Starting phenix.real_space_refine on Sun Aug 9 10:18:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sc1_54746/08_2026/9sc1_54746.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sc1_54746/08_2026/9sc1_54746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sc1_54746/08_2026/9sc1_54746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sc1_54746/08_2026/9sc1_54746.map" model { file = "/net/cci-nas-00/data/ceres_data/9sc1_54746/08_2026/9sc1_54746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sc1_54746/08_2026/9sc1_54746.cif" } resolution = 3.48 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= 0.034 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 100 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 20561 2.51 5 N 5765 2.21 5 O 6465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33083 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10942 Classifications: {'peptide': 1390} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1327} Chain breaks: 6 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 905 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 105.432 70.784 94.961 1.00147.88 S ATOM 479 SG CYS A 70 104.874 67.219 93.593 1.00139.31 S ATOM 532 SG CYS A 77 102.300 69.927 92.931 1.00134.67 S ATOM 762 SG CYS A 107 80.305 76.540 135.079 1.00182.03 S ATOM 786 SG CYS A 110 81.985 73.263 136.005 1.00170.83 S ATOM 1091 SG CYS A 148 78.545 74.017 137.318 1.00189.89 S ATOM 1105 SG CYS A 167 81.551 76.087 138.577 1.00179.49 S ATOM 19603 SG CYS B1163 97.231 58.308 104.935 1.00141.32 S ATOM 19621 SG CYS B1166 95.783 61.671 105.441 1.00153.38 S ATOM 19746 SG CYS B1182 99.609 61.146 104.712 1.00144.42 S ATOM 19765 SG CYS B1185 97.966 60.451 108.133 1.00140.95 S ATOM 20753 SG CYS C 86 91.936 74.940 25.701 1.00200.71 S ATOM 20770 SG CYS C 88 94.122 77.251 27.725 1.00205.78 S ATOM 20803 SG CYS C 92 92.891 78.268 24.294 1.00168.41 S ATOM 20826 SG CYS C 95 90.411 78.098 27.201 1.00158.97 S ATOM 28411 SG CYS I 7 40.112 125.175 128.617 1.00256.76 S ATOM 28436 SG CYS I 10 43.665 124.249 127.955 1.00252.49 S ATOM 28602 SG CYS I 29 41.559 121.771 129.922 1.00268.86 S ATOM 28626 SG CYS I 32 42.501 125.130 131.472 1.00267.19 S ATOM 28953 SG CYS I 75 15.862 115.676 89.991 1.00251.53 S ATOM 28975 SG CYS I 78 15.570 119.191 88.610 1.00257.12 S ATOM 29191 SG CYS I 103 18.861 117.476 88.382 1.00241.90 S ATOM 29211 SG CYS I 106 17.544 118.499 91.831 1.00233.35 S ATOM 29313 SG CYS J 7 62.735 90.310 37.670 1.00116.77 S ATOM 29336 SG CYS J 10 62.200 88.186 34.515 1.00119.98 S ATOM 29616 SG CYS J 45 59.261 89.178 36.629 1.00129.50 S ATOM 29622 SG CYS J 46 61.095 91.653 34.389 1.00123.20 S ATOM 30745 SG CYS L 31 96.271 113.817 53.895 1.00212.54 S ATOM 30765 SG CYS L 34 97.125 115.467 50.570 1.00221.64 S ATOM 30869 SG CYS L 48 99.863 114.666 53.138 1.00230.29 S ATOM 30892 SG CYS L 51 97.484 117.497 53.725 1.00239.32 S Time building chain proxies: 6.81, per 1000 atoms: 0.21 Number of scatterers: 33083 At special positions: 0 Unit cell: (151.241, 154.505, 183.883, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 182 16.00 P 100 15.00 Mg 2 11.99 O 6465 8.00 N 5765 7.00 C 20561 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: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 67 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 167 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 45 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 47 sheets defined 38.5% alpha, 20.0% beta 42 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 4.84 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.990A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.707A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.961A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.814A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.557A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 removed outlier: 3.536A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.601A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 710 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.762A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 843 removed outlier: 4.117A pdb=" N THR A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.649A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.663A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.526A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 removed outlier: 3.540A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1083 removed outlier: 3.523A pdb=" N LEU A1067 " --> pdb=" O MET A1063 " (cutoff:3.500A) Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1084 through 1086 No H-bonds generated for 'chain 'A' and resid 1084 through 1086' Processing helix chain 'A' and resid 1091 through 1107 removed outlier: 4.381A pdb=" N VAL A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Proline residue: A1099 - end of helix Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 4.113A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1220 removed outlier: 3.609A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.595A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.887A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.637A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.143A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 3.524A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.864A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix removed outlier: 3.506A pdb=" N GLU B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 439 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.902A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.924A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.611A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.594A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.616A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 813 removed outlier: 3.905A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 813 " --> pdb=" O GLU B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.154A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.804A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.540A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.532A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.501A pdb=" N TRP C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 removed outlier: 4.148A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.601A pdb=" N ASP C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 132 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 169 removed outlier: 3.820A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.662A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 5 through 27 removed outlier: 3.559A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 55 through 58 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 92 through 104 Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.526A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.532A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.513A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.605A pdb=" N GLU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.573A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.112A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.560A pdb=" N GLY J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 51 removed outlier: 3.875A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.586A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 10.078A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.753A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.566A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.782A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 470 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.568A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.509A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.054A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.755A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1284 through 1292 Processing sheet with id=AB5, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.375A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.010A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.010A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.418A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.418A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.098A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 223 through 227 removed outlier: 4.028A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.924A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 641 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.314A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.512A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.512A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.331A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.561A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.823A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.584A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE2, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE3, first strand: chain 'E' and resid 47 through 48 removed outlier: 4.961A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.451A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.018A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.895A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.554A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.736A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF1, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.130A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 1331 hydrogen bonds defined for protein. 3666 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 109 hydrogen bonds 218 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 11.33 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5413 1.31 - 1.44: 8962 1.44 - 1.56: 19010 1.56 - 1.69: 196 1.69 - 1.82: 292 Bond restraints: 33873 Sorted by residual: bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.181 0.193 1.00e-02 1.00e+04 3.71e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.207 0.163 1.20e-02 6.94e+03 1.84e+02 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.447 -0.110 1.10e-02 8.26e+03 1.00e+02 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.334 0.075 1.00e-02 1.00e+04 5.67e+01 bond pdb=" C2' ATP A1801 " pdb=" C3' ATP A1801 " ideal model delta sigma weight residual 1.531 1.453 0.078 1.20e-02 6.94e+03 4.19e+01 ... (remaining 33868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 46074 4.39 - 8.79: 76 8.79 - 13.18: 0 13.18 - 17.57: 2 17.57 - 21.96: 1 Bond angle restraints: 46153 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 117.91 21.96 1.00e+00 1.00e+00 4.82e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 120.42 16.41 1.00e+00 1.00e+00 2.69e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.37 -13.65 1.00e+00 1.00e+00 1.86e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 120.36 8.33 1.00e+00 1.00e+00 6.94e+01 angle pdb=" N3 ATP A1801 " pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 127.04 133.30 -6.26 1.15e+00 7.59e-01 2.97e+01 ... (remaining 46148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 19927 35.44 - 70.88: 509 70.88 - 106.32: 28 106.32 - 141.76: 2 141.76 - 177.20: 1 Dihedral angle restraints: 20467 sinusoidal: 9132 harmonic: 11335 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PHE A 22 " pdb=" C PHE A 22 " pdb=" N SER A 23 " pdb=" CA SER A 23 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ILE C 38 " pdb=" C ILE C 38 " pdb=" N ALA C 39 " pdb=" CA ALA C 39 " ideal model delta harmonic sigma weight residual -180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 20464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3469 0.036 - 0.071: 1181 0.071 - 0.107: 396 0.107 - 0.142: 132 0.142 - 0.178: 12 Chirality restraints: 5190 Sorted by residual: chirality pdb=" C1' A R 1 " pdb=" O4' A R 1 " pdb=" C2' A R 1 " pdb=" N9 A R 1 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" C3' DG N 58 " pdb=" C4' DG N 58 " pdb=" O3' DG N 58 " pdb=" C2' DG N 58 " both_signs ideal model delta sigma weight residual False -2.73 -2.90 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 5187 not shown) Planarity restraints: 5630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C LEU A 710 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A R 1 " 0.026 2.00e-02 2.50e+03 1.18e-02 3.85e+00 pdb=" N9 A R 1 " -0.028 2.00e-02 2.50e+03 pdb=" C8 A R 1 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A R 1 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A R 1 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A R 1 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A R 1 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A R 1 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A R 1 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A R 1 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A R 1 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 39 " 0.022 2.00e-02 2.50e+03 1.30e-02 3.80e+00 pdb=" N1 DC N 39 " -0.020 2.00e-02 2.50e+03 pdb=" C2 DC N 39 " 0.016 2.00e-02 2.50e+03 pdb=" O2 DC N 39 " -0.016 2.00e-02 2.50e+03 pdb=" N3 DC N 39 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC N 39 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC N 39 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC N 39 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC N 39 " -0.006 2.00e-02 2.50e+03 ... (remaining 5627 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 101 2.41 - 3.03: 19776 3.03 - 3.65: 48950 3.65 - 4.28: 75865 4.28 - 4.90: 126302 Nonbonded interactions: 270994 Sorted by model distance: nonbonded pdb=" O2G ATP A1801 " pdb="MG MG A1802 " model vdw 1.785 2.170 nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1802 " model vdw 1.857 2.170 nonbonded pdb=" O2B ATP A1801 " pdb="MG MG A1802 " model vdw 1.898 2.170 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 2.012 2.170 nonbonded pdb=" OE1 GLU A1062 " pdb=" OH TYR F 88 " model vdw 2.122 3.040 ... (remaining 270989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 42.090 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.005 0.193 33905 Z= 0.319 Angle : 0.615 21.964 46198 Z= 0.418 Chirality : 0.043 0.178 5190 Planarity : 0.003 0.048 5630 Dihedral : 14.241 177.200 13127 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.79 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.50 (0.14), residues: 3854 helix: 1.56 (0.15), residues: 1315 sheet: -0.05 (0.21), residues: 649 loop : -0.35 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1366 TYR 0.029 0.001 TYR B 797 PHE 0.019 0.001 PHE A1174 TRP 0.019 0.001 TRP A1044 HIS 0.008 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.32 (33873) covalent geometry : angle 0.60957 / 0.42 (46153) hydrogen bonds : bond 0.18268 / 12.14 ( 1404) hydrogen bonds : angle 6.83117 / 4.93 ( 3884) metal coordination : bond 0.00455 / 0.29 ( 32) metal coordination : angle 2.65910 / 1.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8960 (tp) cc_final: 0.8725 (tt) REVERT: A 147 VAL cc_start: 0.8536 (t) cc_final: 0.8317 (p) REVERT: A 175 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7892 (tmm-80) REVERT: A 256 GLN cc_start: 0.7384 (mm110) cc_final: 0.6565 (mt0) REVERT: A 261 ASP cc_start: 0.8826 (m-30) cc_final: 0.8388 (m-30) REVERT: A 330 LYS cc_start: 0.8223 (ptmt) cc_final: 0.8011 (pttp) REVERT: A 677 ARG cc_start: 0.8022 (mtt90) cc_final: 0.7809 (ttp80) REVERT: A 716 ASP cc_start: 0.9052 (t70) cc_final: 0.8774 (t0) REVERT: A 789 LYS cc_start: 0.8840 (mttt) cc_final: 0.8618 (mtpp) REVERT: A 812 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7861 (mt-10) REVERT: A 992 ASP cc_start: 0.8224 (m-30) cc_final: 0.7915 (t0) REVERT: A 1144 LYS cc_start: 0.9076 (ttmm) cc_final: 0.8462 (tppt) REVERT: A 1195 LEU cc_start: 0.8805 (mp) cc_final: 0.8588 (mp) REVERT: A 1205 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7817 (mtmm) REVERT: A 1209 MET cc_start: 0.7949 (mmt) cc_final: 0.7710 (mmt) REVERT: A 1285 MET cc_start: 0.8004 (mmt) cc_final: 0.7802 (tpp) REVERT: A 1317 MET cc_start: 0.9392 (ptt) cc_final: 0.9156 (ptp) REVERT: A 1368 MET cc_start: 0.9056 (mtm) cc_final: 0.8797 (mtm) REVERT: A 1419 ASP cc_start: 0.9018 (t0) cc_final: 0.8628 (t70) REVERT: B 183 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8348 (pm20) REVERT: B 267 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7848 (mtt-85) REVERT: B 308 TRP cc_start: 0.8686 (p-90) cc_final: 0.8480 (p-90) REVERT: B 399 ASP cc_start: 0.9015 (m-30) cc_final: 0.8756 (m-30) REVERT: B 445 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8030 (ttmm) REVERT: B 470 LYS cc_start: 0.8939 (mppt) cc_final: 0.8618 (mmtm) REVERT: B 498 THR cc_start: 0.9127 (m) cc_final: 0.8647 (p) REVERT: B 573 GLN cc_start: 0.8763 (tt0) cc_final: 0.7977 (tm-30) REVERT: B 595 ARG cc_start: 0.8483 (ttt180) cc_final: 0.8129 (ttt180) REVERT: B 598 GLU cc_start: 0.8657 (tp30) cc_final: 0.8264 (tm-30) REVERT: B 618 ASP cc_start: 0.8447 (t0) cc_final: 0.7029 (t0) REVERT: B 620 ARG cc_start: 0.8961 (ptp-170) cc_final: 0.8569 (ttp80) REVERT: B 621 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8097 (mp0) REVERT: B 622 LYS cc_start: 0.8775 (mttt) cc_final: 0.8463 (mttp) REVERT: B 764 SER cc_start: 0.9017 (m) cc_final: 0.8813 (p) REVERT: B 1152 MET cc_start: 0.8659 (mmm) cc_final: 0.8447 (mmm) REVERT: B 1222 ARG cc_start: 0.8621 (ptt180) cc_final: 0.8370 (ptt180) REVERT: C 15 LYS cc_start: 0.9135 (ptpt) cc_final: 0.8728 (pttp) REVERT: C 19 ASP cc_start: 0.8441 (t0) cc_final: 0.8066 (t0) REVERT: C 50 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7858 (tt0) REVERT: C 55 THR cc_start: 0.9376 (m) cc_final: 0.9107 (p) REVERT: C 207 CYS cc_start: 0.8934 (m) cc_final: 0.8568 (m) REVERT: D 8 PHE cc_start: 0.7482 (m-80) cc_final: 0.7203 (m-10) REVERT: D 38 ILE cc_start: 0.8225 (mt) cc_final: 0.7711 (mm) REVERT: D 50 LEU cc_start: 0.7576 (mt) cc_final: 0.7349 (mp) REVERT: D 61 GLU cc_start: 0.8595 (pt0) cc_final: 0.8005 (tp30) REVERT: D 134 THR cc_start: 0.8403 (t) cc_final: 0.7925 (p) REVERT: D 140 ASP cc_start: 0.7480 (m-30) cc_final: 0.7262 (m-30) REVERT: D 151 PHE cc_start: 0.4503 (m-80) cc_final: 0.3668 (m-80) REVERT: E 8 ASN cc_start: 0.9201 (m110) cc_final: 0.8658 (m-40) REVERT: E 48 ASP cc_start: 0.8058 (t70) cc_final: 0.7735 (t70) REVERT: E 74 ASP cc_start: 0.9183 (m-30) cc_final: 0.8912 (p0) REVERT: E 177 ARG cc_start: 0.8575 (mtt180) cc_final: 0.8333 (mtm-85) REVERT: F 127 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8879 (mt-10) REVERT: G 33 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7648 (mt-10) REVERT: G 71 ASN cc_start: 0.8639 (t0) cc_final: 0.8262 (t0) REVERT: G 140 LYS cc_start: 0.7054 (mttt) cc_final: 0.6842 (mppt) REVERT: G 151 ILE cc_start: 0.8271 (mt) cc_final: 0.7033 (tt) REVERT: H 9 ILE cc_start: 0.8660 (mp) cc_final: 0.8149 (tt) REVERT: H 19 ARG cc_start: 0.8643 (mmt180) cc_final: 0.8386 (mtp85) REVERT: H 32 THR cc_start: 0.9218 (m) cc_final: 0.8692 (p) REVERT: H 53 ASP cc_start: 0.8501 (m-30) cc_final: 0.8182 (m-30) REVERT: H 80 ARG cc_start: 0.8740 (mtp85) cc_final: 0.8496 (ttm110) REVERT: H 87 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8430 (mmt-90) REVERT: I 1 MET cc_start: 0.5092 (tpt) cc_final: 0.3660 (mmm) REVERT: I 44 TYR cc_start: 0.7824 (t80) cc_final: 0.7616 (t80) REVERT: J 26 GLN cc_start: 0.8971 (tt0) cc_final: 0.8534 (mt0) REVERT: J 49 MET cc_start: 0.9404 (tpp) cc_final: 0.9078 (tpp) REVERT: K 82 ASP cc_start: 0.8193 (t70) cc_final: 0.7859 (t0) REVERT: L 62 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7682 (mptt) REVERT: L 63 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7581 (ptp-170) REVERT: L 64 LEU cc_start: 0.8869 (tp) cc_final: 0.7801 (tp) outliers start: 0 outliers final: 0 residues processed: 682 average time/residue: 0.2655 time to fit residues: 276.7300 Evaluate side-chains 419 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS A 851 HIS A 994 GLN A 996 ASN ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 538 ASN B 786 ASN D 34 GLN D 138 ASN D 146 GLN E 8 ASN G 153 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 46 HIS K 2 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.122587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.083709 restraints weight = 56781.027| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.32 r_work: 0.2884 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33905 Z= 0.235 Angle : 0.638 10.816 46198 Z= 0.337 Chirality : 0.047 0.278 5190 Planarity : 0.005 0.065 5630 Dihedral : 16.786 175.350 5346 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 1.14 % Allowed : 7.25 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.34 (0.14), residues: 3854 helix: 1.42 (0.15), residues: 1346 sheet: -0.15 (0.21), residues: 645 loop : -0.46 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1122 TYR 0.020 0.002 TYR B 811 PHE 0.021 0.002 PHE A 219 TRP 0.014 0.001 TRP A1044 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (33873) covalent geometry : angle 0.62934 / 0.34 (46153) hydrogen bonds : bond 0.04794 / 3.19 ( 1404) hydrogen bonds : angle 5.21356 / 3.75 ( 3884) metal coordination : bond 0.00805 / 0.52 ( 32) metal coordination : angle 3.32306 / 2.18 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 437 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.9248 (tp) cc_final: 0.9032 (tt) REVERT: A 234 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8738 (mtp) REVERT: A 256 GLN cc_start: 0.7610 (mm110) cc_final: 0.6854 (mt0) REVERT: A 708 MET cc_start: 0.8022 (ttm) cc_final: 0.7668 (ttm) REVERT: A 789 LYS cc_start: 0.9163 (mttt) cc_final: 0.8948 (mtpp) REVERT: A 812 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7954 (mt-10) REVERT: A 1144 LYS cc_start: 0.9095 (ttmm) cc_final: 0.8584 (tppt) REVERT: A 1419 ASP cc_start: 0.9027 (t0) cc_final: 0.8818 (t70) REVERT: B 445 LYS cc_start: 0.8820 (mmtm) cc_final: 0.8241 (ttmm) REVERT: B 563 MET cc_start: 0.9018 (ttp) cc_final: 0.8806 (ttt) REVERT: B 573 GLN cc_start: 0.8742 (tt0) cc_final: 0.8105 (tm-30) REVERT: B 621 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8756 (mp0) REVERT: B 764 SER cc_start: 0.9199 (m) cc_final: 0.8994 (p) REVERT: C 15 LYS cc_start: 0.9116 (ptpt) cc_final: 0.8843 (pttp) REVERT: C 19 ASP cc_start: 0.8582 (t0) cc_final: 0.8340 (t0) REVERT: C 207 CYS cc_start: 0.8878 (m) cc_final: 0.8580 (m) REVERT: D 1 MET cc_start: 0.3131 (ptm) cc_final: 0.2815 (ptm) REVERT: D 38 ILE cc_start: 0.8337 (mt) cc_final: 0.8009 (mp) REVERT: D 61 GLU cc_start: 0.8551 (pt0) cc_final: 0.8000 (tp30) REVERT: D 120 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6298 (tp30) REVERT: G 71 ASN cc_start: 0.8999 (t0) cc_final: 0.8569 (t0) REVERT: G 82 PHE cc_start: 0.6041 (m-80) cc_final: 0.5546 (m-80) REVERT: G 151 ILE cc_start: 0.8153 (mt) cc_final: 0.7666 (tt) REVERT: H 9 ILE cc_start: 0.9162 (mp) cc_final: 0.8601 (tt) REVERT: H 37 LYS cc_start: 0.8965 (ptpp) cc_final: 0.8706 (ptpp) REVERT: H 87 ARG cc_start: 0.8625 (mmm-85) cc_final: 0.8410 (mmt-90) REVERT: I 1 MET cc_start: 0.5636 (tpt) cc_final: 0.5123 (mmm) REVERT: I 11 ASN cc_start: 0.7345 (t0) cc_final: 0.7097 (t0) REVERT: J 26 GLN cc_start: 0.8823 (tt0) cc_final: 0.8559 (mt0) REVERT: J 27 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7952 (tm-30) REVERT: J 49 MET cc_start: 0.9288 (tpp) cc_final: 0.8995 (tpp) REVERT: L 28 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8250 (mptt) REVERT: L 30 ILE cc_start: 0.8404 (mt) cc_final: 0.8055 (mm) REVERT: L 57 LEU cc_start: 0.8697 (mp) cc_final: 0.8361 (mt) REVERT: L 62 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7805 (mptt) REVERT: L 63 ARG cc_start: 0.7996 (mtm180) cc_final: 0.7746 (ptp-170) outliers start: 39 outliers final: 27 residues processed: 459 average time/residue: 0.2497 time to fit residues: 180.8755 Evaluate side-chains 410 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 382 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 242 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 373 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 333 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 ASN B1117 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.083443 restraints weight = 56524.153| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.34 r_work: 0.2874 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 33905 Z= 0.209 Angle : 0.594 9.206 46198 Z= 0.313 Chirality : 0.046 0.277 5190 Planarity : 0.004 0.047 5630 Dihedral : 16.706 175.581 5346 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.97 % Favored : 95.90 % Rotamer: Outliers : 1.34 % Allowed : 9.00 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.27 (0.14), residues: 3854 helix: 1.39 (0.15), residues: 1344 sheet: -0.18 (0.20), residues: 634 loop : -0.54 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1122 TYR 0.022 0.001 TYR H 129 PHE 0.021 0.002 PHE A 219 TRP 0.016 0.001 TRP A1228 HIS 0.009 0.001 HIS I 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (33873) covalent geometry : angle 0.58567 / 0.31 (46153) hydrogen bonds : bond 0.04208 / 2.82 ( 1404) hydrogen bonds : angle 4.92248 / 3.53 ( 3884) metal coordination : bond 0.00703 / 0.46 ( 32) metal coordination : angle 3.20199 / 2.14 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 396 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.9249 (tp) cc_final: 0.9038 (tt) REVERT: A 234 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8842 (mtp) REVERT: A 261 ASP cc_start: 0.8240 (t0) cc_final: 0.7761 (t0) REVERT: A 316 GLN cc_start: 0.7558 (tt0) cc_final: 0.7012 (mt0) REVERT: A 708 MET cc_start: 0.7948 (ttm) cc_final: 0.7720 (ttm) REVERT: A 812 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8032 (mt-10) REVERT: A 912 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9218 (pp) REVERT: B 445 LYS cc_start: 0.8828 (mmtm) cc_final: 0.8260 (ttmm) REVERT: B 573 GLN cc_start: 0.8748 (tt0) cc_final: 0.8111 (tm-30) REVERT: B 621 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8757 (mp0) REVERT: C 15 LYS cc_start: 0.9109 (ptpt) cc_final: 0.8778 (pttm) REVERT: C 19 ASP cc_start: 0.8567 (t0) cc_final: 0.8333 (t0) REVERT: C 207 CYS cc_start: 0.8881 (m) cc_final: 0.8551 (m) REVERT: D 61 GLU cc_start: 0.8536 (pt0) cc_final: 0.7946 (tp30) REVERT: D 120 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6306 (tp30) REVERT: D 175 PHE cc_start: 0.7783 (t80) cc_final: 0.7381 (t80) REVERT: F 114 GLU cc_start: 0.8796 (tp30) cc_final: 0.8557 (tp30) REVERT: G 50 ASP cc_start: 0.8731 (t70) cc_final: 0.8054 (t0) REVERT: G 71 ASN cc_start: 0.9000 (t0) cc_final: 0.8549 (t0) REVERT: G 151 ILE cc_start: 0.8227 (mt) cc_final: 0.7710 (tt) REVERT: H 9 ILE cc_start: 0.9163 (mp) cc_final: 0.8621 (tt) REVERT: H 37 LYS cc_start: 0.8918 (ptpp) cc_final: 0.8690 (ptpp) REVERT: H 87 ARG cc_start: 0.8584 (mmm-85) cc_final: 0.8336 (mmt-90) REVERT: I 1 MET cc_start: 0.5685 (tpt) cc_final: 0.5101 (mmm) REVERT: I 91 ARG cc_start: 0.8536 (mmt90) cc_final: 0.8262 (mmm-85) REVERT: J 27 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7993 (tm-30) REVERT: J 29 GLU cc_start: 0.8477 (mp0) cc_final: 0.8272 (mp0) REVERT: J 49 MET cc_start: 0.9298 (tpp) cc_final: 0.9027 (tpp) REVERT: L 28 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8247 (mptt) REVERT: L 30 ILE cc_start: 0.8417 (mt) cc_final: 0.8043 (mm) REVERT: L 57 LEU cc_start: 0.8623 (mp) cc_final: 0.8327 (mt) REVERT: L 62 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7798 (mptt) REVERT: L 63 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7732 (ptp-170) outliers start: 46 outliers final: 32 residues processed: 421 average time/residue: 0.2337 time to fit residues: 157.4137 Evaluate side-chains 404 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 370 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 0 optimal weight: 8.9990 chunk 345 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 216 optimal weight: 0.9990 chunk 286 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 chunk 251 optimal weight: 0.9980 chunk 308 optimal weight: 8.9990 chunk 352 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 GLN ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS A1106 ASN A1110 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.122637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.084508 restraints weight = 56275.865| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.29 r_work: 0.2888 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33905 Z= 0.176 Angle : 0.560 8.619 46198 Z= 0.295 Chirality : 0.044 0.280 5190 Planarity : 0.004 0.046 5630 Dihedral : 16.657 176.342 5346 Min Nonbonded Distance : 1.543 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 1.51 % Allowed : 9.64 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.30 (0.14), residues: 3854 helix: 1.42 (0.15), residues: 1353 sheet: -0.17 (0.20), residues: 634 loop : -0.52 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1122 TYR 0.020 0.001 TYR H 129 PHE 0.021 0.001 PHE A 219 TRP 0.011 0.001 TRP A1044 HIS 0.007 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (33873) covalent geometry : angle 0.55217 / 0.29 (46153) hydrogen bonds : bond 0.03820 / 2.57 ( 1404) hydrogen bonds : angle 4.73494 / 3.39 ( 3884) metal coordination : bond 0.00611 / 0.40 ( 32) metal coordination : angle 3.11708 / 2.10 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 386 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8803 (mmm) cc_final: 0.8538 (tpp) REVERT: A 205 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: A 234 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8903 (mtp) REVERT: A 261 ASP cc_start: 0.8166 (t0) cc_final: 0.7630 (t0) REVERT: A 316 GLN cc_start: 0.7744 (tt0) cc_final: 0.6978 (mt0) REVERT: A 708 MET cc_start: 0.7941 (ttm) cc_final: 0.7696 (ttm) REVERT: A 812 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8070 (mt-10) REVERT: A 1291 VAL cc_start: 0.9351 (t) cc_final: 0.8972 (m) REVERT: B 150 GLU cc_start: 0.8339 (tp30) cc_final: 0.7972 (pp20) REVERT: B 387 LEU cc_start: 0.8937 (mt) cc_final: 0.8736 (mp) REVERT: B 445 LYS cc_start: 0.8844 (mmtm) cc_final: 0.8299 (ttmm) REVERT: B 573 GLN cc_start: 0.8728 (tt0) cc_final: 0.8090 (tm-30) REVERT: B 621 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8714 (mp0) REVERT: C 15 LYS cc_start: 0.9075 (ptpt) cc_final: 0.8757 (pttm) REVERT: D 61 GLU cc_start: 0.8581 (pt0) cc_final: 0.7900 (tp30) REVERT: D 120 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6284 (tp30) REVERT: D 175 PHE cc_start: 0.7513 (t80) cc_final: 0.6994 (t80) REVERT: G 1 MET cc_start: 0.7493 (ttt) cc_final: 0.6839 (tmm) REVERT: G 50 ASP cc_start: 0.8833 (t70) cc_final: 0.8081 (t0) REVERT: G 71 ASN cc_start: 0.8987 (t0) cc_final: 0.8504 (t0) REVERT: G 151 ILE cc_start: 0.8219 (mt) cc_final: 0.7730 (tt) REVERT: H 9 ILE cc_start: 0.9178 (mp) cc_final: 0.8629 (tt) REVERT: I 1 MET cc_start: 0.5637 (tpt) cc_final: 0.5051 (mmm) REVERT: I 91 ARG cc_start: 0.8625 (mmt90) cc_final: 0.8353 (mmm-85) REVERT: J 29 GLU cc_start: 0.8460 (mp0) cc_final: 0.8205 (mp0) REVERT: K 16 GLU cc_start: 0.7786 (mp0) cc_final: 0.7498 (mp0) REVERT: K 49 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8553 (mm-30) REVERT: L 28 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8182 (mptt) REVERT: L 30 ILE cc_start: 0.8454 (mt) cc_final: 0.8072 (mm) REVERT: L 57 LEU cc_start: 0.8616 (mp) cc_final: 0.8326 (mt) REVERT: L 62 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7825 (mptt) REVERT: L 63 ARG cc_start: 0.8000 (mtm180) cc_final: 0.7749 (ptp-170) outliers start: 52 outliers final: 41 residues processed: 418 average time/residue: 0.2413 time to fit residues: 161.8105 Evaluate side-chains 410 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 367 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 1085 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 46 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 136 optimal weight: 0.0670 chunk 106 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 ASN A 706 HIS A1110 ASN A1140 HIS ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.086396 restraints weight = 56247.150| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.43 r_work: 0.2909 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33905 Z= 0.123 Angle : 0.530 8.048 46198 Z= 0.280 Chirality : 0.043 0.286 5190 Planarity : 0.003 0.047 5630 Dihedral : 16.571 177.138 5346 Min Nonbonded Distance : 1.530 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 1.34 % Allowed : 10.72 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.42 (0.14), residues: 3854 helix: 1.54 (0.15), residues: 1348 sheet: -0.12 (0.21), residues: 629 loop : -0.46 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1239 TYR 0.021 0.001 TYR H 129 PHE 0.021 0.001 PHE A 219 TRP 0.025 0.001 TRP B 561 HIS 0.005 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (33873) covalent geometry : angle 0.52328 / 0.28 (46153) hydrogen bonds : bond 0.03463 / 2.33 ( 1404) hydrogen bonds : angle 4.51674 / 3.24 ( 3884) metal coordination : bond 0.00491 / 0.32 ( 32) metal coordination : angle 2.83978 / 1.88 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 400 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8778 (mmm) cc_final: 0.8574 (tpp) REVERT: A 123 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7686 (mtm-85) REVERT: A 234 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8939 (mtp) REVERT: A 261 ASP cc_start: 0.8145 (t0) cc_final: 0.7594 (t0) REVERT: A 316 GLN cc_start: 0.7732 (tt0) cc_final: 0.6932 (mt0) REVERT: A 739 ASP cc_start: 0.8575 (m-30) cc_final: 0.7785 (m-30) REVERT: A 812 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8010 (mt-10) REVERT: A 1291 VAL cc_start: 0.9357 (t) cc_final: 0.8974 (m) REVERT: B 150 GLU cc_start: 0.8334 (tp30) cc_final: 0.7926 (pp20) REVERT: B 445 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8298 (ttmm) REVERT: B 573 GLN cc_start: 0.8739 (tt0) cc_final: 0.8088 (tm-30) REVERT: B 597 MET cc_start: 0.9203 (tpt) cc_final: 0.8690 (tpp) REVERT: B 621 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8650 (mp0) REVERT: B 898 LEU cc_start: 0.8284 (mt) cc_final: 0.8066 (mp) REVERT: C 15 LYS cc_start: 0.9086 (ptpt) cc_final: 0.8740 (pttm) REVERT: D 61 GLU cc_start: 0.8584 (pt0) cc_final: 0.7899 (tp30) REVERT: D 120 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6211 (tp30) REVERT: D 175 PHE cc_start: 0.7471 (t80) cc_final: 0.6539 (t80) REVERT: G 1 MET cc_start: 0.7322 (ttt) cc_final: 0.6164 (mtt) REVERT: G 44 TYR cc_start: 0.7717 (m-80) cc_final: 0.7269 (m-80) REVERT: G 50 ASP cc_start: 0.8855 (t70) cc_final: 0.8029 (t0) REVERT: G 71 ASN cc_start: 0.8985 (t0) cc_final: 0.8459 (t0) REVERT: G 151 ILE cc_start: 0.8161 (mt) cc_final: 0.7651 (tt) REVERT: H 9 ILE cc_start: 0.9149 (mp) cc_final: 0.8613 (tt) REVERT: H 37 LYS cc_start: 0.8976 (ptpp) cc_final: 0.8574 (pttp) REVERT: I 1 MET cc_start: 0.5547 (tpt) cc_final: 0.5038 (mmm) REVERT: I 44 TYR cc_start: 0.7927 (t80) cc_final: 0.7588 (t80) REVERT: J 29 GLU cc_start: 0.8552 (mp0) cc_final: 0.8225 (mp0) REVERT: K 16 GLU cc_start: 0.7837 (mp0) cc_final: 0.7426 (mp0) REVERT: L 28 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8095 (mptt) REVERT: L 30 ILE cc_start: 0.8450 (mt) cc_final: 0.8070 (mm) REVERT: L 36 SER cc_start: 0.7996 (m) cc_final: 0.7723 (p) REVERT: L 57 LEU cc_start: 0.8550 (mp) cc_final: 0.8329 (mt) REVERT: L 62 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7810 (mptt) REVERT: L 63 ARG cc_start: 0.8000 (mtm180) cc_final: 0.7737 (ptp-170) outliers start: 46 outliers final: 35 residues processed: 425 average time/residue: 0.2424 time to fit residues: 164.2425 Evaluate side-chains 412 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 376 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 1085 ILE Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 0.0040 chunk 101 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 742 ASN A1110 ASN A1140 HIS C 203 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.122838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.084053 restraints weight = 56226.148| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.33 r_work: 0.2886 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33905 Z= 0.174 Angle : 0.550 10.359 46198 Z= 0.288 Chirality : 0.044 0.289 5190 Planarity : 0.004 0.048 5630 Dihedral : 16.561 178.097 5346 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 1.72 % Allowed : 11.21 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.39 (0.14), residues: 3854 helix: 1.54 (0.15), residues: 1347 sheet: -0.16 (0.21), residues: 615 loop : -0.49 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 19 TYR 0.021 0.001 TYR B 666 PHE 0.024 0.001 PHE G 121 TRP 0.011 0.001 TRP B 561 HIS 0.007 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (33873) covalent geometry : angle 0.54388 / 0.29 (46153) hydrogen bonds : bond 0.03551 / 2.39 ( 1404) hydrogen bonds : angle 4.51155 / 3.23 ( 3884) metal coordination : bond 0.00581 / 0.38 ( 32) metal coordination : angle 2.77603 / 1.84 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 377 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8797 (mmm) cc_final: 0.8576 (tpp) REVERT: A 123 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7491 (mtm-85) REVERT: A 234 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8923 (mtp) REVERT: A 316 GLN cc_start: 0.7758 (tt0) cc_final: 0.7182 (tt0) REVERT: A 320 ARG cc_start: 0.9322 (ptm-80) cc_final: 0.9036 (ptm-80) REVERT: A 812 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8064 (mt-10) REVERT: A 1291 VAL cc_start: 0.9387 (t) cc_final: 0.9018 (m) REVERT: B 150 GLU cc_start: 0.8347 (tp30) cc_final: 0.7920 (pp20) REVERT: B 387 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8745 (mp) REVERT: B 445 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8328 (ttmm) REVERT: B 573 GLN cc_start: 0.8728 (tt0) cc_final: 0.8092 (tm-30) REVERT: B 597 MET cc_start: 0.9249 (tpt) cc_final: 0.8763 (tpp) REVERT: B 621 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8693 (mp0) REVERT: B 839 MET cc_start: 0.9250 (ptp) cc_final: 0.8982 (ptp) REVERT: B 898 LEU cc_start: 0.8344 (mt) cc_final: 0.8128 (mp) REVERT: C 15 LYS cc_start: 0.9125 (ptpt) cc_final: 0.8770 (pttm) REVERT: D 120 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6277 (tp30) REVERT: D 175 PHE cc_start: 0.7488 (t80) cc_final: 0.6667 (t80) REVERT: F 118 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8701 (tt) REVERT: G 1 MET cc_start: 0.7188 (ttt) cc_final: 0.6260 (mtt) REVERT: G 33 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7594 (mt-10) REVERT: G 44 TYR cc_start: 0.7769 (m-80) cc_final: 0.7302 (m-80) REVERT: G 50 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.7947 (t0) REVERT: G 71 ASN cc_start: 0.8983 (t0) cc_final: 0.8454 (t0) REVERT: G 151 ILE cc_start: 0.8136 (mt) cc_final: 0.7622 (tt) REVERT: H 9 ILE cc_start: 0.9171 (mp) cc_final: 0.8631 (tt) REVERT: I 1 MET cc_start: 0.5597 (tpt) cc_final: 0.5108 (mmm) REVERT: I 44 TYR cc_start: 0.7970 (t80) cc_final: 0.7626 (t80) REVERT: J 29 GLU cc_start: 0.8564 (mp0) cc_final: 0.8223 (mp0) REVERT: L 28 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8180 (mptt) REVERT: L 30 ILE cc_start: 0.8519 (mt) cc_final: 0.8141 (mm) REVERT: L 36 SER cc_start: 0.8034 (m) cc_final: 0.7792 (p) REVERT: L 57 LEU cc_start: 0.8564 (mp) cc_final: 0.8332 (mt) REVERT: L 62 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7872 (mptt) REVERT: L 63 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7708 (ptp-170) outliers start: 59 outliers final: 45 residues processed: 415 average time/residue: 0.2397 time to fit residues: 159.4758 Evaluate side-chains 415 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 366 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 382 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 306 optimal weight: 5.9990 chunk 78 optimal weight: 0.0170 chunk 354 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 357 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 chunk 351 optimal weight: 6.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1110 ASN A1140 HIS ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.122388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.083972 restraints weight = 56627.682| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.32 r_work: 0.2881 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33905 Z= 0.184 Angle : 0.556 10.112 46198 Z= 0.291 Chirality : 0.044 0.291 5190 Planarity : 0.004 0.052 5630 Dihedral : 16.549 178.727 5346 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 1.83 % Allowed : 11.85 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.37 (0.14), residues: 3854 helix: 1.54 (0.15), residues: 1346 sheet: -0.19 (0.21), residues: 592 loop : -0.50 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 92 TYR 0.021 0.001 TYR B 666 PHE 0.022 0.001 PHE G 2 TRP 0.010 0.001 TRP B 561 HIS 0.009 0.001 HIS I 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (33873) covalent geometry : angle 0.54964 / 0.29 (46153) hydrogen bonds : bond 0.03585 / 2.41 ( 1404) hydrogen bonds : angle 4.48486 / 3.21 ( 3884) metal coordination : bond 0.00608 / 0.39 ( 32) metal coordination : angle 2.78908 / 1.84 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 365 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8794 (mmm) cc_final: 0.8579 (tpp) REVERT: A 234 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8949 (mtp) REVERT: A 261 ASP cc_start: 0.8341 (t0) cc_final: 0.7901 (t0) REVERT: A 316 GLN cc_start: 0.7823 (tt0) cc_final: 0.7405 (mt0) REVERT: A 812 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8041 (mt-10) REVERT: A 982 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8361 (p) REVERT: B 150 GLU cc_start: 0.8290 (tp30) cc_final: 0.7906 (pp20) REVERT: B 445 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8318 (ttmm) REVERT: B 573 GLN cc_start: 0.8747 (tt0) cc_final: 0.8089 (tm-30) REVERT: B 597 MET cc_start: 0.9226 (tpt) cc_final: 0.8729 (tpp) REVERT: B 621 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8694 (mp0) REVERT: B 839 MET cc_start: 0.9252 (ptp) cc_final: 0.8997 (ptp) REVERT: B 898 LEU cc_start: 0.8336 (mt) cc_final: 0.8115 (mp) REVERT: C 15 LYS cc_start: 0.9113 (ptpt) cc_final: 0.8765 (pttm) REVERT: D 120 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6212 (tp30) REVERT: F 118 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8687 (tt) REVERT: G 6 ASP cc_start: 0.8276 (m-30) cc_final: 0.7981 (m-30) REVERT: G 44 TYR cc_start: 0.7874 (m-80) cc_final: 0.7338 (m-80) REVERT: G 50 ASP cc_start: 0.8877 (t70) cc_final: 0.7938 (t0) REVERT: G 71 ASN cc_start: 0.8981 (t0) cc_final: 0.8688 (t0) REVERT: G 151 ILE cc_start: 0.8123 (mt) cc_final: 0.7603 (tt) REVERT: H 9 ILE cc_start: 0.9174 (mp) cc_final: 0.8636 (tt) REVERT: I 1 MET cc_start: 0.5422 (tpt) cc_final: 0.4926 (mmm) REVERT: I 44 TYR cc_start: 0.7955 (t80) cc_final: 0.7616 (t80) REVERT: J 29 GLU cc_start: 0.8577 (mp0) cc_final: 0.8214 (mp0) REVERT: K 16 GLU cc_start: 0.7786 (mp0) cc_final: 0.7494 (mp0) REVERT: L 28 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8159 (mptt) REVERT: L 30 ILE cc_start: 0.8421 (mt) cc_final: 0.8043 (mm) REVERT: L 57 LEU cc_start: 0.8493 (mp) cc_final: 0.8255 (mt) REVERT: L 62 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7870 (mptt) REVERT: L 63 ARG cc_start: 0.8023 (mtm180) cc_final: 0.7698 (ptp-170) outliers start: 63 outliers final: 47 residues processed: 403 average time/residue: 0.2426 time to fit residues: 156.4986 Evaluate side-chains 408 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 358 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 363 optimal weight: 7.9990 chunk 243 optimal weight: 0.0470 chunk 331 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 56 optimal weight: 0.0870 chunk 12 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 275 optimal weight: 0.0040 overall best weight: 0.3868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 698 GLN A 706 HIS A 975 HIS A1110 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.125111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.087031 restraints weight = 56065.500| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.32 r_work: 0.2981 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33905 Z= 0.099 Angle : 0.517 10.616 46198 Z= 0.272 Chirality : 0.042 0.299 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.447 179.428 5346 Min Nonbonded Distance : 1.473 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.93 % Favored : 96.96 % Rotamer: Outliers : 1.34 % Allowed : 12.70 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.50 (0.14), residues: 3854 helix: 1.65 (0.15), residues: 1346 sheet: -0.15 (0.21), residues: 590 loop : -0.41 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 92 TYR 0.024 0.001 TYR B 666 PHE 0.020 0.001 PHE A 219 TRP 0.014 0.001 TRP B 561 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (33873) covalent geometry : angle 0.51089 / 0.27 (46153) hydrogen bonds : bond 0.03174 / 2.13 ( 1404) hydrogen bonds : angle 4.30992 / 3.08 ( 3884) metal coordination : bond 0.00387 / 0.25 ( 32) metal coordination : angle 2.56963 / 1.68 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 397 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8807 (mmm) cc_final: 0.8598 (tpp) REVERT: A 234 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8852 (mtm) REVERT: A 316 GLN cc_start: 0.7814 (tt0) cc_final: 0.7434 (tt0) REVERT: A 724 GLU cc_start: 0.8673 (tp30) cc_final: 0.8390 (tp30) REVERT: A 812 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8065 (mt-10) REVERT: A 997 LEU cc_start: 0.9010 (mt) cc_final: 0.8702 (mp) REVERT: A 1291 VAL cc_start: 0.9378 (t) cc_final: 0.9030 (m) REVERT: B 150 GLU cc_start: 0.8281 (tp30) cc_final: 0.7955 (pp20) REVERT: B 387 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8640 (mp) REVERT: B 445 LYS cc_start: 0.8813 (mmtm) cc_final: 0.8302 (ttmm) REVERT: B 573 GLN cc_start: 0.8670 (tt0) cc_final: 0.8022 (tm-30) REVERT: B 618 ASP cc_start: 0.8747 (t0) cc_final: 0.7201 (t0) REVERT: B 620 ARG cc_start: 0.8812 (ttp80) cc_final: 0.8413 (tpp80) REVERT: B 621 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8334 (mp0) REVERT: B 839 MET cc_start: 0.9241 (ptp) cc_final: 0.8989 (ptp) REVERT: C 15 LYS cc_start: 0.9066 (ptpt) cc_final: 0.8749 (pttm) REVERT: D 120 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6167 (tp30) REVERT: F 119 ARG cc_start: 0.8975 (tpp80) cc_final: 0.8763 (mmm-85) REVERT: G 44 TYR cc_start: 0.7860 (m-80) cc_final: 0.7346 (m-80) REVERT: G 50 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.7731 (t0) REVERT: G 71 ASN cc_start: 0.8951 (t0) cc_final: 0.8640 (t0) REVERT: G 151 ILE cc_start: 0.8101 (mt) cc_final: 0.7568 (tt) REVERT: H 9 ILE cc_start: 0.9139 (mp) cc_final: 0.8587 (tt) REVERT: H 35 GLN cc_start: 0.9025 (pt0) cc_final: 0.8761 (pt0) REVERT: I 1 MET cc_start: 0.5509 (tpt) cc_final: 0.4994 (mmm) REVERT: I 44 TYR cc_start: 0.7929 (t80) cc_final: 0.7673 (t80) REVERT: J 29 GLU cc_start: 0.8531 (mp0) cc_final: 0.8151 (mp0) REVERT: K 16 GLU cc_start: 0.7796 (mp0) cc_final: 0.7429 (mp0) REVERT: L 28 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8227 (mptt) REVERT: L 30 ILE cc_start: 0.8497 (mt) cc_final: 0.8127 (mm) REVERT: L 36 SER cc_start: 0.7958 (m) cc_final: 0.7751 (p) REVERT: L 53 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.6372 (t70) REVERT: L 63 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7690 (ptp-170) outliers start: 46 outliers final: 32 residues processed: 416 average time/residue: 0.2365 time to fit residues: 157.5567 Evaluate side-chains 410 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 374 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 1085 ILE Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 58 optimal weight: 5.9990 chunk 377 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 331 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 742 ASN A1140 HIS B 786 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.082017 restraints weight = 56704.000| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.29 r_work: 0.2845 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 33905 Z= 0.305 Angle : 0.644 9.529 46198 Z= 0.332 Chirality : 0.047 0.299 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.567 179.965 5346 Min Nonbonded Distance : 1.513 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.56 % Rotamer: Outliers : 1.40 % Allowed : 13.10 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.27 (0.14), residues: 3854 helix: 1.45 (0.15), residues: 1348 sheet: -0.33 (0.21), residues: 614 loop : -0.54 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 92 TYR 0.015 0.002 TYR H 141 PHE 0.022 0.002 PHE A 219 TRP 0.010 0.001 TRP H 79 HIS 0.012 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.31 (33873) covalent geometry : angle 0.63749 / 0.33 (46153) hydrogen bonds : bond 0.04051 / 2.72 ( 1404) hydrogen bonds : angle 4.58426 / 3.28 ( 3884) metal coordination : bond 0.00974 / 0.61 ( 32) metal coordination : angle 3.05750 / 2.04 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 361 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8810 (mmm) cc_final: 0.8578 (tpp) REVERT: A 234 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8960 (mtp) REVERT: A 812 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8152 (mt-10) REVERT: A 873 MET cc_start: 0.9262 (mmt) cc_final: 0.8221 (mpp) REVERT: B 61 ASP cc_start: 0.8619 (m-30) cc_final: 0.8307 (t0) REVERT: B 150 GLU cc_start: 0.8352 (tp30) cc_final: 0.7960 (pp20) REVERT: B 387 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8728 (mp) REVERT: B 445 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8339 (ttmm) REVERT: B 476 ARG cc_start: 0.8417 (ttm-80) cc_final: 0.8017 (mtm180) REVERT: B 573 GLN cc_start: 0.8748 (tt0) cc_final: 0.8037 (tm-30) REVERT: B 621 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8750 (mp0) REVERT: B 839 MET cc_start: 0.9288 (ptp) cc_final: 0.9054 (ptp) REVERT: B 841 MET cc_start: 0.9361 (ttm) cc_final: 0.8957 (ttt) REVERT: C 15 LYS cc_start: 0.9124 (ptpt) cc_final: 0.8778 (pttm) REVERT: C 264 GLN cc_start: 0.8646 (tp40) cc_final: 0.8013 (tm-30) REVERT: D 120 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6221 (tp30) REVERT: G 50 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.7647 (t0) REVERT: G 71 ASN cc_start: 0.8975 (t0) cc_final: 0.8653 (t0) REVERT: G 151 ILE cc_start: 0.8118 (mt) cc_final: 0.7576 (tt) REVERT: H 9 ILE cc_start: 0.9173 (mp) cc_final: 0.8636 (tt) REVERT: I 44 TYR cc_start: 0.7980 (t80) cc_final: 0.7760 (t80) REVERT: J 29 GLU cc_start: 0.8588 (mp0) cc_final: 0.8193 (mp0) REVERT: K 16 GLU cc_start: 0.7822 (mp0) cc_final: 0.7434 (mp0) REVERT: L 28 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8185 (mptt) REVERT: L 30 ILE cc_start: 0.8500 (mt) cc_final: 0.8171 (mm) REVERT: L 53 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.6334 (t70) REVERT: L 62 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7889 (mptt) REVERT: L 63 ARG cc_start: 0.8055 (mtm180) cc_final: 0.7699 (ptp-170) outliers start: 48 outliers final: 33 residues processed: 391 average time/residue: 0.2425 time to fit residues: 151.2748 Evaluate side-chains 393 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 356 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 308 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 314 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 321 optimal weight: 0.0970 chunk 241 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 706 HIS A 742 ASN A1110 ASN A1140 HIS ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.123940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.085906 restraints weight = 56496.748| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.32 r_work: 0.2911 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33905 Z= 0.112 Angle : 0.533 10.342 46198 Z= 0.278 Chirality : 0.042 0.303 5190 Planarity : 0.004 0.055 5630 Dihedral : 16.455 179.602 5346 Min Nonbonded Distance : 1.280 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % Rotamer: Outliers : 1.05 % Allowed : 13.57 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.43 (0.14), residues: 3854 helix: 1.62 (0.15), residues: 1349 sheet: -0.27 (0.21), residues: 595 loop : -0.46 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 92 TYR 0.017 0.001 TYR H 129 PHE 0.020 0.001 PHE A 219 TRP 0.011 0.001 TRP A1044 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (33873) covalent geometry : angle 0.52661 / 0.28 (46153) hydrogen bonds : bond 0.03331 / 2.24 ( 1404) hydrogen bonds : angle 4.33131 / 3.09 ( 3884) metal coordination : bond 0.00411 / 0.27 ( 32) metal coordination : angle 2.70349 / 1.77 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 365 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8812 (mmm) cc_final: 0.8593 (tpp) REVERT: A 234 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8927 (mtm) REVERT: A 724 GLU cc_start: 0.8694 (tp30) cc_final: 0.8426 (tp30) REVERT: A 812 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 61 ASP cc_start: 0.8539 (m-30) cc_final: 0.8232 (t0) REVERT: B 150 GLU cc_start: 0.8312 (tp30) cc_final: 0.7926 (pp20) REVERT: B 387 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8595 (mp) REVERT: B 573 GLN cc_start: 0.8726 (tt0) cc_final: 0.8042 (tm-30) REVERT: B 597 MET cc_start: 0.9306 (tpt) cc_final: 0.8613 (tpp) REVERT: B 620 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8424 (tpp80) REVERT: B 621 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8712 (mp0) REVERT: B 839 MET cc_start: 0.9286 (ptp) cc_final: 0.9045 (ptp) REVERT: C 15 LYS cc_start: 0.9100 (ptpt) cc_final: 0.8764 (pttm) REVERT: D 1 MET cc_start: 0.1811 (ttt) cc_final: 0.0650 (tpt) REVERT: D 120 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6270 (tp30) REVERT: F 119 ARG cc_start: 0.8991 (tpp80) cc_final: 0.8692 (mmm-85) REVERT: G 44 TYR cc_start: 0.7694 (m-80) cc_final: 0.7345 (m-80) REVERT: G 50 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.7697 (t0) REVERT: G 71 ASN cc_start: 0.8964 (t0) cc_final: 0.8661 (t0) REVERT: G 151 ILE cc_start: 0.8092 (mt) cc_final: 0.7545 (tt) REVERT: H 9 ILE cc_start: 0.9152 (mp) cc_final: 0.8610 (tt) REVERT: H 35 GLN cc_start: 0.9027 (pt0) cc_final: 0.8744 (pt0) REVERT: I 1 MET cc_start: 0.5424 (tpt) cc_final: 0.4920 (mmm) REVERT: I 44 TYR cc_start: 0.7975 (t80) cc_final: 0.7727 (t80) REVERT: J 29 GLU cc_start: 0.8569 (mp0) cc_final: 0.8166 (mp0) REVERT: K 16 GLU cc_start: 0.7829 (mp0) cc_final: 0.7421 (mp0) REVERT: L 28 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8189 (mptt) REVERT: L 30 ILE cc_start: 0.8468 (mt) cc_final: 0.8156 (mm) REVERT: L 36 SER cc_start: 0.7974 (m) cc_final: 0.7723 (p) REVERT: L 53 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.6253 (t70) REVERT: L 63 ARG cc_start: 0.8023 (mtm180) cc_final: 0.7668 (ptp-170) outliers start: 36 outliers final: 25 residues processed: 388 average time/residue: 0.2396 time to fit residues: 148.6656 Evaluate side-chains 386 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 357 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1258 HIS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1373 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 352 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 354 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 374 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 343 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1110 ASN A1140 HIS ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.122391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.084446 restraints weight = 56289.937| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.29 r_work: 0.2882 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33905 Z= 0.182 Angle : 0.560 9.918 46198 Z= 0.291 Chirality : 0.044 0.308 5190 Planarity : 0.004 0.047 5630 Dihedral : 16.432 179.013 5346 Min Nonbonded Distance : 1.231 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.84 % Favored : 96.06 % Rotamer: Outliers : 0.93 % Allowed : 13.89 % Favored : 85.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.41 % 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: 0.38 (0.14), residues: 3854 helix: 1.58 (0.15), residues: 1350 sheet: -0.30 (0.21), residues: 585 loop : -0.48 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 75 TYR 0.014 0.001 TYR H 129 PHE 0.021 0.001 PHE A 219 TRP 0.011 0.001 TRP B 561 HIS 0.007 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (33873) covalent geometry : angle 0.55352 / 0.29 (46153) hydrogen bonds : bond 0.03525 / 2.36 ( 1404) hydrogen bonds : angle 4.37094 / 3.12 ( 3884) metal coordination : bond 0.00622 / 0.39 ( 32) metal coordination : angle 2.69013 / 1.79 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9334.62 seconds wall clock time: 160 minutes 45.26 seconds (9645.26 seconds total)