Starting phenix.real_space_refine on Sun Aug 9 02:55:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qw9_18683/08_2026/8qw9_18683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qw9_18683/08_2026/8qw9_18683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qw9_18683/08_2026/8qw9_18683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qw9_18683/08_2026/8qw9_18683.map" model { file = "/net/cci-nas-00/data/ceres_data/8qw9_18683/08_2026/8qw9_18683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qw9_18683/08_2026/8qw9_18683.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 7 6.06 5 P 37 5.49 5 Mg 1 5.21 5 S 193 5.16 5 C 19923 2.51 5 N 5553 2.21 5 O 5997 1.98 5 H 645 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 253 residue(s): 0.23s 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: 32356 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1371, 10833 Classifications: {'peptide': 1371} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 65, 'TRANS': 1303} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 8802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1106, 8802 Classifications: {'peptide': 1106} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 52, 'TRANS': 1053} Chain breaks: 7 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2039 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 239} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 197} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 623 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 72} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1172 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 143} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 520 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 368 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 213 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "N" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 162 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "R" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1376 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 7, 'GLU:plan': 5, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "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 464 SG CYS A 71 57.404 73.347 92.031 1.00 79.91 S ATOM 486 SG CYS A 74 58.277 70.129 92.411 1.00 80.38 S ATOM 533 SG CYS A 81 61.054 72.580 91.409 1.00 80.19 S ATOM 768 SG CYS A 111 67.021 57.055 45.350 1.00 98.79 S ATOM 790 SG CYS A 114 64.709 54.372 46.513 1.00101.88 S ATOM 20329 SG CYS C 88 96.936 96.172 144.392 1.00 53.40 S ATOM 20342 SG CYS C 90 94.457 97.765 141.906 1.00 64.39 S ATOM 20377 SG CYS C 94 96.394 99.793 144.504 1.00 47.78 S ATOM 20399 SG CYS C 97 98.028 98.335 141.333 1.00 41.58 S ATOM 25203 SG CYS I 17 115.617 95.353 19.306 1.00 86.09 S ATOM 25227 SG CYS I 20 112.378 95.105 21.220 1.00 88.12 S ATOM 25388 SG CYS I 39 113.714 92.052 19.214 1.00 88.51 S ATOM 25410 SG CYS I 42 112.907 94.664 17.081 1.00 91.58 S ATOM 25759 SG CYS I 86 150.020 97.726 49.339 1.00 73.63 S ATOM 25783 SG CYS I 89 150.986 101.425 49.809 1.00 78.19 S ATOM 25969 SG CYS I 114 148.230 99.960 51.895 1.00 58.40 S ATOM 26004 SG CYS I 119 147.732 100.456 48.177 1.00 70.43 S ATOM 26114 SG CYS J 7 121.424 98.841 119.636 1.00 30.55 S ATOM 26138 SG CYS J 10 122.823 97.514 122.932 1.00 26.37 S ATOM 26398 SG CYS J 44 124.761 96.857 119.743 1.00 27.85 S ATOM 26404 SG CYS J 45 124.575 100.255 121.431 1.00 30.50 S ATOM 27541 SG CYS L 19 87.375 123.595 104.173 1.00 66.82 S ATOM 27560 SG CYS L 22 87.745 126.935 106.061 1.00 72.19 S ATOM 27677 SG CYS L 36 84.383 125.670 104.962 1.00 81.62 S Time building chain proxies: 6.61, per 1000 atoms: 0.20 Number of scatterers: 32356 At special positions: 0 Unit cell: (168.387, 143.379, 160.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 7 29.99 S 193 16.00 P 37 15.00 Mg 1 11.99 O 5997 8.00 N 5553 7.00 C 19923 6.00 H 645 1.00 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: 2.82 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " 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 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " Number of angles added : 27 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7380 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 44 sheets defined 39.5% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.893A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 301 through 319 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.774A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.723A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 550 removed outlier: 4.097A pdb=" N ARG A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 Processing helix chain 'A' and resid 588 through 596 removed outlier: 4.142A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 4.123A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.552A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.835A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 897 through 901 removed outlier: 3.681A pdb=" N VAL A 901 " --> pdb=" O GLY A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.513A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.272A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.726A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 5.491A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.827A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1161 Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.645A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1295 Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.531A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1371 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.720A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1422 removed outlier: 3.683A pdb=" N GLN A1422 " --> pdb=" O GLY A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.665A pdb=" N LYS A1429 " --> pdb=" O GLY A1425 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.849A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.535A pdb=" N ALA B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 3.525A pdb=" N LEU B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 306 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 332 through 346 Processing helix chain 'B' and resid 357 through 377 removed outlier: 3.956A pdb=" N TYR B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 425 removed outlier: 3.871A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 Processing helix chain 'B' and resid 436 through 451 removed outlier: 4.370A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.710A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 658 Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.683A pdb=" N VAL B 673 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.707A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.937A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 739 through 743 removed outlier: 3.640A pdb=" N ARG B 743 " --> pdb=" O PHE B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.997A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.728A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.053A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.652A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.744A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.660A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.727A pdb=" N CYS C 88 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.509A pdb=" N TRP C 176 " --> pdb=" O HIS C 173 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 177 " --> pdb=" O ALA C 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 173 through 177' Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.624A pdb=" N GLU C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 203' Processing helix chain 'C' and resid 242 through 268 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 133 through 136 removed outlier: 3.607A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.595A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.725A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.903A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.530A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.578A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'R' and resid 498 through 516 Processing helix chain 'R' and resid 546 through 565 removed outlier: 3.505A pdb=" N ARG R 555 " --> pdb=" O GLU R 551 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU R 556 " --> pdb=" O HIS R 552 " (cutoff:3.500A) Processing helix chain 'R' and resid 577 through 591 Processing helix chain 'R' and resid 593 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.598A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.516A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 94 removed outlier: 6.519A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 192 removed outlier: 3.565A pdb=" N GLU A 201 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.860A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.778A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 501 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.907A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.164A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 603 removed outlier: 3.598A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB4, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.701A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB6, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.676A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1243 through 1247 Processing sheet with id=AB8, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 3.633A pdb=" N LYS A1319 " --> pdb=" O LEU A1331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.419A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.419A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 93 removed outlier: 6.423A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC4, first strand: chain 'B' and resid 197 through 200 Processing sheet with id=AC5, first strand: chain 'B' and resid 205 through 209 removed outlier: 6.634A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC7, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC8, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.403A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 747 through 751 removed outlier: 3.576A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 747 through 751 removed outlier: 3.576A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD3, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.124A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD5, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.952A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.831A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 234 " --> pdb=" O GLY C 181 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 44 through 47 Processing sheet with id=AD8, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.792A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.480A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 64 removed outlier: 6.274A pdb=" N ASP E 70 " --> pdb=" O HIS E 64 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ARG E 101 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE4, first strand: chain 'I' and resid 25 through 29 removed outlier: 3.675A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE6, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.776A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.818A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 118 through 120 1359 hydrogen bonds defined for protein. 3804 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.11 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 157 1.06 - 1.25: 4787 1.25 - 1.44: 9258 1.44 - 1.63: 18510 1.63 - 1.82: 306 Bond restraints: 33018 Sorted by residual: bond pdb=" N HIS R 609 " pdb=" H HIS R 609 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" NE2 HIS R 585 " pdb=" HE2 HIS R 585 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CD2 PHE R 588 " pdb=" HD2 PHE R 588 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N ALA R 537 " pdb=" H ALA R 537 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N LEU R 602 " pdb=" H LEU R 602 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 33013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 44436 2.47 - 4.93: 816 4.93 - 7.40: 138 7.40 - 9.86: 11 9.86 - 12.33: 4 Bond angle restraints: 45405 Sorted by residual: angle pdb=" O4' DG T 28 " pdb=" C4' DG T 28 " pdb=" C3' DG T 28 " ideal model delta sigma weight residual 106.00 102.00 4.00 6.00e-01 2.78e+00 4.44e+01 angle pdb=" N ARG C 228 " pdb=" CA ARG C 228 " pdb=" C ARG C 228 " ideal model delta sigma weight residual 111.74 120.44 -8.70 1.35e+00 5.49e-01 4.15e+01 angle pdb=" N GLY A 973 " pdb=" CA GLY A 973 " pdb=" C GLY A 973 " ideal model delta sigma weight residual 113.76 124.21 -10.45 1.80e+00 3.09e-01 3.37e+01 angle pdb=" CA ASP R 497 " pdb=" CB ASP R 497 " pdb=" CG ASP R 497 " ideal model delta sigma weight residual 112.60 117.59 -4.99 1.00e+00 1.00e+00 2.49e+01 angle pdb=" N PHE C 229 " pdb=" CA PHE C 229 " pdb=" C PHE C 229 " ideal model delta sigma weight residual 110.10 117.40 -7.30 1.49e+00 4.50e-01 2.40e+01 ... (remaining 45400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.25: 19506 32.25 - 64.50: 416 64.50 - 96.75: 47 96.75 - 129.01: 0 129.01 - 161.26: 2 Dihedral angle restraints: 19971 sinusoidal: 8555 harmonic: 11416 Sorted by residual: dihedral pdb=" CA LYS R 516 " pdb=" C LYS R 516 " pdb=" N GLY R 517 " pdb=" CA GLY R 517 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLY R 517 " pdb=" C GLY R 517 " pdb=" N LYS R 518 " pdb=" CA LYS R 518 " ideal model delta harmonic sigma weight residual -180.00 -152.23 -27.77 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 19968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4455 0.083 - 0.166: 487 0.166 - 0.249: 11 0.249 - 0.333: 5 0.333 - 0.416: 2 Chirality restraints: 4960 Sorted by residual: chirality pdb=" CA ARG C 228 " pdb=" N ARG C 228 " pdb=" C ARG C 228 " pdb=" CB ARG C 228 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" P DG T 25 " pdb=" OP1 DG T 25 " pdb=" OP2 DG T 25 " pdb=" O5' DG T 25 " both_signs ideal model delta sigma weight residual True 2.34 -2.75 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" P DG T 28 " pdb=" OP1 DG T 28 " pdb=" OP2 DG T 28 " pdb=" O5' DG T 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.63 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4957 not shown) Planarity restraints: 5654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 504 " -0.156 2.00e-02 2.50e+03 5.26e-02 1.11e+02 pdb=" CG TRP R 504 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP R 504 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP R 504 " 0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP R 504 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TRP R 504 " 0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP R 504 " 0.042 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 504 " -0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 504 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP R 504 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 TRP R 504 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP R 504 " 0.022 2.00e-02 2.50e+03 pdb=" HE3 TRP R 504 " 0.056 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 504 " -0.042 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 504 " 0.020 2.00e-02 2.50e+03 pdb=" HH2 TRP R 504 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 508 " 0.075 2.00e-02 2.50e+03 3.47e-02 3.61e+01 pdb=" CG TYR R 508 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR R 508 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR R 508 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR R 508 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR R 508 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR R 508 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 508 " 0.075 2.00e-02 2.50e+03 pdb=" HD1 TYR R 508 " -0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR R 508 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR R 508 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 TYR R 508 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS R 516 " -0.032 2.00e-02 2.50e+03 5.85e-02 3.43e+01 pdb=" N GLY R 517 " 0.101 2.00e-02 2.50e+03 pdb=" CA GLY R 517 " -0.029 2.00e-02 2.50e+03 pdb=" H GLY R 517 " -0.041 2.00e-02 2.50e+03 ... (remaining 5651 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 82 2.24 - 2.83: 12153 2.83 - 3.42: 36413 3.42 - 4.01: 61630 4.01 - 4.60: 91658 Nonbonded interactions: 201936 Sorted by model distance: nonbonded pdb=" OE2 GLU R 584 " pdb=" HH TYR R 597 " model vdw 1.648 2.450 nonbonded pdb=" O LEU R 583 " pdb=" HG1 THR R 587 " model vdw 1.707 2.450 nonbonded pdb=" OE2 GLU R 536 " pdb=" HE2 HIS R 585 " model vdw 1.770 2.450 nonbonded pdb=" OE2 GLU R 498 " pdb=" HZ2 LYS R 501 " model vdw 1.770 2.450 nonbonded pdb=" OE1 GLU R 536 " pdb="HH21 ARG R 541 " model vdw 1.803 2.450 ... (remaining 201931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.210 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: 0.300 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 37.630 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.006 0.210 32398 Z= 0.296 Angle : 0.726 18.187 43948 Z= 0.451 Chirality : 0.050 0.416 4960 Planarity : 0.005 0.101 5558 Dihedral : 13.284 161.258 12380 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.60 % Rotamer: Outliers : 0.65 % Allowed : 6.40 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: -0.46 (0.13), residues: 3849 helix: 0.65 (0.14), residues: 1377 sheet: -0.36 (0.23), residues: 539 loop : -0.96 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 16 TYR 0.072 0.002 TYR R 508 PHE 0.048 0.002 PHE R 588 TRP 0.107 0.003 TRP R 504 HIS 0.009 0.001 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.29 (32373) covalent geometry : angle 0.70820 / 0.45 (43921) hydrogen bonds : bond 0.16269 / 10.83 ( 1322) hydrogen bonds : angle 6.98173 / 4.90 ( 3804) metal coordination : bond 0.04737 / 2.41 ( 25) metal coordination : angle 6.43335 / 5.11 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 521 is missing expected H atoms. Skipping. Residue ILE 522 is missing expected H atoms. Skipping. Residue LEU 534 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LYS 548 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Evaluate side-chains 895 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 873 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.6016 (m-10) cc_final: 0.5557 (m-80) REVERT: A 105 LYS cc_start: 0.7246 (tppp) cc_final: 0.6496 (mttt) REVERT: A 225 PHE cc_start: 0.6571 (m-80) cc_final: 0.5738 (m-80) REVERT: A 248 MET cc_start: 0.6126 (mtm) cc_final: 0.5524 (mmp) REVERT: A 261 ARG cc_start: 0.5624 (ptt90) cc_final: 0.4628 (mtm180) REVERT: A 340 LYS cc_start: 0.7001 (ttpt) cc_final: 0.6697 (mmtt) REVERT: A 408 ARG cc_start: 0.7595 (mtp180) cc_final: 0.7354 (mtt-85) REVERT: A 434 LYS cc_start: 0.8131 (ptpt) cc_final: 0.7773 (tmtt) REVERT: A 465 HIS cc_start: 0.6585 (p-80) cc_final: 0.6208 (p-80) REVERT: A 614 ASP cc_start: 0.7866 (m-30) cc_final: 0.7507 (m-30) REVERT: A 625 ASP cc_start: 0.8582 (t0) cc_final: 0.8061 (t0) REVERT: A 734 ARG cc_start: 0.7847 (mmt90) cc_final: 0.7375 (mmm-85) REVERT: A 758 LYS cc_start: 0.8526 (mmmt) cc_final: 0.7752 (mttm) REVERT: A 986 MET cc_start: 0.8105 (mtt) cc_final: 0.7770 (mtm) REVERT: A 1094 SER cc_start: 0.8397 (m) cc_final: 0.8150 (t) REVERT: A 1119 LEU cc_start: 0.7902 (mm) cc_final: 0.7689 (mt) REVERT: A 1125 LYS cc_start: 0.6469 (mmtt) cc_final: 0.5206 (mttt) REVERT: A 1309 MET cc_start: 0.8089 (ttt) cc_final: 0.7685 (ttm) REVERT: A 1396 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6754 (mtt-85) REVERT: A 1456 GLU cc_start: 0.6944 (mt-10) cc_final: 0.5911 (mt-10) REVERT: A 1459 MET cc_start: 0.7552 (mtm) cc_final: 0.7296 (ptp) REVERT: B 304 SER cc_start: 0.8681 (m) cc_final: 0.8301 (p) REVERT: B 338 TYR cc_start: 0.7184 (t80) cc_final: 0.6935 (t80) REVERT: B 413 LYS cc_start: 0.7199 (ttpt) cc_final: 0.6704 (tppt) REVERT: B 414 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7928 (mm-30) REVERT: B 445 LYS cc_start: 0.6875 (ttpp) cc_final: 0.6243 (tttm) REVERT: B 463 ARG cc_start: 0.6924 (mtp180) cc_final: 0.5416 (ptt-90) REVERT: B 563 ASP cc_start: 0.7580 (m-30) cc_final: 0.7369 (t0) REVERT: B 609 GLU cc_start: 0.6345 (mm-30) cc_final: 0.6093 (tp30) REVERT: B 667 THR cc_start: 0.8839 (m) cc_final: 0.8548 (p) REVERT: B 909 VAL cc_start: 0.9375 (t) cc_final: 0.9114 (m) REVERT: B 923 VAL cc_start: 0.8590 (t) cc_final: 0.8370 (m) REVERT: B 930 GLN cc_start: 0.6737 (mt0) cc_final: 0.6150 (mt0) REVERT: B 1089 MET cc_start: 0.6283 (mtp) cc_final: 0.6044 (mtt) REVERT: B 1153 TYR cc_start: 0.7690 (t80) cc_final: 0.7458 (t80) REVERT: C 166 LYS cc_start: 0.8406 (mttt) cc_final: 0.8099 (mtpt) REVERT: E 4 GLU cc_start: 0.7385 (mp0) cc_final: 0.6737 (tm-30) REVERT: E 44 PHE cc_start: 0.7202 (m-80) cc_final: 0.6884 (m-80) REVERT: E 61 LEU cc_start: 0.8564 (tp) cc_final: 0.8267 (tt) REVERT: E 73 PHE cc_start: 0.8157 (m-80) cc_final: 0.7700 (m-10) REVERT: E 187 ARG cc_start: 0.8030 (mtp-110) cc_final: 0.7618 (ttm-80) REVERT: F 91 LEU cc_start: 0.8682 (mp) cc_final: 0.8306 (mt) REVERT: H 43 VAL cc_start: 0.8423 (t) cc_final: 0.8216 (p) REVERT: H 87 GLN cc_start: 0.8016 (mp10) cc_final: 0.7798 (mm110) REVERT: H 110 THR cc_start: 0.8816 (p) cc_final: 0.8594 (t) REVERT: I 36 LEU cc_start: 0.7472 (mt) cc_final: 0.7001 (mm) REVERT: K 93 ASP cc_start: 0.7440 (m-30) cc_final: 0.7074 (m-30) REVERT: D 32 LEU cc_start: 0.4097 (mt) cc_final: 0.2695 (mp) REVERT: D 39 MET cc_start: 0.7333 (mtp) cc_final: 0.6969 (mmm) REVERT: D 62 MET cc_start: 0.7444 (mmt) cc_final: 0.7167 (mtt) REVERT: D 78 GLU cc_start: 0.5320 (mt-10) cc_final: 0.5075 (tm-30) REVERT: G 10 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6594 (mp0) REVERT: G 53 ASN cc_start: 0.6854 (t0) cc_final: 0.6426 (t0) REVERT: G 67 LEU cc_start: 0.5976 (tt) cc_final: 0.5670 (tt) REVERT: R 545 LEU cc_start: 0.7960 (tp) cc_final: 0.7603 (tp) REVERT: R 561 LEU cc_start: 0.6003 (mt) cc_final: 0.5787 (mt) REVERT: R 576 LEU cc_start: 0.6466 (tt) cc_final: 0.6213 (pt) REVERT: R 593 VAL cc_start: 0.7448 (m) cc_final: 0.7003 (m) outliers start: 22 outliers final: 4 residues processed: 889 average time/residue: 0.2368 time to fit residues: 319.8165 Evaluate side-chains 504 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 499 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 377 GLN A 459 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 678 ASN A 722 ASN A 804 HIS A1078 GLN A1093 GLN A1172 ASN A1182 GLN A1190 GLN A1194 ASN A1236 ASN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 GLN B1009 GLN B1094 GLN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN H 46 GLN I 46 GLN ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN K 44 ASN D 43 HIS ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS G 14 HIS ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 500 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122984 restraints weight = 58059.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107296 restraints weight = 131497.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104872 restraints weight = 140815.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105021 restraints weight = 140526.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105206 restraints weight = 132165.701| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32398 Z= 0.138 Angle : 0.538 21.809 43948 Z= 0.280 Chirality : 0.042 0.170 4960 Planarity : 0.004 0.069 5558 Dihedral : 9.787 167.683 4696 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: 0.09 (0.14), residues: 3849 helix: 1.46 (0.14), residues: 1386 sheet: -0.29 (0.22), residues: 572 loop : -0.87 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 880 TYR 0.022 0.001 TYR L 41 PHE 0.025 0.001 PHE A1239 TRP 0.013 0.001 TRP B 27 HIS 0.007 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (32373) covalent geometry : angle 0.51039 / 0.28 (43921) hydrogen bonds : bond 0.04230 / 2.83 ( 1322) hydrogen bonds : angle 5.14596 / 3.65 ( 3804) metal coordination : bond 0.00707 / 0.48 ( 25) metal coordination : angle 6.85694 / 6.16 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 521 is missing expected H atoms. Skipping. Residue ILE 522 is missing expected H atoms. Skipping. Residue LEU 534 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LYS 548 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Evaluate side-chains 591 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 591 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.6581 (tppp) cc_final: 0.5908 (mttt) REVERT: A 145 TYR cc_start: 0.5621 (t80) cc_final: 0.5254 (t80) REVERT: A 225 PHE cc_start: 0.6538 (m-80) cc_final: 0.5680 (m-80) REVERT: A 261 ARG cc_start: 0.5699 (ptt90) cc_final: 0.4765 (mtm180) REVERT: A 340 LYS cc_start: 0.7002 (ttpt) cc_final: 0.6613 (mttt) REVERT: A 349 ARG cc_start: 0.7324 (tpp80) cc_final: 0.6122 (tpp80) REVERT: A 434 LYS cc_start: 0.8360 (ptpt) cc_final: 0.8117 (tmtt) REVERT: A 614 ASP cc_start: 0.7408 (m-30) cc_final: 0.7007 (m-30) REVERT: A 625 ASP cc_start: 0.8163 (t0) cc_final: 0.7827 (t0) REVERT: A 734 ARG cc_start: 0.7561 (mmt90) cc_final: 0.7211 (mmm-85) REVERT: A 758 LYS cc_start: 0.8531 (mmmt) cc_final: 0.7686 (mttm) REVERT: A 882 SER cc_start: 0.8708 (p) cc_final: 0.8458 (t) REVERT: A 899 GLU cc_start: 0.6765 (pm20) cc_final: 0.6393 (pm20) REVERT: A 986 MET cc_start: 0.8082 (mtt) cc_final: 0.7789 (mtm) REVERT: A 1094 SER cc_start: 0.8418 (m) cc_final: 0.8037 (t) REVERT: A 1125 LYS cc_start: 0.6533 (mmtt) cc_final: 0.5858 (mttt) REVERT: A 1428 MET cc_start: 0.7961 (mmt) cc_final: 0.7461 (mmm) REVERT: B 407 MET cc_start: 0.8018 (mtt) cc_final: 0.7053 (mmt) REVERT: B 413 LYS cc_start: 0.7295 (ttpt) cc_final: 0.6981 (mttt) REVERT: B 463 ARG cc_start: 0.7395 (mtp180) cc_final: 0.5758 (ptt180) REVERT: B 541 ILE cc_start: 0.8292 (mp) cc_final: 0.7996 (mt) REVERT: B 923 VAL cc_start: 0.8740 (t) cc_final: 0.8428 (m) REVERT: B 1059 ILE cc_start: 0.6708 (tt) cc_final: 0.6491 (tt) REVERT: B 1101 GLN cc_start: 0.6256 (mt0) cc_final: 0.5702 (mt0) REVERT: B 1157 LEU cc_start: 0.7879 (tt) cc_final: 0.7580 (tt) REVERT: C 118 ARG cc_start: 0.8017 (tpp-160) cc_final: 0.7745 (tpp-160) REVERT: C 123 ASN cc_start: 0.7734 (p0) cc_final: 0.7110 (m-40) REVERT: C 166 LYS cc_start: 0.8525 (mttt) cc_final: 0.8083 (mtpt) REVERT: E 44 PHE cc_start: 0.6479 (m-80) cc_final: 0.6211 (m-80) REVERT: E 73 PHE cc_start: 0.7460 (m-80) cc_final: 0.6856 (m-10) REVERT: E 187 ARG cc_start: 0.7835 (mtp-110) cc_final: 0.7340 (ttm-80) REVERT: F 91 LEU cc_start: 0.8814 (mp) cc_final: 0.8216 (mt) REVERT: K 22 ASN cc_start: 0.7519 (t0) cc_final: 0.7288 (t0) REVERT: K 93 ASP cc_start: 0.7342 (m-30) cc_final: 0.7027 (m-30) REVERT: D 38 HIS cc_start: 0.5082 (t-170) cc_final: 0.4613 (t-90) REVERT: D 62 MET cc_start: 0.7414 (mmt) cc_final: 0.7149 (mtt) REVERT: G 18 PHE cc_start: 0.7695 (m-10) cc_final: 0.7235 (m-80) REVERT: G 104 MET cc_start: 0.5213 (ptp) cc_final: 0.3687 (ppp) REVERT: R 576 LEU cc_start: 0.6727 (tt) cc_final: 0.6484 (mp) outliers start: 0 outliers final: 0 residues processed: 591 average time/residue: 0.2167 time to fit residues: 200.9525 Evaluate side-chains 451 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 188 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 228 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 371 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A 722 ASN A1182 GLN A1190 GLN A1194 ASN ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 98 HIS B 144 HIS B 456 GLN B 552 ASN B1003 ASN B1068 GLN B1145 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN I 60 HIS K 2 ASN K 44 ASN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116238 restraints weight = 58534.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.100896 restraints weight = 144046.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.098769 restraints weight = 158466.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.099013 restraints weight = 136808.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.098930 restraints weight = 120327.761| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 32398 Z= 0.255 Angle : 0.644 13.539 43948 Z= 0.332 Chirality : 0.045 0.177 4960 Planarity : 0.005 0.062 5558 Dihedral : 9.935 169.799 4696 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3849 helix: 1.40 (0.14), residues: 1367 sheet: -0.51 (0.21), residues: 580 loop : -0.95 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 40 TYR 0.017 0.002 TYR B 338 PHE 0.028 0.002 PHE B 422 TRP 0.017 0.002 TRP I 123 HIS 0.008 0.002 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.26 (32373) covalent geometry : angle 0.63161 / 0.33 (43921) hydrogen bonds : bond 0.04470 / 2.98 ( 1322) hydrogen bonds : angle 4.95698 / 3.51 ( 3804) metal coordination : bond 0.01044 / 0.75 ( 25) metal coordination : angle 5.02705 / 4.09 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 521 is missing expected H atoms. Skipping. Residue ILE 522 is missing expected H atoms. Skipping. Residue LEU 534 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LYS 548 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Evaluate side-chains 505 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 501 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7587 (mmm) cc_final: 0.7150 (tpt) REVERT: A 105 LYS cc_start: 0.6824 (tppp) cc_final: 0.5915 (mttt) REVERT: A 225 PHE cc_start: 0.6524 (m-80) cc_final: 0.5894 (m-80) REVERT: A 340 LYS cc_start: 0.6963 (ttpt) cc_final: 0.6490 (mttt) REVERT: A 412 GLN cc_start: 0.7644 (mp10) cc_final: 0.7242 (mp10) REVERT: A 465 HIS cc_start: 0.6716 (p-80) cc_final: 0.5819 (p-80) REVERT: A 625 ASP cc_start: 0.8582 (t0) cc_final: 0.8139 (t0) REVERT: A 758 LYS cc_start: 0.8647 (mmmt) cc_final: 0.7815 (mttm) REVERT: A 869 GLU cc_start: 0.6577 (pp20) cc_final: 0.6344 (pp20) REVERT: A 899 GLU cc_start: 0.6854 (pm20) cc_final: 0.6576 (pm20) REVERT: A 986 MET cc_start: 0.8181 (mtt) cc_final: 0.7871 (mtm) REVERT: A 1094 SER cc_start: 0.8467 (m) cc_final: 0.8059 (t) REVERT: A 1125 LYS cc_start: 0.6879 (mmtt) cc_final: 0.6229 (mttt) REVERT: A 1334 TRP cc_start: 0.8264 (m100) cc_final: 0.8055 (m100) REVERT: B 61 ASP cc_start: 0.7441 (m-30) cc_final: 0.7213 (t70) REVERT: B 304 SER cc_start: 0.8563 (m) cc_final: 0.8231 (p) REVERT: B 358 GLU cc_start: 0.7422 (pp20) cc_final: 0.6978 (pm20) REVERT: B 407 MET cc_start: 0.8022 (mtt) cc_final: 0.7277 (mmt) REVERT: B 413 LYS cc_start: 0.7569 (ttpt) cc_final: 0.7126 (mttt) REVERT: B 442 ASP cc_start: 0.7191 (m-30) cc_final: 0.6982 (m-30) REVERT: B 463 ARG cc_start: 0.7490 (mtp180) cc_final: 0.5734 (ptt180) REVERT: B 541 ILE cc_start: 0.8622 (mp) cc_final: 0.8286 (mt) REVERT: B 667 THR cc_start: 0.8880 (m) cc_final: 0.8400 (t) REVERT: B 761 THR cc_start: 0.7485 (m) cc_final: 0.7198 (p) REVERT: B 1059 ILE cc_start: 0.6684 (tt) cc_final: 0.6447 (tt) REVERT: B 1125 MET cc_start: 0.8497 (tmm) cc_final: 0.7170 (ttm) REVERT: B 1165 MET cc_start: 0.7708 (mmm) cc_final: 0.7419 (mmm) REVERT: E 73 PHE cc_start: 0.7707 (m-80) cc_final: 0.7456 (m-10) REVERT: E 120 ASP cc_start: 0.6433 (p0) cc_final: 0.5561 (m-30) REVERT: F 91 LEU cc_start: 0.8676 (mp) cc_final: 0.8315 (mt) REVERT: I 64 GLU cc_start: 0.7227 (mp0) cc_final: 0.6972 (mp0) REVERT: L 29 LYS cc_start: 0.7249 (ttmm) cc_final: 0.6919 (ttmt) REVERT: D 38 HIS cc_start: 0.5249 (t-170) cc_final: 0.4629 (t-90) outliers start: 4 outliers final: 1 residues processed: 505 average time/residue: 0.2161 time to fit residues: 172.4342 Evaluate side-chains 415 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 211 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 384 optimal weight: 9.9990 chunk 370 optimal weight: 0.0070 chunk 212 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 115 optimal weight: 0.0040 chunk 154 optimal weight: 7.9990 overall best weight: 1.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A 757 GLN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN A1194 ASN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS A1422 GLN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B1068 GLN B1071 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN I 121 HIS K 2 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118276 restraints weight = 57643.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102618 restraints weight = 130194.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.100371 restraints weight = 151281.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.100742 restraints weight = 133292.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.100727 restraints weight = 115208.939| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32398 Z= 0.122 Angle : 0.465 12.910 43948 Z= 0.248 Chirality : 0.041 0.140 4960 Planarity : 0.003 0.055 5558 Dihedral : 9.759 166.986 4696 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 23.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 96.00 % Rotamer: Outliers : 0.03 % Allowed : 1.36 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: 3849 helix: 1.77 (0.14), residues: 1364 sheet: -0.32 (0.21), residues: 572 loop : -0.84 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 40 TYR 0.031 0.001 TYR B1048 PHE 0.016 0.001 PHE B 806 TRP 0.011 0.001 TRP B 27 HIS 0.011 0.001 HIS A1384 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (32373) covalent geometry : angle 0.45776 / 0.25 (43921) hydrogen bonds : bond 0.03453 / 2.30 ( 1322) hydrogen bonds : angle 4.55488 / 3.23 ( 3804) metal coordination : bond 0.00467 / 0.34 ( 25) metal coordination : angle 3.26248 / 2.27 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 521 is missing expected H atoms. Skipping. Residue ILE 522 is missing expected H atoms. Skipping. Residue LEU 534 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LYS 548 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Evaluate side-chains 527 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 526 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7684 (mmm) cc_final: 0.7346 (tpt) REVERT: A 105 LYS cc_start: 0.7021 (tppp) cc_final: 0.6292 (mttt) REVERT: A 145 TYR cc_start: 0.5704 (t80) cc_final: 0.5212 (t80) REVERT: A 225 PHE cc_start: 0.6668 (m-80) cc_final: 0.5917 (m-80) REVERT: A 465 HIS cc_start: 0.6858 (p-80) cc_final: 0.6402 (p-80) REVERT: A 625 ASP cc_start: 0.8526 (t0) cc_final: 0.8130 (t0) REVERT: A 758 LYS cc_start: 0.8552 (mmmt) cc_final: 0.7769 (mttm) REVERT: A 962 ASP cc_start: 0.7458 (m-30) cc_final: 0.7187 (m-30) REVERT: A 986 MET cc_start: 0.8186 (mtt) cc_final: 0.7851 (mtm) REVERT: A 1094 SER cc_start: 0.8465 (m) cc_final: 0.8038 (t) REVERT: A 1125 LYS cc_start: 0.6712 (mmtt) cc_final: 0.6134 (mttt) REVERT: B 61 ASP cc_start: 0.7413 (m-30) cc_final: 0.7131 (t70) REVERT: B 299 GLU cc_start: 0.7121 (mp0) cc_final: 0.6897 (mp0) REVERT: B 304 SER cc_start: 0.8616 (m) cc_final: 0.8364 (p) REVERT: B 320 PHE cc_start: 0.7661 (t80) cc_final: 0.7441 (t80) REVERT: B 358 GLU cc_start: 0.7538 (pp20) cc_final: 0.6768 (pm20) REVERT: B 407 MET cc_start: 0.7913 (mtt) cc_final: 0.7297 (mmt) REVERT: B 413 LYS cc_start: 0.7554 (ttpt) cc_final: 0.7024 (mttt) REVERT: B 442 ASP cc_start: 0.7187 (m-30) cc_final: 0.6932 (m-30) REVERT: B 463 ARG cc_start: 0.7618 (mtp180) cc_final: 0.5807 (ptt180) REVERT: B 541 ILE cc_start: 0.8562 (mp) cc_final: 0.8283 (mt) REVERT: B 637 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7793 (tttm) REVERT: B 1125 MET cc_start: 0.8477 (tmm) cc_final: 0.7431 (ttp) REVERT: B 1150 ARG cc_start: 0.6844 (tpp80) cc_final: 0.6186 (mmt180) REVERT: E 73 PHE cc_start: 0.7489 (m-80) cc_final: 0.7275 (m-10) REVERT: E 120 ASP cc_start: 0.6082 (p0) cc_final: 0.5546 (m-30) REVERT: F 91 LEU cc_start: 0.8669 (mp) cc_final: 0.8421 (mt) REVERT: I 36 LEU cc_start: 0.6470 (mm) cc_final: 0.6090 (mm) REVERT: I 64 GLU cc_start: 0.7072 (mp0) cc_final: 0.6839 (mp0) REVERT: K 16 GLU cc_start: 0.7523 (tt0) cc_final: 0.7297 (tt0) REVERT: K 22 ASN cc_start: 0.7506 (t0) cc_final: 0.7299 (t0) REVERT: D 38 HIS cc_start: 0.5162 (t-170) cc_final: 0.4570 (t-90) outliers start: 1 outliers final: 1 residues processed: 527 average time/residue: 0.2132 time to fit residues: 177.3780 Evaluate side-chains 422 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 421 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 119 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 382 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 299 optimal weight: 8.9990 chunk 350 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 380 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 459 ASN A 780 ASN A 791 GLN A1190 GLN A1194 ASN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS K 44 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.120931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.113638 restraints weight = 59079.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.096819 restraints weight = 136917.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.095351 restraints weight = 150092.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.095313 restraints weight = 134190.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.095369 restraints weight = 117139.942| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 32398 Z= 0.282 Angle : 0.640 12.984 43948 Z= 0.332 Chirality : 0.046 0.220 4960 Planarity : 0.005 0.051 5558 Dihedral : 10.011 168.508 4696 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.03 % Favored : 93.95 % Rotamer: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.14 (0.14), residues: 3849 helix: 1.34 (0.14), residues: 1369 sheet: -0.42 (0.21), residues: 583 loop : -1.05 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1072 TYR 0.032 0.002 TYR B1153 PHE 0.029 0.002 PHE A 668 TRP 0.013 0.002 TRP A1192 HIS 0.008 0.002 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.28 (32373) covalent geometry : angle 0.62840 / 0.33 (43921) hydrogen bonds : bond 0.04486 / 2.98 ( 1322) hydrogen bonds : angle 4.84502 / 3.43 ( 3804) metal coordination : bond 0.01093 / 0.76 ( 25) metal coordination : angle 4.86723 / 3.67 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 521 is missing expected H atoms. Skipping. Residue ILE 522 is missing expected H atoms. Skipping. Residue LEU 534 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LYS 548 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Evaluate side-chains 471 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 470 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7791 (mmm) cc_final: 0.7544 (tpt) REVERT: A 105 LYS cc_start: 0.7349 (tppp) cc_final: 0.6388 (mttt) REVERT: A 225 PHE cc_start: 0.6758 (m-80) cc_final: 0.6133 (m-80) REVERT: A 261 ARG cc_start: 0.6478 (ptt90) cc_final: 0.5600 (mtt90) REVERT: A 465 HIS cc_start: 0.6573 (p-80) cc_final: 0.5825 (p-80) REVERT: A 625 ASP cc_start: 0.8649 (t0) cc_final: 0.8180 (t0) REVERT: A 758 LYS cc_start: 0.8683 (mmmt) cc_final: 0.7870 (mttm) REVERT: A 986 MET cc_start: 0.8231 (mtt) cc_final: 0.7890 (mtm) REVERT: A 1094 SER cc_start: 0.8586 (m) cc_final: 0.8233 (t) REVERT: A 1125 LYS cc_start: 0.6744 (mmtt) cc_final: 0.6212 (mttt) REVERT: A 1230 GLN cc_start: 0.7395 (tt0) cc_final: 0.6828 (tt0) REVERT: A 1405 MET cc_start: 0.7984 (mtp) cc_final: 0.7743 (mtp) REVERT: A 1432 PHE cc_start: 0.6045 (t80) cc_final: 0.5831 (t80) REVERT: B 61 ASP cc_start: 0.7617 (m-30) cc_final: 0.7246 (t70) REVERT: B 304 SER cc_start: 0.8789 (m) cc_final: 0.8392 (p) REVERT: B 413 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7242 (mttt) REVERT: B 442 ASP cc_start: 0.7097 (m-30) cc_final: 0.6884 (m-30) REVERT: B 463 ARG cc_start: 0.7490 (mtp180) cc_final: 0.5705 (ptt-90) REVERT: B 637 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7921 (tttm) REVERT: B 667 THR cc_start: 0.8788 (m) cc_final: 0.8325 (t) REVERT: B 1076 GLU cc_start: 0.6979 (tt0) cc_final: 0.5541 (mp0) REVERT: B 1125 MET cc_start: 0.8443 (tmm) cc_final: 0.7286 (ttp) REVERT: B 1150 ARG cc_start: 0.7014 (tpp80) cc_final: 0.6093 (tpt90) REVERT: E 67 ASP cc_start: 0.7739 (t0) cc_final: 0.7169 (t0) REVERT: E 120 ASP cc_start: 0.6217 (p0) cc_final: 0.5866 (m-30) REVERT: F 91 LEU cc_start: 0.8613 (mp) cc_final: 0.8095 (mt) REVERT: I 64 GLU cc_start: 0.7213 (mp0) cc_final: 0.6827 (mp0) REVERT: J 31 GLU cc_start: 0.7286 (mp0) cc_final: 0.6750 (mp0) REVERT: D 38 HIS cc_start: 0.5154 (t-170) cc_final: 0.4597 (t-170) REVERT: G 5 ILE cc_start: 0.6028 (mt) cc_final: 0.5669 (mm) outliers start: 1 outliers final: 0 residues processed: 471 average time/residue: 0.2143 time to fit residues: 159.8054 Evaluate side-chains 402 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 257 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 226 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 0.0070 chunk 151 optimal weight: 0.5980 chunk 327 optimal weight: 0.6980 chunk 312 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN A 780 ASN A 791 GLN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN A1384 HIS A1417 HIS ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 144 HIS B 717 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117648 restraints weight = 57569.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101900 restraints weight = 130474.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.100139 restraints weight = 136965.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.100063 restraints weight = 129750.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.100327 restraints weight = 123439.967| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32398 Z= 0.089 Angle : 0.463 15.598 43948 Z= 0.240 Chirality : 0.040 0.134 4960 Planarity : 0.003 0.063 5558 Dihedral : 9.748 166.703 4696 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 25.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: 3849 helix: 1.87 (0.14), residues: 1365 sheet: -0.27 (0.21), residues: 602 loop : -0.84 (0.15), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 255 TYR 0.026 0.001 TYR B1153 PHE 0.012 0.001 PHE A 458 TRP 0.027 0.001 TRP A1210 HIS 0.008 0.001 HIS A1384 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 (32373) covalent geometry : angle 0.44303 / 0.24 (43921) hydrogen bonds : bond 0.03263 / 2.17 ( 1322) hydrogen bonds : angle 4.42725 / 3.14 ( 3804) metal coordination : bond 0.00701 / 0.50 ( 25) metal coordination : angle 5.50900 / 4.71 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 521 is missing expected H atoms. Skipping. Residue ILE 522 is missing expected H atoms. Skipping. Residue LEU 534 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LYS 548 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Evaluate side-chains 503 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 1.156 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 78 MET cc_start: 0.7709 (mmm) cc_final: 0.7256 (tpt) REVERT: A 105 LYS cc_start: 0.7336 (tppp) cc_final: 0.6366 (mttt) REVERT: A 225 PHE cc_start: 0.6707 (m-80) cc_final: 0.5989 (m-80) REVERT: A 362 SER cc_start: 0.7459 (m) cc_final: 0.6982 (p) REVERT: A 465 HIS cc_start: 0.6857 (p-80) cc_final: 0.6567 (p-80) REVERT: A 625 ASP cc_start: 0.8583 (t0) cc_final: 0.8152 (t0) REVERT: A 758 LYS cc_start: 0.8533 (mmmt) cc_final: 0.7752 (mttm) REVERT: A 962 ASP cc_start: 0.7383 (m-30) cc_final: 0.7090 (m-30) REVERT: A 986 MET cc_start: 0.8111 (mtt) cc_final: 0.7778 (mtm) REVERT: A 1094 SER cc_start: 0.8526 (m) cc_final: 0.8196 (t) REVERT: A 1125 LYS cc_start: 0.6765 (mmtt) cc_final: 0.6180 (mttt) REVERT: A 1405 MET cc_start: 0.7935 (mtp) cc_final: 0.7690 (mtp) REVERT: B 61 ASP cc_start: 0.7491 (m-30) cc_final: 0.7125 (t70) REVERT: B 413 LYS cc_start: 0.7714 (ttpt) cc_final: 0.7172 (mttt) REVERT: B 442 ASP cc_start: 0.7105 (m-30) cc_final: 0.6855 (m-30) REVERT: B 463 ARG cc_start: 0.7611 (mtp180) cc_final: 0.5733 (ptt-90) REVERT: B 667 THR cc_start: 0.8716 (m) cc_final: 0.8427 (t) REVERT: B 1125 MET cc_start: 0.8387 (tmm) cc_final: 0.7144 (ttp) REVERT: B 1150 ARG cc_start: 0.7046 (tpp80) cc_final: 0.6246 (tpt90) REVERT: B 1172 MET cc_start: 0.7703 (mmt) cc_final: 0.7362 (mpp) REVERT: E 67 ASP cc_start: 0.7922 (t0) cc_final: 0.7345 (t0) REVERT: F 91 LEU cc_start: 0.8708 (mp) cc_final: 0.8439 (mt) REVERT: I 64 GLU cc_start: 0.6989 (mp0) cc_final: 0.6744 (mp0) REVERT: K 16 GLU cc_start: 0.7467 (tt0) cc_final: 0.7262 (tt0) REVERT: K 93 ASP cc_start: 0.7948 (m-30) cc_final: 0.7735 (m-30) REVERT: D 38 HIS cc_start: 0.5201 (t-170) cc_final: 0.4505 (t-90) outliers start: 0 outliers final: 0 residues processed: 503 average time/residue: 0.2206 time to fit residues: 174.1879 Evaluate side-chains 406 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 19 optimal weight: 9.9990 chunk 378 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 chunk 335 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 382 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 282 optimal weight: 6.9990 chunk 229 optimal weight: 0.4980 chunk 104 optimal weight: 0.0030 overall best weight: 2.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A1034 GLN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 717 ASN ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115573 restraints weight = 58291.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.099525 restraints weight = 130801.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.097493 restraints weight = 150566.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.097620 restraints weight = 145645.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.097724 restraints weight = 135250.434| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32398 Z= 0.156 Angle : 0.499 12.976 43948 Z= 0.259 Chirality : 0.041 0.143 4960 Planarity : 0.003 0.048 5558 Dihedral : 9.764 166.419 4696 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 25.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.39 % Rotamer: Outliers : 0.03 % Allowed : 0.77 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: 3849 helix: 1.88 (0.14), residues: 1370 sheet: -0.20 (0.21), residues: 591 loop : -0.83 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 863 TYR 0.016 0.001 TYR B 811 PHE 0.031 0.001 PHE G 18 TRP 0.012 0.001 TRP A1192 HIS 0.007 0.001 HIS A1384 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (32373) covalent geometry : angle 0.48567 / 0.26 (43921) hydrogen bonds : bond 0.03477 / 2.31 ( 1322) hydrogen bonds : angle 4.41023 / 3.14 ( 3804) metal coordination : bond 0.00584 / 0.43 ( 25) metal coordination : angle 4.73239 / 3.91 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 521 is missing expected H atoms. Skipping. Residue ILE 522 is missing expected H atoms. Skipping. Residue LEU 534 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LYS 548 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 475 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7727 (mmm) cc_final: 0.7215 (tpt) REVERT: A 105 LYS cc_start: 0.7429 (tppp) cc_final: 0.6404 (mttt) REVERT: A 225 PHE cc_start: 0.6590 (m-80) cc_final: 0.5998 (m-80) REVERT: A 248 MET cc_start: 0.7396 (ttp) cc_final: 0.7082 (ttm) REVERT: A 261 ARG cc_start: 0.6437 (ptt90) cc_final: 0.5587 (mtt90) REVERT: A 362 SER cc_start: 0.7640 (m) cc_final: 0.7068 (p) REVERT: A 465 HIS cc_start: 0.6669 (p-80) cc_final: 0.6356 (p-80) REVERT: A 625 ASP cc_start: 0.8611 (t0) cc_final: 0.8074 (t0) REVERT: A 758 LYS cc_start: 0.8622 (mmmt) cc_final: 0.7849 (mttm) REVERT: A 962 ASP cc_start: 0.7377 (m-30) cc_final: 0.7071 (m-30) REVERT: A 986 MET cc_start: 0.8166 (mtt) cc_final: 0.7813 (mtm) REVERT: A 1094 SER cc_start: 0.8637 (m) cc_final: 0.8422 (p) REVERT: A 1125 LYS cc_start: 0.6534 (mmtt) cc_final: 0.6028 (mttt) REVERT: A 1405 MET cc_start: 0.7865 (mtp) cc_final: 0.7631 (mtp) REVERT: A 1428 MET cc_start: 0.8274 (mmm) cc_final: 0.7745 (mmm) REVERT: B 61 ASP cc_start: 0.7542 (m-30) cc_final: 0.7234 (t70) REVERT: B 128 ILE cc_start: 0.8478 (tp) cc_final: 0.8261 (tp) REVERT: B 413 LYS cc_start: 0.7735 (ttpt) cc_final: 0.7226 (mttt) REVERT: B 463 ARG cc_start: 0.7603 (mtp180) cc_final: 0.5752 (ptt-90) REVERT: B 667 THR cc_start: 0.8946 (m) cc_final: 0.8433 (t) REVERT: B 1125 MET cc_start: 0.8392 (tmm) cc_final: 0.7225 (ttp) REVERT: B 1150 ARG cc_start: 0.7087 (tpp80) cc_final: 0.6409 (tpt90) REVERT: B 1171 MET cc_start: 0.5112 (mtp) cc_final: 0.4903 (mtp) REVERT: B 1172 MET cc_start: 0.7749 (mmt) cc_final: 0.7291 (mpp) REVERT: E 67 ASP cc_start: 0.7888 (t0) cc_final: 0.7427 (t0) REVERT: F 91 LEU cc_start: 0.8739 (mp) cc_final: 0.8235 (mt) REVERT: I 64 GLU cc_start: 0.7036 (mp0) cc_final: 0.6774 (mp0) outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.2132 time to fit residues: 161.1915 Evaluate side-chains 401 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 337 optimal weight: 0.9980 chunk 286 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 305 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN A 459 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112399 restraints weight = 58226.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.097250 restraints weight = 137043.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.095998 restraints weight = 162584.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.095861 restraints weight = 140858.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.095748 restraints weight = 135795.839| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 32398 Z= 0.272 Angle : 0.626 14.077 43948 Z= 0.325 Chirality : 0.045 0.179 4960 Planarity : 0.005 0.047 5558 Dihedral : 9.978 165.943 4696 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 27.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.50 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3849 helix: 1.43 (0.14), residues: 1384 sheet: -0.32 (0.22), residues: 585 loop : -1.00 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1072 TYR 0.039 0.002 TYR B1048 PHE 0.040 0.002 PHE G 18 TRP 0.014 0.002 TRP A1192 HIS 0.006 0.001 HIS A1417 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.27 (32373) covalent geometry : angle 0.61203 / 0.32 (43921) hydrogen bonds : bond 0.04287 / 2.86 ( 1322) hydrogen bonds : angle 4.72678 / 3.36 ( 3804) metal coordination : bond 0.01067 / 0.73 ( 25) metal coordination : angle 5.39842 / 4.34 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 521 is missing expected H atoms. Skipping. Residue ILE 522 is missing expected H atoms. Skipping. Residue LEU 534 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LYS 548 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Evaluate side-chains 460 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.7396 (tppp) cc_final: 0.6381 (mttt) REVERT: A 225 PHE cc_start: 0.6754 (m-80) cc_final: 0.6071 (m-80) REVERT: A 248 MET cc_start: 0.7412 (ttp) cc_final: 0.7102 (ttm) REVERT: A 465 HIS cc_start: 0.6653 (p-80) cc_final: 0.6343 (p-80) REVERT: A 625 ASP cc_start: 0.8704 (t0) cc_final: 0.8238 (t0) REVERT: A 758 LYS cc_start: 0.8709 (mmmt) cc_final: 0.7952 (mttm) REVERT: A 962 ASP cc_start: 0.7545 (m-30) cc_final: 0.7162 (m-30) REVERT: A 1125 LYS cc_start: 0.6672 (mmtt) cc_final: 0.5929 (mttt) REVERT: A 1405 MET cc_start: 0.7930 (mtp) cc_final: 0.7667 (mtp) REVERT: A 1428 MET cc_start: 0.8375 (mmm) cc_final: 0.7691 (mmm) REVERT: B 61 ASP cc_start: 0.7605 (m-30) cc_final: 0.7373 (t70) REVERT: B 413 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7320 (mttt) REVERT: B 463 ARG cc_start: 0.7529 (mtp180) cc_final: 0.5724 (ptt-90) REVERT: B 667 THR cc_start: 0.8780 (m) cc_final: 0.8409 (t) REVERT: B 1076 GLU cc_start: 0.6952 (tt0) cc_final: 0.5924 (mp0) REVERT: B 1125 MET cc_start: 0.8414 (tmm) cc_final: 0.8205 (tmm) REVERT: B 1150 ARG cc_start: 0.7046 (tpp80) cc_final: 0.6205 (tpt90) REVERT: B 1172 MET cc_start: 0.7821 (mmt) cc_final: 0.7406 (mpp) REVERT: C 123 ASN cc_start: 0.7470 (p0) cc_final: 0.7227 (m-40) REVERT: I 64 GLU cc_start: 0.7053 (mp0) cc_final: 0.6793 (mp0) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.2167 time to fit residues: 158.3453 Evaluate side-chains 382 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 98 optimal weight: 4.9990 chunk 300 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 202 optimal weight: 0.5980 chunk 177 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 163 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 234 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN A 459 ASN A 678 ASN A1034 GLN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN L 26 ASN D 34 ASN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115798 restraints weight = 57380.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100369 restraints weight = 141873.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.097490 restraints weight = 145222.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.097733 restraints weight = 127975.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.097714 restraints weight = 126883.895| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 32398 Z= 0.095 Angle : 0.458 11.273 43948 Z= 0.241 Chirality : 0.040 0.153 4960 Planarity : 0.003 0.050 5558 Dihedral : 9.743 163.634 4696 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 26.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.30 % Rotamer: Outliers : 0.06 % Allowed : 0.21 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: 0.45 (0.14), residues: 3849 helix: 1.92 (0.14), residues: 1378 sheet: -0.16 (0.22), residues: 595 loop : -0.78 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1153 TYR 0.014 0.001 TYR B1153 PHE 0.030 0.001 PHE G 18 TRP 0.036 0.001 TRP A1334 HIS 0.008 0.001 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (32373) covalent geometry : angle 0.44657 / 0.24 (43921) hydrogen bonds : bond 0.03220 / 2.15 ( 1322) hydrogen bonds : angle 4.36337 / 3.11 ( 3804) metal coordination : bond 0.00370 / 0.26 ( 25) metal coordination : angle 4.20122 / 3.36 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 521 is missing expected H atoms. Skipping. Residue ILE 522 is missing expected H atoms. Skipping. Residue LEU 534 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LYS 548 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 474 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.7401 (tppp) cc_final: 0.6405 (mttt) REVERT: A 225 PHE cc_start: 0.6841 (m-80) cc_final: 0.6106 (m-80) REVERT: A 248 MET cc_start: 0.7379 (ttp) cc_final: 0.7080 (ttm) REVERT: A 261 ARG cc_start: 0.6443 (ptt90) cc_final: 0.5512 (mtt90) REVERT: A 362 SER cc_start: 0.7495 (m) cc_final: 0.7013 (p) REVERT: A 465 HIS cc_start: 0.6847 (p-80) cc_final: 0.6499 (p-80) REVERT: A 625 ASP cc_start: 0.8687 (t0) cc_final: 0.8209 (t0) REVERT: A 758 LYS cc_start: 0.8672 (mmmt) cc_final: 0.7913 (mttm) REVERT: A 1125 LYS cc_start: 0.6624 (mmtt) cc_final: 0.5974 (mttt) REVERT: A 1344 MET cc_start: 0.7278 (tpt) cc_final: 0.7025 (tpp) REVERT: A 1405 MET cc_start: 0.7901 (mtp) cc_final: 0.7655 (mtp) REVERT: B 61 ASP cc_start: 0.7622 (m-30) cc_final: 0.7346 (t70) REVERT: B 413 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7213 (mttt) REVERT: B 463 ARG cc_start: 0.7503 (mtp180) cc_final: 0.5729 (ptt-90) REVERT: B 667 THR cc_start: 0.8776 (m) cc_final: 0.8445 (t) REVERT: B 895 PHE cc_start: 0.7870 (m-80) cc_final: 0.7645 (m-80) REVERT: B 1125 MET cc_start: 0.8428 (tmm) cc_final: 0.8196 (tmm) REVERT: B 1150 ARG cc_start: 0.7097 (tpp80) cc_final: 0.6225 (tpt90) REVERT: B 1172 MET cc_start: 0.7685 (mmt) cc_final: 0.7204 (mpp) REVERT: I 64 GLU cc_start: 0.7070 (mp0) cc_final: 0.6833 (mp0) REVERT: D 38 HIS cc_start: 0.5312 (t-170) cc_final: 0.4876 (t70) outliers start: 2 outliers final: 1 residues processed: 475 average time/residue: 0.2120 time to fit residues: 160.9228 Evaluate side-chains 386 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 284 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 327 optimal weight: 0.0970 chunk 326 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 337 optimal weight: 0.0870 chunk 161 optimal weight: 0.4980 chunk 328 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 379 optimal weight: 0.1980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** 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 = 0.3531 r_free = 0.3531 target = 0.124402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116924 restraints weight = 57473.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.101490 restraints weight = 128212.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.099552 restraints weight = 143344.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.099497 restraints weight = 136444.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099710 restraints weight = 125060.751| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32398 Z= 0.078 Angle : 0.422 9.815 43948 Z= 0.222 Chirality : 0.039 0.162 4960 Planarity : 0.003 0.058 5558 Dihedral : 9.573 162.413 4696 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.03 % Allowed : 0.09 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % 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: 0.82 (0.14), residues: 3849 helix: 2.31 (0.15), residues: 1381 sheet: -0.05 (0.21), residues: 602 loop : -0.60 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 255 TYR 0.023 0.001 TYR B1153 PHE 0.015 0.001 PHE R 507 TRP 0.024 0.001 TRP A1210 HIS 0.008 0.001 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00169 / 0.08 (32373) covalent geometry : angle 0.41291 / 0.22 (43921) hydrogen bonds : bond 0.02751 / 1.84 ( 1322) hydrogen bonds : angle 4.09484 / 2.92 ( 3804) metal coordination : bond 0.00291 / 0.19 ( 25) metal coordination : angle 3.45355 / 2.73 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 521 is missing expected H atoms. Skipping. Residue ILE 522 is missing expected H atoms. Skipping. Residue LEU 534 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue VAL 547 is missing expected H atoms. Skipping. Residue LYS 548 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LEU 596 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Evaluate side-chains 472 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 471 time to evaluate : 1.287 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 105 LYS cc_start: 0.7385 (tppp) cc_final: 0.6376 (mttt) REVERT: A 225 PHE cc_start: 0.6708 (m-80) cc_final: 0.5995 (m-80) REVERT: A 248 MET cc_start: 0.7328 (ttp) cc_final: 0.7066 (ttm) REVERT: A 261 ARG cc_start: 0.6260 (ptt90) cc_final: 0.5504 (mtt90) REVERT: A 467 MET cc_start: 0.7147 (mmt) cc_final: 0.6921 (mmm) REVERT: A 625 ASP cc_start: 0.8645 (t0) cc_final: 0.8195 (t0) REVERT: A 758 LYS cc_start: 0.8594 (mmmt) cc_final: 0.7820 (mttm) REVERT: A 962 ASP cc_start: 0.7283 (m-30) cc_final: 0.6991 (m-30) REVERT: A 986 MET cc_start: 0.8274 (mtt) cc_final: 0.7784 (mtm) REVERT: A 1125 LYS cc_start: 0.6490 (mmtt) cc_final: 0.5876 (mttt) REVERT: A 1405 MET cc_start: 0.7832 (mtp) cc_final: 0.7535 (mtp) REVERT: B 61 ASP cc_start: 0.7467 (m-30) cc_final: 0.7245 (t70) REVERT: B 128 ILE cc_start: 0.8501 (tp) cc_final: 0.8280 (tp) REVERT: B 413 LYS cc_start: 0.7724 (ttpt) cc_final: 0.7207 (mttt) REVERT: B 463 ARG cc_start: 0.7578 (mtp180) cc_final: 0.5855 (ptt-90) REVERT: B 667 THR cc_start: 0.8821 (m) cc_final: 0.8583 (t) REVERT: B 1150 ARG cc_start: 0.6954 (tpp80) cc_final: 0.6311 (tpt90) REVERT: B 1172 MET cc_start: 0.7775 (mmt) cc_final: 0.7331 (mpp) REVERT: F 91 LEU cc_start: 0.8832 (mp) cc_final: 0.8554 (mt) REVERT: I 64 GLU cc_start: 0.6912 (mp0) cc_final: 0.6699 (mp0) REVERT: D 38 HIS cc_start: 0.5226 (t-170) cc_final: 0.4853 (t70) outliers start: 1 outliers final: 0 residues processed: 472 average time/residue: 0.2032 time to fit residues: 154.5846 Evaluate side-chains 393 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 12 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 315 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 299 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 361 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112504 restraints weight = 58134.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.096487 restraints weight = 138559.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.094762 restraints weight = 158662.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.094677 restraints weight = 138586.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.094863 restraints weight = 126298.082| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 32398 Z= 0.272 Angle : 0.608 11.256 43948 Z= 0.315 Chirality : 0.045 0.183 4960 Planarity : 0.005 0.047 5558 Dihedral : 9.844 163.236 4696 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 28.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.29 (0.14), residues: 3849 helix: 1.75 (0.14), residues: 1378 sheet: -0.22 (0.22), residues: 592 loop : -0.85 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 924 TYR 0.023 0.002 TYR B 811 PHE 0.032 0.002 PHE G 18 TRP 0.040 0.002 TRP A1334 HIS 0.010 0.001 HIS A1163 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.27 (32373) covalent geometry : angle 0.59691 / 0.31 (43921) hydrogen bonds : bond 0.04125 / 2.76 ( 1322) hydrogen bonds : angle 4.56597 / 3.25 ( 3804) metal coordination : bond 0.00999 / 0.72 ( 25) metal coordination : angle 4.70756 / 3.54 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5136.11 seconds wall clock time: 90 minutes 10.14 seconds (5410.14 seconds total)