Starting phenix.real_space_refine on Wed Oct 28 23:00:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28jc_56542/10_2026/28jc_56542.cif Found real_map, /net/cci-nas-00/data/ceres_data/28jc_56542/10_2026/28jc_56542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28jc_56542/10_2026/28jc_56542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28jc_56542/10_2026/28jc_56542.map" model { file = "/net/cci-nas-00/data/ceres_data/28jc_56542/10_2026/28jc_56542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28jc_56542/10_2026/28jc_56542.cif" } resolution = 2.94 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= 0.002 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 169 5.16 5 C 18654 2.51 5 N 5114 2.21 5 O 5549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29492 Number of models: 1 Model: "" Number of chains: 19 Chain: "D" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1063 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 515 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1082 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain breaks: 2 Chain: "A" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8206 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 43, 'TRANS': 985} Chain breaks: 6 Chain: "B" Number of atoms: 8128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 8128 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 48, 'TRANS': 966} Chain breaks: 3 Chain: "C" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2135 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 15, 'TRANS': 249} Chain breaks: 1 Chain: "N" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1250 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5998 SG CYS I 17 42.642 51.443 22.604 1.00108.24 S ATOM 6022 SG CYS I 20 45.957 50.006 22.946 1.00114.35 S ATOM 6183 SG CYS I 39 45.986 53.718 22.405 1.00121.08 S ATOM 6208 SG CYS I 42 44.699 51.422 19.579 1.00122.74 S ATOM 6560 SG CYS I 86 12.161 59.977 52.142 1.00 98.59 S ATOM 6584 SG CYS I 89 10.420 56.534 52.078 1.00109.13 S ATOM 6788 SG CYS I 114 13.482 57.316 54.437 1.00 82.02 S ATOM 6823 SG CYS I 119 13.478 56.679 50.583 1.00105.73 S ATOM 6933 SG CYS J 7 45.016 60.929 118.956 1.00 38.51 S ATOM 6957 SG CYS J 10 44.155 62.750 122.190 1.00 38.74 S ATOM 7221 SG CYS J 44 42.189 63.561 118.995 1.00 40.35 S ATOM 7227 SG CYS J 45 41.827 60.370 121.122 1.00 41.85 S ATOM 8355 SG CYS L 19 71.399 27.592 104.985 1.00 76.77 S ATOM 8374 SG CYS L 22 70.412 26.073 108.149 1.00 85.41 S ATOM 8491 SG CYS L 36 73.659 24.941 106.513 1.00 96.54 S ATOM 8517 SG CYS L 39 70.346 23.685 105.351 1.00 97.11 S ATOM 26796 SG CYS C 88 70.958 60.908 141.555 1.00 87.25 S ATOM 26809 SG CYS C 90 73.095 58.176 140.149 1.00113.21 S ATOM 26844 SG CYS C 94 70.261 57.075 141.811 1.00 77.75 S ATOM 26866 SG CYS C 97 69.431 58.763 138.658 1.00 70.12 S ATOM 28696 SG CYS N 100 74.650 92.408 18.000 1.00156.71 S ATOM 28733 SG CYS N 105 74.751 91.931 14.284 1.00162.73 S ATOM 28990 SG CYS N 136 71.707 93.382 16.058 1.00165.47 S ATOM 29021 SG CYS N 140 72.818 89.522 16.468 1.00164.34 S Time building chain proxies: 5.47, per 1000 atoms: 0.19 Number of scatterers: 29492 At special positions: 0 Unit cell: (169.05, 156.45, 160.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 169 16.00 O 5549 8.00 N 5114 7.00 C 18654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN N 701 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 100 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 105 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 136 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 140 " Number of angles added : 36 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6952 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 41 sheets defined 40.4% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.454A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 29' Processing helix chain 'D' and resid 33 through 51 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 117 through 121 removed outlier: 4.149A pdb=" N GLY D 120 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.660A pdb=" N GLN D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.759A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 34' Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.622A pdb=" N LEU E 58 " --> pdb=" O ARG E 55 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 55 through 59' Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 4.331A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 removed outlier: 3.848A pdb=" N ILE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 4.061A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.588A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE H 88 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 132 removed outlier: 3.608A pdb=" N ASN H 131 " --> pdb=" O ASP H 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.569A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 73 removed outlier: 3.594A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 69 through 73' Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.515A pdb=" N ALA J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA J 27 " --> pdb=" O GLY J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 4.560A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.681A pdb=" N GLU K 8 " --> pdb=" O PRO K 5 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.533A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 removed outlier: 3.630A pdb=" N ASP K 111 " --> pdb=" O VAL K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 37 removed outlier: 3.894A pdb=" N ASN M 37 " --> pdb=" O ARG M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 42 removed outlier: 3.907A pdb=" N ILE M 41 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS M 42 " --> pdb=" O GLU M 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 37 through 42' Processing helix chain 'M' and resid 48 through 73 Processing helix chain 'M' and resid 229 through 241 removed outlier: 3.607A pdb=" N ASN M 241 " --> pdb=" O MET M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 316 removed outlier: 4.329A pdb=" N ALA M 311 " --> pdb=" O GLU M 307 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN M 313 " --> pdb=" O SER M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 316 through 334 removed outlier: 3.504A pdb=" N TYR M 320 " --> pdb=" O GLN M 316 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET M 323 " --> pdb=" O ASN M 319 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA M 325 " --> pdb=" O GLU M 321 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS M 326 " --> pdb=" O GLU M 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 398 through 409 removed outlier: 4.132A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 541 through 549 Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.782A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.596A pdb=" N ASP A 614 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 4.029A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.577A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.840A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 920 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 944 removed outlier: 4.357A pdb=" N SER A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.549A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 removed outlier: 3.534A pdb=" N THR A1038 " --> pdb=" O GLN A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.808A pdb=" N SER A1147 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.667A pdb=" N ASP A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1190 through 1197 Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 4.061A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET A1296 " --> pdb=" O MET A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1347 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1407 Processing helix chain 'A' and resid 1476 through 1481 removed outlier: 3.794A pdb=" N CYS A1480 " --> pdb=" O ASP A1476 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1476 through 1481' Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.228A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.872A pdb=" N GLU B 307 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.785A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 436 through 451 removed outlier: 4.705A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 491 through 496 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.535A pdb=" N LEU B 505 " --> pdb=" O HIS B 502 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 506' Processing helix chain 'B' and resid 538 through 549 removed outlier: 3.626A pdb=" N LEU B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 556 removed outlier: 3.820A pdb=" N ILE B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.705A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 4.181A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.878A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 649 removed outlier: 3.667A pdb=" N ASN B 649 " --> pdb=" O ARG B 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 646 through 649' Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.746A pdb=" N LEU B 682 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.592A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 732 removed outlier: 3.847A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 removed outlier: 3.521A pdb=" N ILE B 972 " --> pdb=" O PRO B 969 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 969 through 972' Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.284A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1055 through 1061 Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.633A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 4.442A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 65 Processing helix chain 'N' and resid 71 through 79 removed outlier: 3.686A pdb=" N LEU N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET N 76 " --> pdb=" O GLU N 72 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU N 77 " --> pdb=" O GLU N 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS N 78 " --> pdb=" O PHE N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 97 removed outlier: 3.692A pdb=" N VAL N 91 " --> pdb=" O TYR N 87 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP N 92 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU N 93 " --> pdb=" O ASP N 89 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG N 94 " --> pdb=" O VAL N 90 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER N 95 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL N 97 " --> pdb=" O GLU N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 135 Processing helix chain 'N' and resid 137 through 151 removed outlier: 3.586A pdb=" N TYR N 141 " --> pdb=" O SER N 137 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN N 142 " --> pdb=" O ASN N 138 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA N 143 " --> pdb=" O PHE N 139 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER N 144 " --> pdb=" O CYS N 140 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN N 150 " --> pdb=" O PHE N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 194 removed outlier: 3.970A pdb=" N ILE N 194 " --> pdb=" O THR N 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.355A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL E 74 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE E 73 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.276A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 115 through 118 Processing sheet with id=AA4, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.613A pdb=" N ILE G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 7 " --> pdb=" O TYR G 72 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR G 72 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL G 70 " --> pdb=" O HIS G 9 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR G 68 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY G 43 " --> pdb=" O THR G 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.613A pdb=" N ILE G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 7 " --> pdb=" O TYR G 72 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR G 72 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL G 70 " --> pdb=" O HIS G 9 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR G 68 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 142 through 146 removed outlier: 7.755A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 117 through 119 removed outlier: 3.652A pdb=" N TYR G 128 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 15 removed outlier: 5.851A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP H 14 " --> pdb=" O HIS H 29 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP H 8 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AB1, first strand: chain 'I' and resid 52 through 57 removed outlier: 3.643A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'K' and resid 19 through 23 removed outlier: 3.637A pdb=" N THR K 34 " --> pdb=" O THR K 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 25 through 26 removed outlier: 4.079A pdb=" N TYR L 17 " --> pdb=" O ASN L 26 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 816 " --> pdb=" O CYS B 919 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.616A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 54 through 56 removed outlier: 5.797A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 455 through 458 Processing sheet with id=AB8, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.848A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AC1, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.798A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AC3, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.740A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AC5, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 4.071A pdb=" N GLN A1299 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1304 through 1307 removed outlier: 4.369A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC8, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.904A pdb=" N ILE B 65 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 86 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 67 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR B 84 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.904A pdb=" N ILE B 65 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 86 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 67 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR B 84 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AD2, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AD3, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AD4, first strand: chain 'B' and resid 205 through 209 removed outlier: 3.645A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 223 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD6, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD7, first strand: chain 'B' and resid 565 through 569 removed outlier: 3.733A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 604 through 606 Processing sheet with id=AD9, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AE1, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.520A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 826 through 829 removed outlier: 3.780A pdb=" N GLU B 826 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.687A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 113 through 116 removed outlier: 3.635A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 117 through 120 1213 hydrogen bonds defined for protein. 3390 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.73 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9746 1.34 - 1.46: 5835 1.46 - 1.58: 14192 1.58 - 1.70: 0 1.70 - 1.82: 266 Bond restraints: 30039 Sorted by residual: bond pdb=" C LYS A 581 " pdb=" N PRO A 582 " ideal model delta sigma weight residual 1.335 1.379 -0.044 1.36e-02 5.41e+03 1.03e+01 bond pdb=" CA GLU K 16 " pdb=" CB GLU K 16 " ideal model delta sigma weight residual 1.530 1.565 -0.035 1.69e-02 3.50e+03 4.23e+00 bond pdb=" N ASN N 69 " pdb=" CA ASN N 69 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.54e-02 4.22e+03 2.93e+00 bond pdb=" C TYR A 413 " pdb=" N PRO A 414 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.57e+00 bond pdb=" CB GLN J 26 " pdb=" CG GLN J 26 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.40e+00 ... (remaining 30034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 39765 2.52 - 5.03: 648 5.03 - 7.55: 114 7.55 - 10.07: 22 10.07 - 12.59: 7 Bond angle restraints: 40556 Sorted by residual: angle pdb=" N ASN B 649 " pdb=" CA ASN B 649 " pdb=" C ASN B 649 " ideal model delta sigma weight residual 114.56 105.71 8.85 1.27e+00 6.20e-01 4.85e+01 angle pdb=" CA GLU K 16 " pdb=" CB GLU K 16 " pdb=" CG GLU K 16 " ideal model delta sigma weight residual 114.10 125.52 -11.42 2.00e+00 2.50e-01 3.26e+01 angle pdb=" N VAL A1185 " pdb=" CA VAL A1185 " pdb=" C VAL A1185 " ideal model delta sigma weight residual 113.53 108.52 5.01 9.80e-01 1.04e+00 2.61e+01 angle pdb=" C GLU A1302 " pdb=" N GLN A1303 " pdb=" CA GLN A1303 " ideal model delta sigma weight residual 122.08 129.09 -7.01 1.47e+00 4.63e-01 2.27e+01 angle pdb=" N VAL N 97 " pdb=" CA VAL N 97 " pdb=" C VAL N 97 " ideal model delta sigma weight residual 111.91 108.04 3.87 8.90e-01 1.26e+00 1.89e+01 ... (remaining 40551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 16529 17.81 - 35.62: 1568 35.62 - 53.42: 276 53.42 - 71.23: 58 71.23 - 89.04: 35 Dihedral angle restraints: 18466 sinusoidal: 7745 harmonic: 10721 Sorted by residual: dihedral pdb=" CA ASN G 124 " pdb=" C ASN G 124 " pdb=" N PRO G 125 " pdb=" CA PRO G 125 " ideal model delta harmonic sigma weight residual 180.00 142.16 37.84 0 5.00e+00 4.00e-02 5.73e+01 dihedral pdb=" CA MET B 976 " pdb=" C MET B 976 " pdb=" N THR B 977 " pdb=" CA THR B 977 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA HIS A1410 " pdb=" C HIS A1410 " pdb=" N LEU A1411 " pdb=" CA LEU A1411 " ideal model delta harmonic sigma weight residual -180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 18463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3814 0.070 - 0.140: 668 0.140 - 0.210: 34 0.210 - 0.280: 9 0.280 - 0.350: 2 Chirality restraints: 4527 Sorted by residual: chirality pdb=" CB ILE H 99 " pdb=" CA ILE H 99 " pdb=" CG1 ILE H 99 " pdb=" CG2 ILE H 99 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CB ILE F 92 " pdb=" CA ILE F 92 " pdb=" CG1 ILE F 92 " pdb=" CG2 ILE F 92 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB THR A1357 " pdb=" CA THR A1357 " pdb=" OG1 THR A1357 " pdb=" CG2 THR A1357 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 4524 not shown) Planarity restraints: 5258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 15 " -0.416 9.50e-02 1.11e+02 1.86e-01 2.16e+01 pdb=" NE ARG I 15 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG I 15 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG I 15 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG I 15 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 395 " -0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 396 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 910 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO A 911 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 911 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 911 " -0.041 5.00e-02 4.00e+02 ... (remaining 5255 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8021 2.81 - 3.34: 27398 3.34 - 3.86: 49625 3.86 - 4.38: 57307 4.38 - 4.90: 98660 Nonbonded interactions: 241011 Sorted by model distance: nonbonded pdb=" OD1 ASP A 695 " pdb=" OG1 THR A 698 " model vdw 2.292 3.040 nonbonded pdb=" OD2 ASP D 16 " pdb=" OG SER D 18 " model vdw 2.307 3.040 nonbonded pdb=" O GLU B 600 " pdb=" NH2 ARG B 620 " model vdw 2.308 3.120 nonbonded pdb=" OD1 ASP H 11 " pdb=" NZ LYS H 13 " model vdw 2.320 3.120 nonbonded pdb=" OE2 GLU B 959 " pdb=" OH TYR B1020 " model vdw 2.320 3.040 ... (remaining 241006 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 28.720 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 0.053 30063 Z= 0.172 Angle : 0.824 15.065 40592 Z= 0.412 Chirality : 0.051 0.350 4527 Planarity : 0.007 0.186 5258 Dihedral : 14.587 89.037 11514 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 3616 helix: -0.34 (0.14), residues: 1287 sheet: -0.75 (0.24), residues: 504 loop : -1.08 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 122 TYR 0.046 0.002 TYR B 752 PHE 0.037 0.002 PHE N 147 TRP 0.043 0.002 TRP B 548 HIS 0.013 0.001 HIS N 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (30039) covalent geometry : angle 0.80392 / 0.41 (40556) hydrogen bonds : bond 0.17489 / 11.39 ( 1198) hydrogen bonds : angle 6.85423 / 4.88 ( 3390) metal coordination : bond 0.00754 / 0.46 ( 24) metal coordination : angle 6.18866 / 3.52 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 MET cc_start: 0.8078 (ppp) cc_final: 0.7745 (ppp) REVERT: E 121 MET cc_start: 0.7265 (ptm) cc_final: 0.7065 (ppp) REVERT: G 164 MET cc_start: 0.7281 (mpp) cc_final: 0.6969 (mpm) REVERT: I 25 TYR cc_start: 0.8577 (m-80) cc_final: 0.8247 (m-80) REVERT: L 16 ILE cc_start: 0.9318 (mm) cc_final: 0.8127 (mm) REVERT: L 47 LYS cc_start: 0.8729 (mmmm) cc_final: 0.8486 (mmmm) REVERT: M 27 MET cc_start: 0.9079 (mpp) cc_final: 0.8866 (mpt) REVERT: M 237 MET cc_start: 0.7885 (tpt) cc_final: 0.7683 (tpt) REVERT: M 319 ASN cc_start: 0.8426 (m-40) cc_final: 0.7993 (m110) REVERT: A 561 MET cc_start: 0.8837 (mmt) cc_final: 0.8440 (mpt) REVERT: A 1339 ASP cc_start: 0.8572 (t0) cc_final: 0.8290 (t0) REVERT: B 442 ASP cc_start: 0.7278 (m-30) cc_final: 0.7046 (m-30) REVERT: C 111 GLN cc_start: 0.7962 (pp30) cc_final: 0.7687 (pp30) REVERT: N 92 ASP cc_start: 0.8792 (m-30) cc_final: 0.8471 (m-30) outliers start: 0 outliers final: 4 residues processed: 415 average time/residue: 0.5914 time to fit residues: 294.3179 Evaluate side-chains 342 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 338 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain N residue 74 PHE Chi-restraints excluded: chain N residue 147 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.0970 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 107 GLN E 174 GLN G 53 ASN G 60 GLN G 139 GLN I 74 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS K 2 ASN K 113 GLN M 319 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS A 472 HIS A 516 GLN A 590 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN A 735 GLN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS A 904 GLN A1032 GLN A1082 HIS A1146 GLN A1163 HIS A1190 GLN B 90 GLN B 111 ASN B 144 HIS B 430 ASN B 582 GLN B 593 GLN B 649 ASN B 699 HIS B 755 GLN B 777 ASN B 906 GLN B 939 HIS ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 51 GLN C 114 HIS C 260 GLN N 174 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.117364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.073969 restraints weight = 62181.506| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.96 r_work: 0.2904 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30063 Z= 0.159 Angle : 0.641 14.832 40592 Z= 0.315 Chirality : 0.044 0.189 4527 Planarity : 0.005 0.073 5258 Dihedral : 5.291 155.360 4010 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.41 % Allowed : 9.96 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.53 (0.14), residues: 3616 helix: 0.52 (0.14), residues: 1298 sheet: -0.68 (0.23), residues: 522 loop : -0.84 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 122 TYR 0.028 0.002 TYR B 752 PHE 0.023 0.001 PHE B 429 TRP 0.034 0.002 TRP B 548 HIS 0.005 0.001 HIS A 809 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (30039) covalent geometry : angle 0.61376 / 0.31 (40556) hydrogen bonds : bond 0.03934 / 2.56 ( 1198) hydrogen bonds : angle 4.97131 / 3.50 ( 3390) metal coordination : bond 0.00898 / 0.54 ( 24) metal coordination : angle 6.27617 / 3.47 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 373 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 LEU cc_start: 0.9380 (mt) cc_final: 0.9037 (pp) REVERT: E 94 MET cc_start: 0.8751 (mmp) cc_final: 0.8536 (mmm) REVERT: E 121 MET cc_start: 0.8007 (ptm) cc_final: 0.7284 (ppp) REVERT: F 101 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8468 (tttm) REVERT: F 109 TYR cc_start: 0.8801 (m-10) cc_final: 0.8487 (m-10) REVERT: G 1 MET cc_start: 0.8668 (pmm) cc_final: 0.7451 (mtt) REVERT: G 164 MET cc_start: 0.8238 (mpp) cc_final: 0.7969 (mpm) REVERT: H 126 GLN cc_start: 0.8191 (mm110) cc_final: 0.7734 (mm-40) REVERT: I 32 ASN cc_start: 0.9251 (t0) cc_final: 0.8918 (t0) REVERT: I 33 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7738 (tpt-90) REVERT: I 56 ASN cc_start: 0.9089 (t0) cc_final: 0.8556 (t0) REVERT: I 99 SER cc_start: 0.8733 (m) cc_final: 0.8392 (t) REVERT: J 31 GLU cc_start: 0.8541 (mp0) cc_final: 0.8291 (mt-10) REVERT: K 38 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8250 (mp0) REVERT: L 32 ASP cc_start: 0.8821 (t0) cc_final: 0.8595 (t0) REVERT: M 41 ILE cc_start: 0.9369 (mp) cc_final: 0.9141 (pp) REVERT: M 237 MET cc_start: 0.8703 (tpt) cc_final: 0.8309 (tpt) REVERT: M 315 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8704 (tm-30) REVERT: A 470 MET cc_start: 0.7865 (tpp) cc_final: 0.7606 (tpp) REVERT: A 501 MET cc_start: 0.6247 (OUTLIER) cc_final: 0.4987 (tpt) REVERT: A 1102 MET cc_start: 0.5608 (mtm) cc_final: 0.5182 (mtm) REVERT: A 1196 TYR cc_start: 0.8881 (t80) cc_final: 0.8617 (t80) REVERT: A 1228 MET cc_start: 0.8898 (mmp) cc_final: 0.8670 (mpp) REVERT: A 1233 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8516 (tp30) REVERT: A 1247 PHE cc_start: 0.8482 (p90) cc_final: 0.8246 (p90) REVERT: A 1259 ILE cc_start: 0.9148 (mt) cc_final: 0.8940 (mp) REVERT: A 1296 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6362 (ttm) REVERT: A 1339 ASP cc_start: 0.9056 (t0) cc_final: 0.8826 (t0) REVERT: B 368 MET cc_start: 0.9314 (mtp) cc_final: 0.9031 (mtm) REVERT: B 438 ARG cc_start: 0.8076 (tpm170) cc_final: 0.7854 (tmm-80) REVERT: B 603 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8545 (mtp) REVERT: B 648 TYR cc_start: 0.7959 (p90) cc_final: 0.7755 (p90) REVERT: B 975 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8341 (ttm110) REVERT: N 76 MET cc_start: 0.8378 (mmm) cc_final: 0.8147 (mmm) REVERT: N 78 CYS cc_start: 0.9063 (p) cc_final: 0.8725 (p) REVERT: N 87 TYR cc_start: 0.8074 (t80) cc_final: 0.7834 (t80) REVERT: N 92 ASP cc_start: 0.9299 (m-30) cc_final: 0.8962 (m-30) outliers start: 46 outliers final: 11 residues processed: 391 average time/residue: 0.6229 time to fit residues: 288.3535 Evaluate side-chains 363 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 347 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 975 ARG Chi-restraints excluded: chain N residue 74 PHE Chi-restraints excluded: chain N residue 83 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: [358, 215, 132, 7, 127, 76, 257, 78, 41, 2, 288] chunk 358 optimal weight: 4.9990 chunk 215 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 288 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 116 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN I 98 GLN I 100 HIS K 2 ASN ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN A1163 HIS A1299 GLN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 111 ASN B 227 ASN B 906 GLN ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 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 = 0.3836 r_free = 0.3836 target = 0.114732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.070564 restraints weight = 61736.073| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.97 r_work: 0.2823 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 30063 Z= 0.202 Angle : 0.645 17.036 40592 Z= 0.316 Chirality : 0.045 0.203 4527 Planarity : 0.005 0.072 5258 Dihedral : 4.504 39.766 4003 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.93 % Allowed : 12.26 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.18 (0.14), residues: 3616 helix: 0.91 (0.15), residues: 1290 sheet: -0.53 (0.23), residues: 515 loop : -0.70 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 64 TYR 0.025 0.002 TYR I 54 PHE 0.019 0.002 PHE B 429 TRP 0.014 0.002 TRP C 49 HIS 0.006 0.001 HIS L 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (30039) covalent geometry : angle 0.61520 / 0.31 (40556) hydrogen bonds : bond 0.03815 / 2.49 ( 1198) hydrogen bonds : angle 4.74839 / 3.34 ( 3390) metal coordination : bond 0.01084 / 0.67 ( 24) metal coordination : angle 6.55718 / 3.57 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 377 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 LEU cc_start: 0.9413 (mt) cc_final: 0.9083 (pp) REVERT: E 94 MET cc_start: 0.8724 (mmp) cc_final: 0.8451 (mtp) REVERT: E 110 MET cc_start: 0.8676 (ttp) cc_final: 0.8419 (ttp) REVERT: E 121 MET cc_start: 0.8120 (ptm) cc_final: 0.7213 (ppp) REVERT: F 101 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8591 (tttt) REVERT: F 107 ARG cc_start: 0.8493 (ttm170) cc_final: 0.8118 (ttm170) REVERT: F 109 TYR cc_start: 0.8809 (m-10) cc_final: 0.8403 (m-10) REVERT: F 117 ASP cc_start: 0.8447 (m-30) cc_final: 0.8184 (m-30) REVERT: G 1 MET cc_start: 0.8387 (pmm) cc_final: 0.7468 (mtt) REVERT: G 164 MET cc_start: 0.8125 (mpp) cc_final: 0.7850 (mpm) REVERT: H 147 LYS cc_start: 0.9266 (mtmt) cc_final: 0.9039 (mtmm) REVERT: I 32 ASN cc_start: 0.9263 (t0) cc_final: 0.8909 (t0) REVERT: I 56 ASN cc_start: 0.9054 (t0) cc_final: 0.8853 (t0) REVERT: I 63 ASP cc_start: 0.7378 (t0) cc_final: 0.6761 (t0) REVERT: I 64 GLU cc_start: 0.8264 (mp0) cc_final: 0.7819 (mm-30) REVERT: J 31 GLU cc_start: 0.8540 (mp0) cc_final: 0.8229 (mt-10) REVERT: K 112 LYS cc_start: 0.9286 (tptp) cc_final: 0.8984 (tptt) REVERT: L 25 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7958 (mm-30) REVERT: L 32 ASP cc_start: 0.8889 (t0) cc_final: 0.8655 (t0) REVERT: L 35 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.8132 (mmm-85) REVERT: M 27 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9129 (mtm) REVERT: M 41 ILE cc_start: 0.9411 (mp) cc_final: 0.9200 (pp) REVERT: M 52 PHE cc_start: 0.9362 (m-80) cc_final: 0.8979 (m-80) REVERT: M 237 MET cc_start: 0.8745 (tpt) cc_final: 0.8307 (tpt) REVERT: M 315 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8719 (tm-30) REVERT: M 319 ASN cc_start: 0.8271 (m-40) cc_final: 0.7917 (m-40) REVERT: M 323 MET cc_start: 0.7713 (ppp) cc_final: 0.7506 (ppp) REVERT: A 470 MET cc_start: 0.7922 (tpp) cc_final: 0.7648 (tpp) REVERT: A 501 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.4742 (tpt) REVERT: A 1102 MET cc_start: 0.5987 (mtm) cc_final: 0.5637 (mtm) REVERT: A 1233 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8575 (tp30) REVERT: A 1247 PHE cc_start: 0.8654 (p90) cc_final: 0.8226 (p90) REVERT: A 1259 ILE cc_start: 0.9190 (mt) cc_final: 0.8963 (mp) REVERT: A 1296 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6529 (ttm) REVERT: A 1339 ASP cc_start: 0.9063 (t0) cc_final: 0.8766 (t0) REVERT: A 1484 MET cc_start: 0.6390 (pmm) cc_final: 0.6146 (pmm) REVERT: B 438 ARG cc_start: 0.8271 (tpm170) cc_final: 0.8000 (tmm-80) REVERT: B 890 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7663 (tpp-160) REVERT: B 975 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8509 (ttp80) REVERT: N 76 MET cc_start: 0.8633 (mmm) cc_final: 0.8322 (mmm) REVERT: N 78 CYS cc_start: 0.9085 (p) cc_final: 0.8810 (p) REVERT: N 89 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8307 (t0) REVERT: N 92 ASP cc_start: 0.9292 (m-30) cc_final: 0.9020 (m-30) outliers start: 63 outliers final: 22 residues processed: 406 average time/residue: 0.6240 time to fit residues: 300.0787 Evaluate side-chains 370 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 342 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 975 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 89 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: [2, 87, 75, 221, 64, 303, 28, 260, 321, 9, 278] chunk 2 optimal weight: 9.9990 chunk 87 optimal weight: 0.2980 chunk 75 optimal weight: 7.9990 chunk 221 optimal weight: 0.1980 chunk 64 optimal weight: 6.9990 chunk 303 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 321 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 278 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN I 100 HIS K 2 ASN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 315 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 649 ASN B 718 GLN ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.116689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.072941 restraints weight = 61481.700| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.98 r_work: 0.2881 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30063 Z= 0.114 Angle : 0.595 14.618 40592 Z= 0.288 Chirality : 0.043 0.228 4527 Planarity : 0.004 0.069 5258 Dihedral : 4.270 30.552 4001 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.96 % Allowed : 13.48 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.01 (0.14), residues: 3616 helix: 1.08 (0.15), residues: 1290 sheet: -0.45 (0.23), residues: 524 loop : -0.61 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 416 TYR 0.023 0.001 TYR M 320 PHE 0.019 0.001 PHE N 74 TRP 0.013 0.001 TRP C 49 HIS 0.007 0.001 HIS B 980 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (30039) covalent geometry : angle 0.57093 / 0.29 (40556) hydrogen bonds : bond 0.03288 / 2.15 ( 1198) hydrogen bonds : angle 4.55500 / 3.19 ( 3390) metal coordination : bond 0.00633 / 0.39 ( 24) metal coordination : angle 5.62838 / 3.09 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 374 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 LEU cc_start: 0.9354 (mt) cc_final: 0.9044 (pp) REVERT: E 72 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.9017 (ttp) REVERT: E 94 MET cc_start: 0.8683 (mmp) cc_final: 0.8440 (mtp) REVERT: E 111 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.7828 (m) REVERT: E 121 MET cc_start: 0.8083 (ptm) cc_final: 0.7204 (ppp) REVERT: F 109 TYR cc_start: 0.8768 (m-10) cc_final: 0.8379 (m-10) REVERT: G 1 MET cc_start: 0.8010 (pmm) cc_final: 0.7171 (mtt) REVERT: G 164 MET cc_start: 0.8110 (mpp) cc_final: 0.7842 (mpm) REVERT: I 32 ASN cc_start: 0.9240 (t0) cc_final: 0.8867 (t0) REVERT: I 41 ASN cc_start: 0.8526 (t0) cc_final: 0.8221 (t0) REVERT: I 63 ASP cc_start: 0.7465 (t0) cc_final: 0.6967 (t0) REVERT: I 64 GLU cc_start: 0.8043 (mp0) cc_final: 0.7748 (mm-30) REVERT: J 31 GLU cc_start: 0.8515 (mp0) cc_final: 0.8147 (mt-10) REVERT: K 38 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8181 (mp0) REVERT: L 25 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7750 (mm-30) REVERT: L 32 ASP cc_start: 0.8902 (t0) cc_final: 0.8621 (t0) REVERT: L 35 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8091 (mmm-85) REVERT: M 41 ILE cc_start: 0.9390 (mp) cc_final: 0.9167 (pp) REVERT: M 52 PHE cc_start: 0.9302 (m-80) cc_final: 0.8869 (m-80) REVERT: M 237 MET cc_start: 0.8703 (tpt) cc_final: 0.8275 (tpt) REVERT: M 315 GLN cc_start: 0.8998 (tm130) cc_final: 0.8687 (tm-30) REVERT: M 319 ASN cc_start: 0.8376 (m-40) cc_final: 0.8011 (m-40) REVERT: A 470 MET cc_start: 0.7751 (tpp) cc_final: 0.7464 (tpp) REVERT: A 501 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.4667 (tpt) REVERT: A 561 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8165 (mmt) REVERT: A 1102 MET cc_start: 0.6032 (mtm) cc_final: 0.5655 (mtm) REVERT: A 1199 MET cc_start: 0.8436 (pp-130) cc_final: 0.8080 (ppp) REVERT: A 1233 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8533 (tp30) REVERT: A 1259 ILE cc_start: 0.9160 (mt) cc_final: 0.8946 (mp) REVERT: A 1339 ASP cc_start: 0.9006 (t0) cc_final: 0.8699 (t0) REVERT: A 1351 ASP cc_start: 0.8580 (m-30) cc_final: 0.7918 (t70) REVERT: B 438 ARG cc_start: 0.8332 (tpm170) cc_final: 0.8008 (tmm-80) REVERT: B 508 MET cc_start: 0.9463 (mmt) cc_final: 0.9134 (mmt) REVERT: B 674 MET cc_start: 0.9380 (tpt) cc_final: 0.9028 (tpt) REVERT: B 890 ARG cc_start: 0.8036 (tpp-160) cc_final: 0.7588 (tpp-160) REVERT: B 916 TYR cc_start: 0.8471 (m-80) cc_final: 0.8199 (m-10) REVERT: B 975 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8368 (ttp80) REVERT: N 76 MET cc_start: 0.8661 (mmm) cc_final: 0.8312 (mmm) REVERT: N 78 CYS cc_start: 0.9052 (p) cc_final: 0.8840 (p) REVERT: N 87 TYR cc_start: 0.7869 (t80) cc_final: 0.7664 (t80) REVERT: N 89 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8141 (t0) REVERT: N 92 ASP cc_start: 0.9238 (m-30) cc_final: 0.8934 (m-30) outliers start: 64 outliers final: 22 residues processed: 405 average time/residue: 0.5997 time to fit residues: 289.2323 Evaluate side-chains 367 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 339 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 225 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 975 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 89 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: [299, 150, 240, 311, 125, 243, 273, 245, 298, 284, 265] chunk 299 optimal weight: 0.0010 chunk 150 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 311 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 273 optimal weight: 0.0980 chunk 245 optimal weight: 0.7980 chunk 298 optimal weight: 0.0570 chunk 284 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 overall best weight: 0.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS I 60 HIS I 74 GLN K 2 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 503 ASN ** B 939 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 = 0.3877 r_free = 0.3877 target = 0.117382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.073913 restraints weight = 61770.703| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.99 r_work: 0.2908 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30063 Z= 0.104 Angle : 0.582 12.859 40592 Z= 0.282 Chirality : 0.042 0.247 4527 Planarity : 0.004 0.071 5258 Dihedral : 4.109 30.903 4001 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.02 % Allowed : 14.55 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: 0.06 (0.14), residues: 3616 helix: 1.17 (0.15), residues: 1302 sheet: -0.48 (0.23), residues: 519 loop : -0.59 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 64 TYR 0.025 0.001 TYR M 320 PHE 0.014 0.001 PHE N 146 TRP 0.012 0.001 TRP C 49 HIS 0.005 0.001 HIS B 980 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (30039) covalent geometry : angle 0.56217 / 0.28 (40556) hydrogen bonds : bond 0.03084 / 2.02 ( 1198) hydrogen bonds : angle 4.41581 / 3.09 ( 3390) metal coordination : bond 0.00518 / 0.31 ( 24) metal coordination : angle 5.08085 / 2.79 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 372 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 LEU cc_start: 0.9371 (mt) cc_final: 0.9072 (pp) REVERT: E 73 PHE cc_start: 0.7963 (m-10) cc_final: 0.7703 (m-10) REVERT: E 111 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.7801 (m) REVERT: E 121 MET cc_start: 0.7888 (ptm) cc_final: 0.7235 (ppp) REVERT: F 109 TYR cc_start: 0.8779 (m-10) cc_final: 0.8393 (m-10) REVERT: F 125 ILE cc_start: 0.7842 (pt) cc_final: 0.7429 (tp) REVERT: G 1 MET cc_start: 0.7740 (pmm) cc_final: 0.6893 (mtt) REVERT: G 164 MET cc_start: 0.8099 (mpp) cc_final: 0.7860 (mpm) REVERT: H 126 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8086 (mm110) REVERT: I 32 ASN cc_start: 0.9212 (t0) cc_final: 0.8829 (t0) REVERT: I 41 ASN cc_start: 0.8518 (t0) cc_final: 0.8194 (t0) REVERT: J 31 GLU cc_start: 0.8524 (mp0) cc_final: 0.8154 (mt-10) REVERT: K 38 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8226 (mp0) REVERT: L 25 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7652 (mm-30) REVERT: L 32 ASP cc_start: 0.8882 (t0) cc_final: 0.8578 (t0) REVERT: L 35 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.8005 (mmm-85) REVERT: M 27 MET cc_start: 0.9454 (mtm) cc_final: 0.9206 (mtt) REVERT: M 52 PHE cc_start: 0.9335 (m-80) cc_final: 0.8889 (m-80) REVERT: M 232 MET cc_start: 0.9257 (mmm) cc_final: 0.9057 (mmm) REVERT: M 237 MET cc_start: 0.8655 (tpt) cc_final: 0.8247 (tpt) REVERT: M 315 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8720 (tm-30) REVERT: M 319 ASN cc_start: 0.8395 (m-40) cc_final: 0.7921 (m-40) REVERT: A 1102 MET cc_start: 0.6091 (mtm) cc_final: 0.5694 (mtm) REVERT: A 1228 MET cc_start: 0.8934 (mmp) cc_final: 0.8624 (mmt) REVERT: A 1233 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8502 (tp30) REVERT: A 1339 ASP cc_start: 0.8953 (t0) cc_final: 0.8695 (t0) REVERT: A 1351 ASP cc_start: 0.8504 (m-30) cc_final: 0.7771 (t70) REVERT: B 198 GLU cc_start: 0.8721 (tt0) cc_final: 0.8519 (tt0) REVERT: B 438 ARG cc_start: 0.8272 (tpm170) cc_final: 0.7968 (tmm-80) REVERT: B 452 ASN cc_start: 0.9016 (m110) cc_final: 0.8760 (m110) REVERT: B 486 ASN cc_start: 0.9044 (t0) cc_final: 0.8676 (t0) REVERT: B 489 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8427 (tt) REVERT: B 508 MET cc_start: 0.9468 (mmt) cc_final: 0.9106 (mmt) REVERT: B 674 MET cc_start: 0.9370 (tpt) cc_final: 0.8997 (tpt) REVERT: B 890 ARG cc_start: 0.8113 (tpp-160) cc_final: 0.7771 (tpp-160) REVERT: B 916 TYR cc_start: 0.8401 (m-80) cc_final: 0.8182 (m-10) REVERT: N 76 MET cc_start: 0.8751 (mmm) cc_final: 0.8345 (mmm) REVERT: N 78 CYS cc_start: 0.9105 (p) cc_final: 0.8857 (p) REVERT: N 89 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8217 (t0) REVERT: N 92 ASP cc_start: 0.9234 (m-30) cc_final: 0.8919 (m-30) REVERT: N 102 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.7249 (t80) outliers start: 66 outliers final: 25 residues processed: 407 average time/residue: 0.6083 time to fit residues: 294.4603 Evaluate side-chains 370 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 339 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 225 THR Chi-restraints excluded: chain M residue 315 GLN Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 904 GLN Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 102 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: [147, 18, 180, 211, 54, 248, 188, 124, 218, 220, 76] chunk 147 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 124 optimal weight: 0.0470 chunk 218 optimal weight: 0.7980 chunk 220 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN K 2 ASN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.116928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.073321 restraints weight = 61412.564| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.98 r_work: 0.2889 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30063 Z= 0.118 Angle : 0.592 12.014 40592 Z= 0.287 Chirality : 0.043 0.243 4527 Planarity : 0.004 0.070 5258 Dihedral : 4.061 29.746 4001 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.74 % Allowed : 15.95 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3616 helix: 1.30 (0.15), residues: 1288 sheet: -0.51 (0.23), residues: 522 loop : -0.51 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 416 TYR 0.023 0.001 TYR I 54 PHE 0.022 0.001 PHE N 74 TRP 0.012 0.001 TRP C 49 HIS 0.009 0.001 HIS B 980 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (30039) covalent geometry : angle 0.57232 / 0.29 (40556) hydrogen bonds : bond 0.03080 / 2.02 ( 1198) hydrogen bonds : angle 4.34722 / 3.05 ( 3390) metal coordination : bond 0.00577 / 0.35 ( 24) metal coordination : angle 5.12018 / 2.78 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 348 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 LEU cc_start: 0.9378 (mt) cc_final: 0.9113 (pp) REVERT: E 72 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.9060 (ttt) REVERT: E 111 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.7728 (m) REVERT: E 121 MET cc_start: 0.7865 (ptm) cc_final: 0.7216 (ppp) REVERT: F 57 MET cc_start: 0.9278 (tmt) cc_final: 0.8938 (tmt) REVERT: F 86 GLU cc_start: 0.6982 (pp20) cc_final: 0.5957 (pm20) REVERT: F 109 TYR cc_start: 0.8827 (m-10) cc_final: 0.8355 (m-10) REVERT: F 125 ILE cc_start: 0.7884 (pt) cc_final: 0.7483 (tp) REVERT: G 1 MET cc_start: 0.7751 (pmm) cc_final: 0.6901 (mtt) REVERT: G 164 MET cc_start: 0.8114 (mpp) cc_final: 0.7819 (mpm) REVERT: H 98 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8339 (ptp-170) REVERT: H 126 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8171 (mm110) REVERT: I 32 ASN cc_start: 0.9178 (t0) cc_final: 0.8837 (t0) REVERT: I 41 ASN cc_start: 0.8535 (t0) cc_final: 0.8194 (t0) REVERT: I 64 GLU cc_start: 0.8295 (mp0) cc_final: 0.7978 (mm-30) REVERT: L 32 ASP cc_start: 0.8846 (t0) cc_final: 0.8531 (t0) REVERT: L 35 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.8118 (mmm-85) REVERT: M 52 PHE cc_start: 0.9343 (m-80) cc_final: 0.8924 (m-80) REVERT: M 237 MET cc_start: 0.8644 (tpt) cc_final: 0.8231 (tpt) REVERT: M 315 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8725 (tm-30) REVERT: M 319 ASN cc_start: 0.8465 (m-40) cc_final: 0.8010 (m-40) REVERT: A 470 MET cc_start: 0.7947 (tpp) cc_final: 0.7531 (tpp) REVERT: A 501 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.4899 (tpt) REVERT: A 561 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8215 (mmt) REVERT: A 1102 MET cc_start: 0.6140 (mtm) cc_final: 0.5721 (mtm) REVERT: A 1199 MET cc_start: 0.8336 (pp-130) cc_final: 0.7996 (ppp) REVERT: A 1228 MET cc_start: 0.8986 (mmp) cc_final: 0.8705 (mmt) REVERT: A 1233 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8518 (tp30) REVERT: A 1339 ASP cc_start: 0.8951 (t0) cc_final: 0.8714 (t0) REVERT: B 438 ARG cc_start: 0.8269 (tpm170) cc_final: 0.7956 (tmm-80) REVERT: B 486 ASN cc_start: 0.9019 (t0) cc_final: 0.8683 (t0) REVERT: B 489 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8389 (tt) REVERT: B 508 MET cc_start: 0.9493 (mmt) cc_final: 0.9155 (mmt) REVERT: B 552 ASN cc_start: 0.7587 (m-40) cc_final: 0.7265 (m-40) REVERT: B 674 MET cc_start: 0.9389 (tpt) cc_final: 0.9048 (tpt) REVERT: B 890 ARG cc_start: 0.8127 (tpp-160) cc_final: 0.7856 (tpp-160) REVERT: B 975 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8359 (ttp80) REVERT: N 76 MET cc_start: 0.8781 (mmm) cc_final: 0.8337 (mmm) REVERT: N 78 CYS cc_start: 0.9121 (p) cc_final: 0.8861 (p) REVERT: N 89 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8162 (t0) REVERT: N 102 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.7216 (t80) outliers start: 57 outliers final: 27 residues processed: 383 average time/residue: 0.6167 time to fit residues: 280.1851 Evaluate side-chains 367 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 329 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 225 THR Chi-restraints excluded: chain M residue 315 GLN Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 904 GLN Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 975 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 102 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: [334, 203, 4, 169, 50, 19, 318, 71, 9, 133, 137] chunk 334 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 4 optimal weight: 30.0000 chunk 169 optimal weight: 0.9990 chunk 50 optimal weight: 0.0970 chunk 19 optimal weight: 4.9990 chunk 318 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 9 optimal weight: 30.0000 chunk 133 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN M 316 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.116864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073287 restraints weight = 61566.141| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.94 r_work: 0.2893 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30063 Z= 0.116 Angle : 0.599 11.632 40592 Z= 0.290 Chirality : 0.043 0.245 4527 Planarity : 0.004 0.071 5258 Dihedral : 4.020 30.101 4001 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.11 % Allowed : 16.17 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: 0.22 (0.14), residues: 3616 helix: 1.32 (0.15), residues: 1294 sheet: -0.50 (0.23), residues: 519 loop : -0.47 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 416 TYR 0.023 0.001 TYR I 54 PHE 0.012 0.001 PHE N 146 TRP 0.012 0.001 TRP C 49 HIS 0.009 0.001 HIS B 980 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (30039) covalent geometry : angle 0.58027 / 0.29 (40556) hydrogen bonds : bond 0.03059 / 2.01 ( 1198) hydrogen bonds : angle 4.31256 / 3.01 ( 3390) metal coordination : bond 0.00578 / 0.35 ( 24) metal coordination : angle 5.05388 / 2.77 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 355 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 LEU cc_start: 0.9401 (mt) cc_final: 0.9111 (pp) REVERT: E 72 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.9078 (ttt) REVERT: E 111 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.7780 (m) REVERT: E 121 MET cc_start: 0.7755 (ptm) cc_final: 0.7146 (ppp) REVERT: F 57 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.8942 (tmt) REVERT: F 109 TYR cc_start: 0.8812 (m-10) cc_final: 0.8411 (m-10) REVERT: F 125 ILE cc_start: 0.7867 (pt) cc_final: 0.7417 (tp) REVERT: G 1 MET cc_start: 0.7790 (pmm) cc_final: 0.6772 (mpt) REVERT: G 164 MET cc_start: 0.8089 (mpp) cc_final: 0.7791 (mpm) REVERT: H 55 LYS cc_start: 0.8863 (tppt) cc_final: 0.8631 (tppp) REVERT: H 98 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8438 (ptp-170) REVERT: H 126 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8151 (mm110) REVERT: I 32 ASN cc_start: 0.9186 (t0) cc_final: 0.8782 (t0) REVERT: I 41 ASN cc_start: 0.8591 (t0) cc_final: 0.8245 (t0) REVERT: I 64 GLU cc_start: 0.8296 (mp0) cc_final: 0.7955 (mm-30) REVERT: J 31 GLU cc_start: 0.8560 (mp0) cc_final: 0.8110 (mt-10) REVERT: L 32 ASP cc_start: 0.8819 (t0) cc_final: 0.8494 (t0) REVERT: L 35 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.8056 (mmm-85) REVERT: L 42 ARG cc_start: 0.8705 (mmm-85) cc_final: 0.8182 (mmt-90) REVERT: M 27 MET cc_start: 0.9463 (mtm) cc_final: 0.9188 (mtt) REVERT: M 52 PHE cc_start: 0.9353 (m-80) cc_final: 0.8878 (m-80) REVERT: M 237 MET cc_start: 0.8639 (tpt) cc_final: 0.8239 (tpt) REVERT: M 315 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8710 (tm-30) REVERT: M 316 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8492 (mt0) REVERT: M 319 ASN cc_start: 0.8467 (m-40) cc_final: 0.7999 (m-40) REVERT: A 470 MET cc_start: 0.7921 (tpp) cc_final: 0.7399 (tpp) REVERT: A 501 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.4838 (tpt) REVERT: A 561 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8171 (mmt) REVERT: A 1102 MET cc_start: 0.6157 (mtm) cc_final: 0.5779 (mtm) REVERT: A 1199 MET cc_start: 0.8363 (pp-130) cc_final: 0.8001 (ppp) REVERT: A 1233 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8506 (tp30) REVERT: A 1339 ASP cc_start: 0.8928 (t0) cc_final: 0.8675 (t0) REVERT: A 1351 ASP cc_start: 0.8547 (m-30) cc_final: 0.7849 (t70) REVERT: B 438 ARG cc_start: 0.8301 (tpm170) cc_final: 0.7977 (tmm-80) REVERT: B 486 ASN cc_start: 0.9026 (t0) cc_final: 0.8701 (t0) REVERT: B 489 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8407 (tt) REVERT: B 508 MET cc_start: 0.9515 (mmt) cc_final: 0.9140 (mmt) REVERT: B 552 ASN cc_start: 0.7646 (m-40) cc_final: 0.7317 (m-40) REVERT: B 603 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8447 (mtp) REVERT: B 674 MET cc_start: 0.9406 (tpt) cc_final: 0.9093 (tpt) REVERT: B 890 ARG cc_start: 0.8104 (tpp-160) cc_final: 0.7851 (tpp-160) REVERT: B 916 TYR cc_start: 0.8103 (m-10) cc_final: 0.7668 (m-80) REVERT: B 975 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8108 (ttp80) REVERT: B 976 MET cc_start: 0.8826 (ttt) cc_final: 0.8548 (ttt) REVERT: N 76 MET cc_start: 0.8829 (mmm) cc_final: 0.8364 (mmm) REVERT: N 78 CYS cc_start: 0.9096 (p) cc_final: 0.8851 (p) REVERT: N 89 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8170 (t0) outliers start: 69 outliers final: 31 residues processed: 391 average time/residue: 0.6038 time to fit residues: 282.5660 Evaluate side-chains 379 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 335 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 225 THR Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 315 GLN Chi-restraints excluded: chain M residue 316 GLN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 904 GLN Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain B residue 975 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain N residue 74 PHE Chi-restraints excluded: chain N residue 89 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: [169, 1, 160, 275, 327, 12, 332, 128, 285, 92, 27] chunk 169 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 327 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 332 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 285 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 95 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN K 2 ASN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.116502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.072731 restraints weight = 61430.512| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.96 r_work: 0.2877 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30063 Z= 0.127 Angle : 0.616 12.356 40592 Z= 0.297 Chirality : 0.043 0.235 4527 Planarity : 0.004 0.070 5258 Dihedral : 4.027 29.368 4001 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.77 % Allowed : 16.84 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3616 helix: 1.33 (0.15), residues: 1294 sheet: -0.46 (0.24), residues: 514 loop : -0.45 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 64 TYR 0.024 0.001 TYR N 87 PHE 0.016 0.001 PHE B 429 TRP 0.012 0.001 TRP C 49 HIS 0.008 0.001 HIS B 980 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (30039) covalent geometry : angle 0.59781 / 0.30 (40556) hydrogen bonds : bond 0.03072 / 2.02 ( 1198) hydrogen bonds : angle 4.32320 / 3.02 ( 3390) metal coordination : bond 0.00615 / 0.38 ( 24) metal coordination : angle 5.08287 / 2.79 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 345 time to evaluate : 1.245 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: D 40 LEU cc_start: 0.9381 (mt) cc_final: 0.9128 (pp) REVERT: E 72 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.9097 (ttt) REVERT: E 111 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.7819 (m) REVERT: E 121 MET cc_start: 0.7812 (ptm) cc_final: 0.7180 (ppp) REVERT: F 57 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.8960 (tmt) REVERT: F 109 TYR cc_start: 0.8806 (m-10) cc_final: 0.8392 (m-10) REVERT: F 125 ILE cc_start: 0.7936 (pt) cc_final: 0.7487 (tp) REVERT: G 1 MET cc_start: 0.7744 (pmm) cc_final: 0.6786 (mpt) REVERT: G 164 MET cc_start: 0.8120 (mpp) cc_final: 0.7828 (mpm) REVERT: H 98 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8451 (ptp-170) REVERT: H 126 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8102 (mm110) REVERT: I 32 ASN cc_start: 0.9188 (t0) cc_final: 0.8785 (t0) REVERT: I 33 ARG cc_start: 0.8133 (mtp180) cc_final: 0.7468 (tpt-90) REVERT: I 41 ASN cc_start: 0.8615 (t0) cc_final: 0.8281 (t0) REVERT: I 64 GLU cc_start: 0.8166 (mp0) cc_final: 0.7858 (mm-30) REVERT: J 31 GLU cc_start: 0.8591 (mp0) cc_final: 0.8091 (mt-10) REVERT: L 32 ASP cc_start: 0.8817 (t0) cc_final: 0.8518 (t0) REVERT: L 35 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8142 (mmm-85) REVERT: M 52 PHE cc_start: 0.9368 (m-80) cc_final: 0.8924 (m-80) REVERT: M 237 MET cc_start: 0.8672 (tpt) cc_final: 0.8258 (tpt) REVERT: M 315 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8738 (tm-30) REVERT: M 319 ASN cc_start: 0.8436 (m-40) cc_final: 0.7968 (m-40) REVERT: A 470 MET cc_start: 0.7945 (tpp) cc_final: 0.7407 (tpp) REVERT: A 501 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.4830 (tpt) REVERT: A 561 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8082 (mmt) REVERT: A 1102 MET cc_start: 0.6173 (mtm) cc_final: 0.5819 (mtm) REVERT: A 1233 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8526 (tp30) REVERT: A 1339 ASP cc_start: 0.8893 (t0) cc_final: 0.8659 (t0) REVERT: A 1351 ASP cc_start: 0.8573 (m-30) cc_final: 0.7879 (t70) REVERT: B 438 ARG cc_start: 0.8353 (tpm170) cc_final: 0.8005 (tmm-80) REVERT: B 486 ASN cc_start: 0.9019 (t0) cc_final: 0.8688 (t0) REVERT: B 489 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8410 (tt) REVERT: B 508 MET cc_start: 0.9525 (mmt) cc_final: 0.9316 (mmt) REVERT: B 552 ASN cc_start: 0.7742 (m-40) cc_final: 0.7392 (m-40) REVERT: B 603 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8444 (mtp) REVERT: B 674 MET cc_start: 0.9416 (tpt) cc_final: 0.9107 (tpt) REVERT: B 890 ARG cc_start: 0.8108 (tpp-160) cc_final: 0.7862 (tpp-160) REVERT: N 76 MET cc_start: 0.8879 (mmm) cc_final: 0.8408 (mmm) REVERT: N 78 CYS cc_start: 0.9100 (p) cc_final: 0.8834 (p) REVERT: N 80 ARG cc_start: 0.9026 (pmm-80) cc_final: 0.8558 (pmm-80) REVERT: N 89 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8178 (t0) REVERT: N 102 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7334 (t80) outliers start: 58 outliers final: 28 residues processed: 378 average time/residue: 0.6217 time to fit residues: 281.0047 Evaluate side-chains 369 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 225 THR Chi-restraints excluded: chain M residue 315 GLN Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 904 GLN Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 102 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: [41, 52, 141, 258, 186, 24, 69, 139, 279, 5, 71] chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 40.0000 chunk 141 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 186 optimal weight: 0.0870 chunk 24 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 5 optimal weight: 40.0000 chunk 71 optimal weight: 7.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** M 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS B 98 HIS B 503 ASN ** B 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 906 GLN ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 66 HIS C 157 GLN ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.112021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.067273 restraints weight = 61189.340| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.91 r_work: 0.2754 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 30063 Z= 0.306 Angle : 0.758 21.931 40592 Z= 0.367 Chirality : 0.047 0.243 4527 Planarity : 0.005 0.070 5258 Dihedral : 4.467 29.579 4001 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.74 % Allowed : 17.11 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3616 helix: 1.16 (0.15), residues: 1299 sheet: -0.50 (0.24), residues: 515 loop : -0.48 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 64 TYR 0.029 0.002 TYR N 87 PHE 0.034 0.002 PHE C 63 TRP 0.015 0.002 TRP B 548 HIS 0.011 0.001 HIS B 980 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.31 (30039) covalent geometry : angle 0.72845 / 0.37 (40556) hydrogen bonds : bond 0.03926 / 2.57 ( 1198) hydrogen bonds : angle 4.65192 / 3.27 ( 3390) metal coordination : bond 0.01526 / 0.96 ( 24) metal coordination : angle 7.03459 / 3.69 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 347 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 72 MET cc_start: 0.9486 (OUTLIER) cc_final: 0.9098 (ttp) REVERT: E 111 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7802 (m) REVERT: E 121 MET cc_start: 0.8161 (ptm) cc_final: 0.7398 (ppp) REVERT: F 101 LYS cc_start: 0.8829 (tttt) cc_final: 0.8628 (tttt) REVERT: F 109 TYR cc_start: 0.8777 (m-10) cc_final: 0.8433 (m-10) REVERT: G 1 MET cc_start: 0.7802 (pmm) cc_final: 0.6908 (mpt) REVERT: G 164 MET cc_start: 0.8093 (mpp) cc_final: 0.7799 (mpm) REVERT: H 98 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8462 (ptp-170) REVERT: I 23 MET cc_start: 0.8916 (ptt) cc_final: 0.8578 (ptm) REVERT: I 32 ASN cc_start: 0.9216 (t0) cc_final: 0.8819 (t0) REVERT: I 41 ASN cc_start: 0.8712 (t0) cc_final: 0.8448 (t0) REVERT: I 64 GLU cc_start: 0.8233 (mp0) cc_final: 0.7852 (mm-30) REVERT: L 32 ASP cc_start: 0.8828 (t0) cc_final: 0.8565 (t0) REVERT: L 35 ARG cc_start: 0.8868 (mmm-85) cc_final: 0.8588 (mmm-85) REVERT: M 52 PHE cc_start: 0.9358 (m-80) cc_final: 0.9001 (m-80) REVERT: M 315 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8717 (tm-30) REVERT: M 319 ASN cc_start: 0.8553 (m-40) cc_final: 0.8022 (m110) REVERT: A 501 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.5107 (tpt) REVERT: A 510 GLU cc_start: 0.8635 (tp30) cc_final: 0.8088 (mm-30) REVERT: A 1102 MET cc_start: 0.6459 (mtm) cc_final: 0.6147 (mtm) REVERT: A 1233 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8707 (tp30) REVERT: A 1339 ASP cc_start: 0.8961 (t0) cc_final: 0.8739 (t0) REVERT: B 438 ARG cc_start: 0.8452 (tpm170) cc_final: 0.8147 (tmm-80) REVERT: B 508 MET cc_start: 0.9488 (mmt) cc_final: 0.9116 (mmt) REVERT: B 552 ASN cc_start: 0.8342 (m-40) cc_final: 0.7890 (m-40) REVERT: B 674 MET cc_start: 0.9507 (tpt) cc_final: 0.9209 (tpt) REVERT: B 890 ARG cc_start: 0.8096 (tpp-160) cc_final: 0.7840 (tpp-160) REVERT: N 76 MET cc_start: 0.8892 (mmm) cc_final: 0.8471 (mmm) REVERT: N 89 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8420 (t0) REVERT: N 92 ASP cc_start: 0.9325 (m-30) cc_final: 0.9048 (m-30) REVERT: N 102 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.7257 (t80) outliers start: 57 outliers final: 25 residues processed: 384 average time/residue: 0.6208 time to fit residues: 284.8355 Evaluate side-chains 360 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 328 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 315 GLN Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 904 GLN Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 102 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: [237, 61, 340, 95, 3, 345, 174, 38, 33, 114, 156] chunk 237 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 340 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 345 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 156 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN I 100 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 755 GLN ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 66 HIS C 157 GLN ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.114630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.070932 restraints weight = 60745.765| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.90 r_work: 0.2836 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30063 Z= 0.138 Angle : 0.687 14.783 40592 Z= 0.330 Chirality : 0.044 0.288 4527 Planarity : 0.004 0.070 5258 Dihedral : 4.299 29.175 4001 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.28 % Allowed : 18.28 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3616 helix: 1.27 (0.15), residues: 1287 sheet: -0.42 (0.24), residues: 508 loop : -0.42 (0.15), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 64 TYR 0.031 0.001 TYR N 87 PHE 0.016 0.001 PHE B 429 TRP 0.013 0.001 TRP C 49 HIS 0.008 0.001 HIS B 980 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (30039) covalent geometry : angle 0.66544 / 0.33 (40556) hydrogen bonds : bond 0.03323 / 2.17 ( 1198) hydrogen bonds : angle 4.50561 / 3.16 ( 3390) metal coordination : bond 0.00755 / 0.47 ( 24) metal coordination : angle 5.83700 / 3.15 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 342 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 72 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9094 (ttp) REVERT: E 111 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.7840 (m) REVERT: E 121 MET cc_start: 0.8036 (ptm) cc_final: 0.7116 (ppp) REVERT: F 109 TYR cc_start: 0.8800 (m-10) cc_final: 0.8402 (m-10) REVERT: G 1 MET cc_start: 0.7677 (pmm) cc_final: 0.6782 (mpt) REVERT: G 164 MET cc_start: 0.8162 (mpp) cc_final: 0.7862 (mpm) REVERT: H 98 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8432 (ptp-170) REVERT: I 32 ASN cc_start: 0.9172 (t0) cc_final: 0.8802 (t0) REVERT: I 41 ASN cc_start: 0.8618 (t0) cc_final: 0.8345 (t0) REVERT: I 64 GLU cc_start: 0.8235 (mp0) cc_final: 0.7897 (mm-30) REVERT: J 31 GLU cc_start: 0.8612 (mp0) cc_final: 0.8148 (mt-10) REVERT: L 32 ASP cc_start: 0.8779 (t0) cc_final: 0.8501 (t0) REVERT: M 27 MET cc_start: 0.9199 (mtm) cc_final: 0.8756 (mpt) REVERT: M 52 PHE cc_start: 0.9333 (m-80) cc_final: 0.8989 (m-80) REVERT: M 315 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8692 (tm-30) REVERT: M 319 ASN cc_start: 0.8530 (m-40) cc_final: 0.8004 (m-40) REVERT: A 470 MET cc_start: 0.7983 (tpp) cc_final: 0.7612 (tpp) REVERT: A 501 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.4941 (tpt) REVERT: A 1102 MET cc_start: 0.6449 (mtm) cc_final: 0.6109 (mtm) REVERT: A 1199 MET cc_start: 0.8273 (pp-130) cc_final: 0.7943 (ppp) REVERT: A 1228 MET cc_start: 0.9051 (mmp) cc_final: 0.8715 (mpp) REVERT: A 1233 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8682 (tp30) REVERT: A 1339 ASP cc_start: 0.8915 (t0) cc_final: 0.8625 (t0) REVERT: A 1484 MET cc_start: 0.6852 (pmm) cc_final: 0.6332 (pmm) REVERT: B 53 MET cc_start: 0.8878 (mmm) cc_final: 0.8581 (mpp) REVERT: B 438 ARG cc_start: 0.8408 (tpm170) cc_final: 0.8147 (tmm-80) REVERT: B 486 ASN cc_start: 0.9127 (t0) cc_final: 0.8803 (t0) REVERT: B 489 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8413 (tt) REVERT: B 508 MET cc_start: 0.9494 (mmt) cc_final: 0.9109 (mmt) REVERT: B 546 GLU cc_start: 0.8345 (tp30) cc_final: 0.8073 (tp30) REVERT: B 552 ASN cc_start: 0.8195 (m-40) cc_final: 0.7654 (m-40) REVERT: B 674 MET cc_start: 0.9375 (tpt) cc_final: 0.9092 (tpt) REVERT: B 890 ARG cc_start: 0.8106 (tpp-160) cc_final: 0.7868 (tpp-160) REVERT: B 916 TYR cc_start: 0.8164 (m-80) cc_final: 0.7765 (m-10) REVERT: C 94 CYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7576 (p) REVERT: N 56 ARG cc_start: 0.9140 (ptp-110) cc_final: 0.8751 (mtm110) REVERT: N 73 GLU cc_start: 0.9205 (tp30) cc_final: 0.8896 (pm20) REVERT: N 76 MET cc_start: 0.8937 (mmm) cc_final: 0.8629 (mmm) REVERT: N 89 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8350 (t0) REVERT: N 92 ASP cc_start: 0.9292 (m-30) cc_final: 0.9000 (m-30) outliers start: 42 outliers final: 22 residues processed: 367 average time/residue: 0.6001 time to fit residues: 264.7489 Evaluate side-chains 357 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 327 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 315 GLN Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 904 GLN Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 TRP Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 939 HIS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain N residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: [200, 233, 41, 206, 75, 264, 132, 294, 201, 311, 93] chunk 200 optimal weight: 7.9990 chunk 233 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 206 optimal weight: 0.0010 chunk 75 optimal weight: 0.9990 chunk 264 optimal weight: 0.0670 chunk 132 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 311 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.5726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN I 100 HIS K 2 ASN M 316 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS A 989 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN ** B 939 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.115638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.071907 restraints weight = 61320.107| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.92 r_work: 0.2859 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30063 Z= 0.122 Angle : 0.666 15.607 40592 Z= 0.323 Chirality : 0.044 0.498 4527 Planarity : 0.004 0.070 5258 Dihedral : 4.190 29.234 4001 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.34 % Allowed : 18.25 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3616 helix: 1.25 (0.15), residues: 1296 sheet: -0.55 (0.24), residues: 507 loop : -0.42 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 64 TYR 0.026 0.001 TYR I 54 PHE 0.018 0.001 PHE N 54 TRP 0.012 0.001 TRP C 49 HIS 0.010 0.001 HIS B 980 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (30039) covalent geometry : angle 0.64680 / 0.32 (40556) hydrogen bonds : bond 0.03175 / 2.08 ( 1198) hydrogen bonds : angle 4.42174 / 3.10 ( 3390) metal coordination : bond 0.00617 / 0.37 ( 24) metal coordination : angle 5.31255 / 2.91 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10817.06 seconds wall clock time: 184 minutes 42.89 seconds (11082.89 seconds total)