 LYS cc_start: 0.8715 (mttt) cc_final: 0.8373 (mmtm) REVERT: B 1181 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: C 78 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7414 (mp0) REVERT: C 102 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: D 122 GLU cc_start: 0.1909 (OUTLIER) cc_final: 0.1081 (tp30) REVERT: E 43 LYS cc_start: 0.7222 (mtmt) cc_final: 0.6973 (mtpm) REVERT: E 93 MET cc_start: 0.6933 (tpp) cc_final: 0.6636 (tpp) REVERT: E 121 MET cc_start: 0.6899 (mmm) cc_final: 0.6621 (mmm) REVERT: E 172 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8348 (mt-10) REVERT: E 192 ARG cc_start: 0.8051 (ttt180) cc_final: 0.7808 (ttm-80) REVERT: E 201 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8492 (mmtt) REVERT: F 78 GLN cc_start: 0.7954 (mt0) cc_final: 0.7699 (mt0) REVERT: G 22 MET cc_start: 0.7971 (ttp) cc_final: 0.7431 (ttp) REVERT: G 107 LYS cc_start: 0.3883 (ttmm) cc_final: 0.3569 (mmtt) REVERT: H 7 ASP cc_start: 0.7800 (t0) cc_final: 0.7528 (t0) REVERT: I 87 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.6216 (mp10) REVERT: I 93 LYS cc_start: 0.6324 (mppt) cc_final: 0.5918 (ptmt) REVERT: K 20 LYS cc_start: 0.8444 (tmmt) cc_final: 0.8138 (ttmt) REVERT: L 28 LYS cc_start: 0.7797 (mptt) cc_final: 0.7189 (mtmp) REVERT: L 36 SER cc_start: 0.8421 (m) cc_final: 0.7917 (t) REVERT: L 54 ARG cc_start: 0.8108 (mtt-85) cc_final: 0.7723 (mtp85) outliers start: 35 outliers final: 16 residues processed: 469 average time/residue: 0.9515 time to fit residues: 517.8066 Evaluate side-chains 479 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 451 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1300 LYS Chi-restraints excluded: chain A residue 1391 ARG Chi-restraints excluded: chain A residue 1449 SER Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 80 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 219 optimal weight: 6.9990 chunk 334 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 47 optimal weight: 0.0870 chunk 252 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 321 optimal weight: 0.1980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 GLN A 965 GLN A1048 ASN A1052 GLN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 ASN B1178 ASN G 71 ASN I 108 HIS K 110 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.198654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127709 restraints weight = 24100.941| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.34 r_work: 0.3262 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 34508 Z= 0.109 Angle : 0.526 13.430 47015 Z= 0.287 Chirality : 0.043 0.282 5286 Planarity : 0.004 0.041 5733 Dihedral : 16.377 161.614 5429 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 0.97 % Allowed : 10.64 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.95 (0.14), residues: 3927 helix: 1.67 (0.14), residues: 1380 sheet: 0.34 (0.20), residues: 631 loop : 0.04 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 677 TYR 0.015 0.001 TYR B 486 PHE 0.027 0.001 PHE A 219 TRP 0.014 0.001 TRP C 192 HIS 0.006 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (34474) covalent geometry : angle 0.51737 / 0.29 (46966) SS BOND : bond 0.00119 / 0.07 ( 2) SS BOND : angle 3.35043 / 1.49 ( 4) hydrogen bonds : bond 0.03951 / 2.64 ( 1512) hydrogen bonds : angle 4.55411 / 3.28 ( 4166) metal coordination : bond 0.00379 / 0.23 ( 32) metal coordination : angle 3.04168 / 2.14 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 452 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8004 (mmm) cc_final: 0.7629 (mmm) REVERT: A 141 LEU cc_start: 0.8381 (mt) cc_final: 0.8144 (mp) REVERT: A 277 GLU cc_start: 0.7532 (tt0) cc_final: 0.7260 (mt-10) REVERT: A 291 GLU cc_start: 0.7243 (tt0) cc_final: 0.6824 (pp20) REVERT: A 383 TYR cc_start: 0.8287 (m-80) cc_final: 0.7989 (m-80) REVERT: A 427 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: A 771 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7911 (mm-30) REVERT: A 822 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: A 900 ASP cc_start: 0.7426 (t0) cc_final: 0.7179 (t0) REVERT: A 915 SER cc_start: 0.7552 (p) cc_final: 0.7180 (t) REVERT: A 934 LYS cc_start: 0.8377 (tttm) cc_final: 0.8041 (mttp) REVERT: A 938 LYS cc_start: 0.8478 (ttmt) cc_final: 0.8276 (tttp) REVERT: A 1005 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7737 (mp0) REVERT: A 1048 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8369 (t0) REVERT: A 1112 LYS cc_start: 0.7865 (mptt) cc_final: 0.7481 (mtmm) REVERT: A 1138 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7772 (mt) REVERT: A 1297 GLU cc_start: 0.8282 (pm20) cc_final: 0.7734 (pm20) REVERT: A 1300 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8080 (ttmt) REVERT: B 115 GLN cc_start: 0.8661 (pp30) cc_final: 0.8249 (tp40) REVERT: B 133 LYS cc_start: 0.7079 (mtpt) cc_final: 0.6549 (ttpp) REVERT: B 193 LYS cc_start: 0.8654 (mmtp) cc_final: 0.8258 (mmtt) REVERT: B 199 MET cc_start: 0.8434 (mtt) cc_final: 0.8215 (mtp) REVERT: B 325 GLN cc_start: 0.6228 (OUTLIER) cc_final: 0.5720 (mt0) REVERT: B 393 LYS cc_start: 0.7330 (mtpt) cc_final: 0.6835 (mptt) REVERT: B 422 LYS cc_start: 0.8258 (mmtp) cc_final: 0.7938 (mttm) REVERT: B 432 MET cc_start: 0.6731 (ttp) cc_final: 0.6486 (mtp) REVERT: B 510 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7511 (tptp) REVERT: B 531 GLN cc_start: 0.7709 (tt0) cc_final: 0.7297 (tm-30) REVERT: B 552 MET cc_start: 0.8030 (mmm) cc_final: 0.7537 (tpp) REVERT: B 619 ILE cc_start: 0.8120 (mm) cc_final: 0.7900 (mm) REVERT: B 662 MET cc_start: 0.8069 (mtm) cc_final: 0.7606 (mmm) REVERT: B 908 GLU cc_start: 0.7108 (mp0) cc_final: 0.6527 (mm-30) REVERT: B 1057 LYS cc_start: 0.8782 (mttt) cc_final: 0.8536 (mmtm) REVERT: B 1181 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: C 15 LYS cc_start: 0.7390 (ptmm) cc_final: 0.7135 (tttm) REVERT: C 78 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7535 (mp0) REVERT: D 122 GLU cc_start: 0.1871 (OUTLIER) cc_final: 0.1061 (tp30) REVERT: D 206 GLU cc_start: 0.3666 (OUTLIER) cc_final: 0.3282 (tt0) REVERT: E 43 LYS cc_start: 0.7280 (mtmt) cc_final: 0.7042 (mtpm) REVERT: E 93 MET cc_start: 0.6917 (tpp) cc_final: 0.6630 (tpp) REVERT: E 121 MET cc_start: 0.6915 (mmm) cc_final: 0.6659 (mmm) REVERT: E 172 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8409 (mt-10) REVERT: E 192 ARG cc_start: 0.8061 (ttt180) cc_final: 0.7856 (ttm-80) REVERT: E 201 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8547 (mmtt) REVERT: F 78 GLN cc_start: 0.7967 (mt0) cc_final: 0.7740 (mt0) REVERT: G 22 MET cc_start: 0.7967 (ttp) cc_final: 0.7546 (ttp) REVERT: G 107 LYS cc_start: 0.3906 (ttmm) cc_final: 0.3546 (mmtt) REVERT: I 87 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6273 (mp10) REVERT: K 20 LYS cc_start: 0.8398 (tmmt) cc_final: 0.8115 (ttmt) REVERT: K 84 LYS cc_start: 0.8603 (mtpm) cc_final: 0.8336 (mtmm) REVERT: L 28 LYS cc_start: 0.7810 (mptt) cc_final: 0.7197 (mtmp) REVERT: L 36 SER cc_start: 0.8415 (m) cc_final: 0.8016 (t) REVERT: L 54 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7774 (mtp85) outliers start: 34 outliers final: 16 residues processed: 472 average time/residue: 0.9193 time to fit residues: 504.1081 Evaluate side-chains 471 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 444 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1300 LYS Chi-restraints excluded: chain A residue 1449 SER Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 310 optimal weight: 0.1980 chunk 288 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 399 optimal weight: 0.0980 chunk 208 optimal weight: 0.5980 chunk 225 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 GLN A 965 GLN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 ASN B1178 ASN G 71 ASN K 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.196575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127210 restraints weight = 23924.731| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.27 r_work: 0.3212 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 34508 Z= 0.148 Angle : 0.585 14.746 47015 Z= 0.318 Chirality : 0.045 0.279 5286 Planarity : 0.005 0.060 5733 Dihedral : 16.425 161.973 5429 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.30 % Rotamer: Outliers : 0.91 % Allowed : 10.93 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.89 (0.13), residues: 3927 helix: 1.56 (0.14), residues: 1382 sheet: 0.40 (0.20), residues: 623 loop : 0.03 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 77 TYR 0.021 0.002 TYR B 486 PHE 0.030 0.002 PHE A 219 TRP 0.015 0.002 TRP B 31 HIS 0.008 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (34474) covalent geometry : angle 0.57480 / 0.32 (46966) SS BOND : bond 0.00142 / 0.09 ( 2) SS BOND : angle 3.22628 / 1.44 ( 4) hydrogen bonds : bond 0.04776 / 3.21 ( 1512) hydrogen bonds : angle 4.72923 / 3.40 ( 4166) metal coordination : bond 0.00491 / 0.30 ( 32) metal coordination : angle 3.42443 / 2.37 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 445 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8046 (mmm) cc_final: 0.7658 (mmm) REVERT: A 141 LEU cc_start: 0.8340 (mt) cc_final: 0.8098 (mp) REVERT: A 277 GLU cc_start: 0.7515 (tt0) cc_final: 0.7208 (mt-10) REVERT: A 291 GLU cc_start: 0.7188 (tt0) cc_final: 0.6807 (pp20) REVERT: A 320 ARG cc_start: 0.7151 (ttp80) cc_final: 0.6878 (ttp80) REVERT: A 383 TYR cc_start: 0.8300 (m-80) cc_final: 0.7999 (m-80) REVERT: A 427 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: A 677 ARG cc_start: 0.6895 (ttp80) cc_final: 0.6649 (ttp-110) REVERT: A 691 LEU cc_start: 0.8619 (tp) cc_final: 0.8162 (tm) REVERT: A 771 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7853 (mm-30) REVERT: A 822 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: A 900 ASP cc_start: 0.7410 (t0) cc_final: 0.7156 (t0) REVERT: A 915 SER cc_start: 0.7593 (p) cc_final: 0.7202 (t) REVERT: A 934 LYS cc_start: 0.8335 (tttm) cc_final: 0.7912 (mttp) REVERT: A 938 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8195 (tttp) REVERT: A 1005 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7640 (mp0) REVERT: A 1048 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8359 (t0) REVERT: A 1112 LYS cc_start: 0.7915 (mptt) cc_final: 0.7513 (mtmm) REVERT: A 1138 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7701 (mt) REVERT: A 1297 GLU cc_start: 0.8295 (pm20) cc_final: 0.7733 (pm20) REVERT: A 1300 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7916 (ttpp) REVERT: B 115 GLN cc_start: 0.8638 (pp30) cc_final: 0.8061 (tp40) REVERT: B 133 LYS cc_start: 0.7080 (mtpt) cc_final: 0.6536 (ttpp) REVERT: B 193 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8158 (mmtt) REVERT: B 199 MET cc_start: 0.8421 (mtt) cc_final: 0.8178 (mtp) REVERT: B 325 GLN cc_start: 0.6207 (OUTLIER) cc_final: 0.5666 (mt0) REVERT: B 393 LYS cc_start: 0.7287 (mtpt) cc_final: 0.6790 (mptt) REVERT: B 422 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7954 (mttp) REVERT: B 432 MET cc_start: 0.6725 (ttp) cc_final: 0.6454 (mtp) REVERT: B 510 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7429 (tptt) REVERT: B 531 GLN cc_start: 0.7671 (tt0) cc_final: 0.7207 (tm-30) REVERT: B 552 MET cc_start: 0.7966 (mmm) cc_final: 0.7498 (tpp) REVERT: B 619 ILE cc_start: 0.8120 (mm) cc_final: 0.7899 (mm) REVERT: B 908 GLU cc_start: 0.7098 (mp0) cc_final: 0.6495 (mm-30) REVERT: B 1057 LYS cc_start: 0.8732 (mttt) cc_final: 0.8394 (mmtm) REVERT: B 1181 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: C 78 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7429 (mp0) REVERT: D 122 GLU cc_start: 0.1892 (OUTLIER) cc_final: 0.1065 (tp30) REVERT: D 206 GLU cc_start: 0.3681 (OUTLIER) cc_final: 0.3299 (tt0) REVERT: E 43 LYS cc_start: 0.7262 (mtmt) cc_final: 0.7019 (mtpm) REVERT: E 63 ASN cc_start: 0.8380 (m-40) cc_final: 0.8083 (m-40) REVERT: E 93 MET cc_start: 0.6941 (tpp) cc_final: 0.6648 (tpp) REVERT: E 121 MET cc_start: 0.6897 (mmm) cc_final: 0.6637 (mmm) REVERT: E 172 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8374 (mt-10) REVERT: E 192 ARG cc_start: 0.8091 (ttt180) cc_final: 0.7839 (ttm-80) REVERT: E 201 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8489 (mmtt) REVERT: F 78 GLN cc_start: 0.7963 (mt0) cc_final: 0.7725 (mt0) REVERT: G 22 MET cc_start: 0.7964 (ttp) cc_final: 0.7494 (ttp) REVERT: G 107 LYS cc_start: 0.3890 (ttmm) cc_final: 0.3523 (mmtt) REVERT: I 87 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6201 (mp10) REVERT: K 20 LYS cc_start: 0.8451 (tmmt) cc_final: 0.8146 (ttmt) REVERT: L 28 LYS cc_start: 0.7794 (mptt) cc_final: 0.7169 (mtmp) REVERT: L 36 SER cc_start: 0.8387 (m) cc_final: 0.7960 (t) REVERT: L 54 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7725 (mtp85) outliers start: 32 outliers final: 16 residues processed: 462 average time/residue: 0.8768 time to fit residues: 469.9599 Evaluate side-chains 473 residues out of total 3505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 445 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1300 LYS Chi-restraints excluded: chain A residue 1449 SER Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 167 optimal weight: 2.9990 chunk 370 optimal weight: 0.7980 chunk 345 optimal weight: 10.0000 chunk 379 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 394 optimal weight: 10.0000 chunk 304 optimal weight: 0.0040 chunk 112 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 overall best weight: 2.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 390 GLN A 706 HIS A 965 GLN A1048 ASN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 ASN B1178 ASN G 71 ASN K 110 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.195034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122590 restraints weight = 23671.595| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.53 r_work: 0.3195 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 34508 Z= 0.200 Angle : 0.667 15.308 47015 Z= 0.361 Chirality : 0.048 0.318 5286 Planarity : 0.006 0.096 5733 Dihedral : 16.514 162.675 5429 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 1.00 % Allowed : 10.73 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.68 (0.13), residues: 3927 helix: 1.31 (0.14), residues: 1383 sheet: 0.27 (0.20), residues: 633 loop : -0.03 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 344 TYR 0.022 0.003 TYR B 486 PHE 0.032 0.002 PHE A 219 TRP 0.018 0.002 TRP B 31 HIS 0.011 0.002 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (34474) covalent geometry : angle 0.65527 / 0.36 (46966) SS BOND : bond 0.00167 / 0.10 ( 2) SS BOND : angle 3.29746 / 1.47 ( 4) hydrogen bonds : bond 0.05603 / 3.77 ( 1512) hydrogen bonds : angle 4.97995 / 3.57 ( 4166) metal coordination : bond 0.00699 / 0.42 ( 32) metal coordination : angle 3.89290 / 2.66 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24747.79 seconds wall clock time: 419 minutes 0.58 seconds (25140.58 seconds total)