Starting phenix.real_space_refine on Thu May 29 14:28:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qw9_18683/05_2025/8qw9_18683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qw9_18683/05_2025/8qw9_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_18683/05_2025/8qw9_18683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qw9_18683/05_2025/8qw9_18683.map" model { file = "/net/cci-nas-00/data/ceres_data/8qw9_18683/05_2025/8qw9_18683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qw9_18683/05_2025/8qw9_18683.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ASP:plan': 1, 'GLU:plan': 3} 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP: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: {'GLN:plan1': 1, 'ARG:plan': 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: {'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 3, 'GLU:plan': 5, '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: {'GLU:plan': 1, 'ASN:plan1': 2, '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, 'GLU:plan': 5, 'ARG:plan': 7, '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: 16.43, per 1000 atoms: 0.51 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: 8.41 Conformation dependent library (CDL) restraints added in 4.3 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: 5.25 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: 15.03 Time building geometry restraints manager: 9.79 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: 44472 2.47 - 4.93: 780 4.93 - 7.40: 138 7.40 - 9.86: 11 9.86 - 12.33: 4 Bond angle restraints: 45405 Sorted by residual: 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 angle pdb=" N ALA L 57 " pdb=" CA ALA L 57 " pdb=" C ALA L 57 " ideal model delta sigma weight residual 112.72 107.30 5.42 1.14e+00 7.69e-01 2.26e+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: 4486 0.083 - 0.166: 457 0.166 - 0.249: 10 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 2.35 -2.75 -0.40 2.00e-01 2.50e+01 4.07e+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 2.35 -2.63 -0.28 2.00e-01 2.50e+01 2.00e+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: 3.230 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: 0.890 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 80.260 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.120 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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= 0.280 Angle : 0.717 18.187 43948 Z= 0.431 Chirality : 0.049 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 : 10.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.107 0.003 TRP R 504 HIS 0.009 0.001 HIS G 14 PHE 0.048 0.002 PHE R 588 TYR 0.072 0.002 TYR R 508 ARG 0.007 0.001 ARG G 16 Details of bonding type rmsd hydrogen bonds : bond 0.16269 ( 1322) hydrogen bonds : angle 6.98173 ( 3804) metal coordination : bond 0.04737 ( 25) metal coordination : angle 6.43335 ( 27) covalent geometry : bond 0.00580 (32373) covalent geometry : angle 0.69951 (43921) *********************** 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 : 3.565 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: 0.5556 (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: 0.4627 (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: 0.5207 (mttt) REVERT: A 1309 MET cc_start: 0.8088 (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: 0.7551 (mtm) cc_final: 0.7297 (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: 0.6934 (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: 0.6045 (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: 0.8017 (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: 0.7000 (mm) REVERT: K 93 ASP cc_start: 0.7440 (m-30) cc_final: 0.7074 (m-30) REVERT: D 32 LEU cc_start: 0.4098 (mt) cc_final: 0.2694 (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: 0.6855 (t0) cc_final: 0.6426 (t0) REVERT: G 67 LEU cc_start: 0.5976 (tt) cc_final: 0.5671 (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: 0.7447 (m) cc_final: 0.7003 (m) outliers start: 22 outliers final: 4 residues processed: 889 average time/residue: 0.5186 time to fit residues: 692.7791 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 : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 325 optimal weight: 0.7980 chunk 292 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 302 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 222 HIS ** 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 ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 98 HIS B 456 GLN B1003 ASN B1009 GLN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 GLN 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 I 98 GLN K 44 ASN D 43 HIS ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 500 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119141 restraints weight = 57846.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102939 restraints weight = 136325.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.100517 restraints weight = 143518.749| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 32398 Z= 0.198 Angle : 0.584 17.061 43948 Z= 0.302 Chirality : 0.043 0.156 4960 Planarity : 0.004 0.065 5558 Dihedral : 9.786 165.666 4696 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.77 % Rotamer: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3849 helix: 1.48 (0.14), residues: 1369 sheet: -0.40 (0.22), residues: 565 loop : -0.90 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 27 HIS 0.007 0.001 HIS D 43 PHE 0.025 0.002 PHE B 806 TYR 0.027 0.002 TYR B1048 ARG 0.012 0.001 ARG J 47 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 1322) hydrogen bonds : angle 5.00956 ( 3804) metal coordination : bond 0.00867 ( 25) metal coordination : angle 5.93049 ( 27) covalent geometry : bond 0.00462 (32373) covalent geometry : angle 0.56513 (43921) *********************** 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 571 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 569 time to evaluate : 3.253 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: 0.7574 (mmm) cc_final: 0.7153 (tpt) REVERT: A 105 LYS cc_start: 0.6692 (tppp) cc_final: 0.5804 (mttt) REVERT: A 225 PHE cc_start: 0.6583 (m-80) cc_final: 0.5820 (m-80) REVERT: A 340 LYS cc_start: 0.6983 (ttpt) cc_final: 0.6665 (mttt) REVERT: A 349 ARG cc_start: 0.7397 (tpp80) cc_final: 0.6533 (tpp80) REVERT: A 465 HIS cc_start: 0.6843 (p-80) cc_final: 0.6382 (p-80) REVERT: A 614 ASP cc_start: 0.7329 (m-30) cc_final: 0.6975 (m-30) REVERT: A 625 ASP cc_start: 0.8419 (t0) cc_final: 0.8027 (t0) REVERT: A 734 ARG cc_start: 0.7616 (mmt90) cc_final: 0.7208 (mmm-85) REVERT: A 758 LYS cc_start: 0.8629 (mmmt) cc_final: 0.7763 (mttm) REVERT: A 986 MET cc_start: 0.8144 (mtt) cc_final: 0.7838 (mtm) REVERT: A 1094 SER cc_start: 0.8505 (m) cc_final: 0.8081 (t) REVERT: A 1125 LYS cc_start: 0.6812 (mmtt) cc_final: 0.6240 (mttt) REVERT: A 1186 VAL cc_start: 0.7791 (t) cc_final: 0.7477 (m) REVERT: A 1405 MET cc_start: 0.8366 (mtm) cc_final: 0.8123 (mtp) REVERT: B 61 ASP cc_start: 0.7371 (m-30) cc_final: 0.7090 (t70) REVERT: B 226 GLU cc_start: 0.4858 (tm-30) cc_final: 0.4602 (tm-30) REVERT: B 407 MET cc_start: 0.8022 (mtt) cc_final: 0.7153 (mmt) REVERT: B 413 LYS cc_start: 0.7368 (ttpt) cc_final: 0.6976 (mttt) REVERT: B 442 ASP cc_start: 0.7104 (m-30) cc_final: 0.6878 (m-30) REVERT: B 463 ARG cc_start: 0.7578 (mtp180) cc_final: 0.5852 (ptt180) REVERT: B 541 ILE cc_start: 0.8543 (mp) cc_final: 0.8262 (mt) REVERT: B 1059 ILE cc_start: 0.6759 (tt) cc_final: 0.6410 (tt) REVERT: B 1101 GLN cc_start: 0.6135 (mt0) cc_final: 0.5633 (mt0) REVERT: C 123 ASN cc_start: 0.7838 (p0) cc_final: 0.7327 (m-40) REVERT: E 4 GLU cc_start: 0.7230 (mp0) cc_final: 0.6955 (tm-30) REVERT: E 73 PHE cc_start: 0.7605 (m-80) cc_final: 0.6921 (m-10) REVERT: F 91 LEU cc_start: 0.8829 (mp) cc_final: 0.8275 (mt) REVERT: H 110 THR cc_start: 0.8820 (p) cc_final: 0.8587 (t) REVERT: I 36 LEU cc_start: 0.7179 (mt) cc_final: 0.6841 (mt) REVERT: K 22 ASN cc_start: 0.7592 (t0) cc_final: 0.7387 (t0) REVERT: D 38 HIS cc_start: 0.5440 (t-170) cc_final: 0.4940 (t-90) REVERT: D 78 GLU cc_start: 0.5131 (mt-10) cc_final: 0.4922 (tm-30) REVERT: G 1 MET cc_start: 0.0812 (ptp) cc_final: 0.0609 (ptm) REVERT: G 104 MET cc_start: 0.4814 (ptp) cc_final: 0.3641 (ppp) REVERT: R 561 LEU cc_start: 0.6046 (mt) cc_final: 0.5834 (mt) outliers start: 2 outliers final: 0 residues processed: 571 average time/residue: 0.5040 time to fit residues: 449.2884 Evaluate side-chains 437 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 221 optimal weight: 6.9990 chunk 339 optimal weight: 0.8980 chunk 368 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 322 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN A 791 GLN A1182 GLN A1190 GLN A1194 ASN A1384 HIS ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 GLN B 552 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 ASN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 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 = 0.3522 r_free = 0.3522 target = 0.123872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116662 restraints weight = 58079.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.100085 restraints weight = 127739.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.098195 restraints weight = 130538.713| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 32398 Z= 0.197 Angle : 0.539 12.814 43948 Z= 0.280 Chirality : 0.042 0.173 4960 Planarity : 0.004 0.056 5558 Dihedral : 9.676 165.164 4696 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3849 helix: 1.63 (0.14), residues: 1371 sheet: -0.39 (0.21), residues: 575 loop : -0.83 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1334 HIS 0.011 0.001 HIS A1384 PHE 0.020 0.002 PHE B 422 TYR 0.015 0.002 TYR B 752 ARG 0.017 0.001 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 1322) hydrogen bonds : angle 4.66026 ( 3804) metal coordination : bond 0.00730 ( 25) metal coordination : angle 4.74465 ( 27) covalent geometry : bond 0.00454 (32373) covalent geometry : angle 0.52632 (43921) *********************** 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 515 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 514 time to evaluate : 3.731 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: 0.7772 (mmm) cc_final: 0.7353 (tpt) REVERT: A 105 LYS cc_start: 0.7020 (tppp) cc_final: 0.6127 (mttt) REVERT: A 225 PHE cc_start: 0.6722 (m-80) cc_final: 0.6060 (m-80) REVERT: A 340 LYS cc_start: 0.7007 (ttpt) cc_final: 0.6534 (mttt) REVERT: A 465 HIS cc_start: 0.6641 (p-80) cc_final: 0.6183 (p-80) REVERT: A 625 ASP cc_start: 0.8517 (t0) cc_final: 0.8067 (t0) REVERT: A 734 ARG cc_start: 0.7731 (mmt90) cc_final: 0.7472 (mmt90) REVERT: A 758 LYS cc_start: 0.8602 (mmmt) cc_final: 0.7832 (mttm) REVERT: A 962 ASP cc_start: 0.7566 (m-30) cc_final: 0.7252 (m-30) REVERT: A 986 MET cc_start: 0.8194 (mtt) cc_final: 0.7829 (mtm) REVERT: A 1094 SER cc_start: 0.8536 (m) cc_final: 0.8078 (t) REVERT: A 1125 LYS cc_start: 0.6845 (mmtt) cc_final: 0.6201 (mttt) REVERT: A 1186 VAL cc_start: 0.7813 (t) cc_final: 0.7538 (m) REVERT: A 1405 MET cc_start: 0.8373 (mtm) cc_final: 0.8148 (mtp) REVERT: A 1428 MET cc_start: 0.8120 (mmm) cc_final: 0.7597 (mmm) REVERT: B 61 ASP cc_start: 0.7595 (m-30) cc_final: 0.7235 (t70) REVERT: B 300 MET cc_start: 0.7915 (ttm) cc_final: 0.7715 (ttm) REVERT: B 407 MET cc_start: 0.8047 (mtt) cc_final: 0.7340 (mmt) REVERT: B 413 LYS cc_start: 0.7472 (ttpt) cc_final: 0.7019 (mttt) REVERT: B 442 ASP cc_start: 0.7258 (m-30) cc_final: 0.7043 (m-30) REVERT: B 463 ARG cc_start: 0.7511 (mtp180) cc_final: 0.5723 (ptt180) REVERT: B 541 ILE cc_start: 0.8573 (mp) cc_final: 0.8249 (mt) REVERT: B 667 THR cc_start: 0.8817 (m) cc_final: 0.8346 (t) REVERT: B 761 THR cc_start: 0.7635 (m) cc_final: 0.7169 (p) REVERT: B 1059 ILE cc_start: 0.6659 (tt) cc_final: 0.6381 (tt) REVERT: B 1150 ARG cc_start: 0.7082 (tpp80) cc_final: 0.6127 (tpt90) REVERT: C 123 ASN cc_start: 0.7829 (p0) cc_final: 0.7331 (m-40) REVERT: E 73 PHE cc_start: 0.7611 (m-80) cc_final: 0.7391 (m-10) REVERT: E 120 ASP cc_start: 0.6205 (p0) cc_final: 0.5584 (m-30) REVERT: E 187 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7875 (ttm-80) REVERT: I 32 ASN cc_start: 0.8206 (m-40) cc_final: 0.7960 (m-40) REVERT: I 36 LEU cc_start: 0.7209 (mt) cc_final: 0.6778 (mt) REVERT: K 16 GLU cc_start: 0.7567 (tt0) cc_final: 0.7336 (tt0) REVERT: D 38 HIS cc_start: 0.5242 (t-170) cc_final: 0.4658 (t-90) REVERT: D 78 GLU cc_start: 0.5018 (mt-10) cc_final: 0.4669 (tm-30) outliers start: 1 outliers final: 0 residues processed: 515 average time/residue: 0.4745 time to fit residues: 379.7994 Evaluate side-chains 410 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 333 optimal weight: 3.9990 chunk 330 optimal weight: 2.9990 chunk 274 optimal weight: 10.0000 chunk 198 optimal weight: 0.2980 chunk 379 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 281 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1384 HIS ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN B1071 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116101 restraints weight = 58242.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.100882 restraints weight = 148076.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.098295 restraints weight = 152999.889| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32398 Z= 0.149 Angle : 0.484 13.266 43948 Z= 0.254 Chirality : 0.041 0.152 4960 Planarity : 0.004 0.048 5558 Dihedral : 9.542 162.889 4696 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.57 % Favored : 95.40 % Rotamer: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3849 helix: 1.86 (0.14), residues: 1370 sheet: -0.33 (0.21), residues: 583 loop : -0.78 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1210 HIS 0.005 0.001 HIS K 69 PHE 0.017 0.001 PHE A 458 TYR 0.030 0.001 TYR B1153 ARG 0.008 0.000 ARG I 40 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 1322) hydrogen bonds : angle 4.44433 ( 3804) metal coordination : bond 0.00541 ( 25) metal coordination : angle 3.26060 ( 27) covalent geometry : bond 0.00350 (32373) covalent geometry : angle 0.47748 (43921) *********************** 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 503 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 502 time to evaluate : 3.422 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: 0.7876 (mmm) cc_final: 0.7611 (tpt) REVERT: A 105 LYS cc_start: 0.7270 (tppp) cc_final: 0.6361 (mttt) REVERT: A 225 PHE cc_start: 0.6686 (m-80) cc_final: 0.6001 (m-80) REVERT: A 447 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7768 (mt-10) REVERT: A 465 HIS cc_start: 0.6572 (p-80) cc_final: 0.6239 (p-80) REVERT: A 467 MET cc_start: 0.7265 (mmt) cc_final: 0.6584 (mmm) REVERT: A 625 ASP cc_start: 0.8503 (t0) cc_final: 0.8150 (t0) REVERT: A 758 LYS cc_start: 0.8604 (mmmt) cc_final: 0.7796 (mttm) REVERT: A 962 ASP cc_start: 0.7531 (m-30) cc_final: 0.7223 (m-30) REVERT: A 986 MET cc_start: 0.8162 (mtt) cc_final: 0.7834 (mtm) REVERT: A 1094 SER cc_start: 0.8545 (m) cc_final: 0.8214 (t) REVERT: A 1125 LYS cc_start: 0.6709 (mmtt) cc_final: 0.6148 (mttt) REVERT: A 1186 VAL cc_start: 0.7901 (t) cc_final: 0.7644 (m) REVERT: A 1344 MET cc_start: 0.7320 (tpt) cc_final: 0.7054 (tpp) REVERT: A 1405 MET cc_start: 0.8421 (mtm) cc_final: 0.8113 (mtp) REVERT: A 1428 MET cc_start: 0.8230 (mmm) cc_final: 0.7691 (mmm) REVERT: B 61 ASP cc_start: 0.7521 (m-30) cc_final: 0.7236 (t70) REVERT: B 413 LYS cc_start: 0.7714 (ttpt) cc_final: 0.7150 (mttt) REVERT: B 442 ASP cc_start: 0.7205 (m-30) cc_final: 0.6963 (m-30) REVERT: B 463 ARG cc_start: 0.7578 (mtp180) cc_final: 0.5757 (ptt-90) REVERT: B 541 ILE cc_start: 0.8604 (mp) cc_final: 0.8311 (mt) REVERT: B 667 THR cc_start: 0.8853 (m) cc_final: 0.8483 (t) REVERT: B 1125 MET cc_start: 0.8280 (tmm) cc_final: 0.7387 (ttp) REVERT: B 1150 ARG cc_start: 0.7010 (tpp80) cc_final: 0.6040 (tpt90) REVERT: B 1172 MET cc_start: 0.7825 (mmt) cc_final: 0.7378 (mpp) REVERT: C 123 ASN cc_start: 0.7774 (p0) cc_final: 0.7343 (m-40) REVERT: E 67 ASP cc_start: 0.7384 (t0) cc_final: 0.6877 (t0) REVERT: E 73 PHE cc_start: 0.7535 (m-80) cc_final: 0.7283 (m-10) REVERT: E 120 ASP cc_start: 0.6194 (p0) cc_final: 0.5864 (m-30) REVERT: E 187 ARG cc_start: 0.8141 (mtp180) cc_final: 0.7672 (ttm-80) REVERT: I 32 ASN cc_start: 0.8389 (m-40) cc_final: 0.7892 (m-40) REVERT: K 16 GLU cc_start: 0.7542 (tt0) cc_final: 0.7241 (tt0) REVERT: D 38 HIS cc_start: 0.4900 (t70) cc_final: 0.4698 (t-90) outliers start: 1 outliers final: 0 residues processed: 503 average time/residue: 0.4596 time to fit residues: 364.1596 Evaluate side-chains 416 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 362 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 273 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 385 optimal weight: 9.9990 chunk 277 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 315 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN A 757 GLN A 780 ASN A1310 HIS ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B1003 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.111556 restraints weight = 58398.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.094987 restraints weight = 131892.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.093331 restraints weight = 133061.855| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 32398 Z= 0.315 Angle : 0.685 12.368 43948 Z= 0.355 Chirality : 0.047 0.182 4960 Planarity : 0.005 0.050 5558 Dihedral : 9.968 165.824 4696 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 27.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.60 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3849 helix: 1.17 (0.14), residues: 1367 sheet: -0.51 (0.22), residues: 565 loop : -1.11 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1210 HIS 0.006 0.002 HIS K 69 PHE 0.034 0.002 PHE A 668 TYR 0.039 0.002 TYR B1048 ARG 0.013 0.001 ARG I 40 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 1322) hydrogen bonds : angle 5.00269 ( 3804) metal coordination : bond 0.01304 ( 25) metal coordination : angle 4.72839 ( 27) covalent geometry : bond 0.00754 (32373) covalent geometry : angle 0.67477 (43921) *********************** 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 455 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 3.781 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: 0.7856 (mmm) cc_final: 0.7612 (tpt) REVERT: A 105 LYS cc_start: 0.7445 (tppp) cc_final: 0.6562 (mtmt) REVERT: A 225 PHE cc_start: 0.6862 (m-80) cc_final: 0.6119 (m-80) REVERT: A 625 ASP cc_start: 0.8694 (t0) cc_final: 0.8239 (t0) REVERT: A 758 LYS cc_start: 0.8657 (mmmt) cc_final: 0.7868 (mttm) REVERT: A 962 ASP cc_start: 0.7567 (m-30) cc_final: 0.7174 (m-30) REVERT: A 1094 SER cc_start: 0.8575 (m) cc_final: 0.8230 (t) REVERT: A 1125 LYS cc_start: 0.6769 (mmtt) cc_final: 0.6351 (mttt) REVERT: A 1186 VAL cc_start: 0.8194 (t) cc_final: 0.7816 (m) REVERT: A 1230 GLN cc_start: 0.7756 (tt0) cc_final: 0.7163 (tt0) REVERT: A 1405 MET cc_start: 0.8352 (mtm) cc_final: 0.8070 (mtp) REVERT: A 1428 MET cc_start: 0.7995 (mmm) cc_final: 0.7383 (mmm) REVERT: A 1432 PHE cc_start: 0.6065 (t80) cc_final: 0.5692 (t80) REVERT: B 61 ASP cc_start: 0.7862 (m-30) cc_final: 0.7442 (t70) REVERT: B 413 LYS cc_start: 0.7751 (ttpt) cc_final: 0.7204 (mttt) REVERT: B 463 ARG cc_start: 0.7457 (mtp180) cc_final: 0.5638 (ptt-90) REVERT: B 667 THR cc_start: 0.8739 (m) cc_final: 0.8302 (t) REVERT: B 1076 GLU cc_start: 0.6643 (tt0) cc_final: 0.5682 (mp0) REVERT: B 1150 ARG cc_start: 0.7366 (tpp80) cc_final: 0.6392 (tpt90) REVERT: B 1172 MET cc_start: 0.7790 (mmt) cc_final: 0.7392 (mpp) REVERT: C 18 ASN cc_start: 0.8168 (t0) cc_final: 0.7886 (t0) REVERT: C 123 ASN cc_start: 0.7459 (p0) cc_final: 0.7210 (m-40) REVERT: E 67 ASP cc_start: 0.8041 (t0) cc_final: 0.7833 (t0) REVERT: E 187 ARG cc_start: 0.8132 (mtp180) cc_final: 0.7786 (ttm-80) REVERT: F 94 MET cc_start: 0.7966 (tpp) cc_final: 0.7757 (tpp) REVERT: I 32 ASN cc_start: 0.8285 (m-40) cc_final: 0.7990 (m-40) REVERT: J 31 GLU cc_start: 0.7248 (mp0) cc_final: 0.6755 (mp0) REVERT: D 38 HIS cc_start: 0.4222 (t70) cc_final: 0.3595 (t-170) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.4618 time to fit residues: 330.3954 Evaluate side-chains 378 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 345 optimal weight: 30.0000 chunk 201 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 270 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 167 optimal weight: 0.0970 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 342 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 294 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN A1384 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B1003 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 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** G 4 HIS G 9 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116114 restraints weight = 57898.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100882 restraints weight = 146780.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.099666 restraints weight = 150567.942| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4605 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= 0.087 Angle : 0.451 12.362 43948 Z= 0.237 Chirality : 0.040 0.134 4960 Planarity : 0.003 0.061 5558 Dihedral : 9.517 164.237 4696 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3849 helix: 1.87 (0.14), residues: 1372 sheet: -0.19 (0.22), residues: 582 loop : -0.80 (0.15), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1210 HIS 0.004 0.001 HIS K 69 PHE 0.009 0.001 PHE A 668 TYR 0.018 0.001 TYR B1153 ARG 0.005 0.000 ARG I 40 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 1322) hydrogen bonds : angle 4.37570 ( 3804) metal coordination : bond 0.00370 ( 25) metal coordination : angle 3.35427 ( 27) covalent geometry : bond 0.00189 (32373) covalent geometry : angle 0.44333 (43921) *********************** 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 485 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7816 (mmm) cc_final: 0.7393 (tpt) REVERT: A 105 LYS cc_start: 0.7616 (tppp) cc_final: 0.6558 (mttt) REVERT: A 225 PHE cc_start: 0.6666 (m-80) cc_final: 0.6034 (m-80) REVERT: A 362 SER cc_start: 0.7570 (m) cc_final: 0.7077 (p) REVERT: A 465 HIS cc_start: 0.6846 (p-80) cc_final: 0.6518 (p-80) REVERT: A 467 MET cc_start: 0.7360 (mmt) cc_final: 0.7066 (mmm) REVERT: A 625 ASP cc_start: 0.8651 (t0) cc_final: 0.8169 (t0) REVERT: A 758 LYS cc_start: 0.8652 (mmmt) cc_final: 0.7844 (mttm) REVERT: A 769 MET cc_start: 0.8278 (mtm) cc_final: 0.8007 (mtm) REVERT: A 1094 SER cc_start: 0.8466 (m) cc_final: 0.8114 (t) REVERT: A 1125 LYS cc_start: 0.6613 (mmtt) cc_final: 0.6086 (mttt) REVERT: A 1405 MET cc_start: 0.8289 (mtm) cc_final: 0.8038 (mtp) REVERT: A 1428 MET cc_start: 0.8155 (mmm) cc_final: 0.7676 (mmm) REVERT: B 61 ASP cc_start: 0.7519 (m-30) cc_final: 0.7255 (t70) REVERT: B 128 ILE cc_start: 0.8376 (tp) cc_final: 0.8163 (tp) REVERT: B 200 MET cc_start: 0.8766 (mmm) cc_final: 0.8524 (tpp) REVERT: B 299 GLU cc_start: 0.6522 (mp0) cc_final: 0.6162 (mp0) REVERT: B 413 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7306 (mttt) REVERT: B 463 ARG cc_start: 0.7607 (mtp180) cc_final: 0.5852 (ptt-90) REVERT: B 667 THR cc_start: 0.8797 (m) cc_final: 0.8533 (t) REVERT: B 1125 MET cc_start: 0.8379 (tmm) cc_final: 0.6583 (mmt) REVERT: B 1150 ARG cc_start: 0.7194 (tpp80) cc_final: 0.6218 (tpt90) REVERT: B 1172 MET cc_start: 0.7825 (mmt) cc_final: 0.7441 (mpp) REVERT: C 123 ASN cc_start: 0.7435 (p0) cc_final: 0.7206 (m-40) REVERT: E 187 ARG cc_start: 0.8141 (mtp180) cc_final: 0.7826 (ttm-80) REVERT: H 37 MET cc_start: 0.7853 (mtt) cc_final: 0.7639 (mtt) REVERT: I 32 ASN cc_start: 0.8222 (m-40) cc_final: 0.7894 (m-40) REVERT: D 38 HIS cc_start: 0.4013 (t70) cc_final: 0.3382 (t-170) outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.4634 time to fit residues: 355.6505 Evaluate side-chains 388 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 301 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 288 optimal weight: 0.3980 chunk 357 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 351 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A 780 ASN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113389 restraints weight = 58024.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098812 restraints weight = 129840.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.097577 restraints weight = 162427.538| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32398 Z= 0.180 Angle : 0.515 11.099 43948 Z= 0.268 Chirality : 0.042 0.142 4960 Planarity : 0.004 0.048 5558 Dihedral : 9.563 165.495 4696 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 27.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3849 helix: 1.78 (0.14), residues: 1376 sheet: -0.21 (0.22), residues: 576 loop : -0.84 (0.15), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1192 HIS 0.005 0.001 HIS A1163 PHE 0.018 0.002 PHE A 668 TYR 0.033 0.001 TYR B1153 ARG 0.005 0.000 ARG B 924 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 1322) hydrogen bonds : angle 4.47268 ( 3804) metal coordination : bond 0.00682 ( 25) metal coordination : angle 3.55764 ( 27) covalent geometry : bond 0.00427 (32373) covalent geometry : angle 0.50719 (43921) *********************** 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 451 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 3.546 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: A 78 MET cc_start: 0.7780 (mmm) cc_final: 0.7352 (tpt) REVERT: A 105 LYS cc_start: 0.7657 (tppp) cc_final: 0.6583 (mttt) REVERT: A 225 PHE cc_start: 0.6793 (m-80) cc_final: 0.6176 (m-80) REVERT: A 287 ASN cc_start: 0.5411 (t0) cc_final: 0.5172 (t0) REVERT: A 465 HIS cc_start: 0.6946 (p-80) cc_final: 0.6636 (p-80) REVERT: A 467 MET cc_start: 0.7310 (mmt) cc_final: 0.6965 (mmm) REVERT: A 625 ASP cc_start: 0.8667 (t0) cc_final: 0.8160 (t0) REVERT: A 758 LYS cc_start: 0.8621 (mmmt) cc_final: 0.7805 (mttm) REVERT: A 769 MET cc_start: 0.8284 (mtm) cc_final: 0.7994 (mtm) REVERT: A 1125 LYS cc_start: 0.6591 (mmtt) cc_final: 0.6218 (mttt) REVERT: A 1405 MET cc_start: 0.8264 (mtm) cc_final: 0.7968 (mtp) REVERT: A 1428 MET cc_start: 0.8320 (mmm) cc_final: 0.7577 (mmm) REVERT: B 61 ASP cc_start: 0.7586 (m-30) cc_final: 0.7284 (t70) REVERT: B 413 LYS cc_start: 0.7861 (ttpt) cc_final: 0.7322 (mttt) REVERT: B 442 ASP cc_start: 0.7059 (m-30) cc_final: 0.6828 (m-30) REVERT: B 463 ARG cc_start: 0.7569 (mtp180) cc_final: 0.5832 (ptt-90) REVERT: B 667 THR cc_start: 0.8778 (m) cc_final: 0.8467 (t) REVERT: B 897 ARG cc_start: 0.6850 (mmm160) cc_final: 0.6578 (mmm160) REVERT: B 1076 GLU cc_start: 0.6841 (tt0) cc_final: 0.5796 (mp0) REVERT: B 1150 ARG cc_start: 0.7107 (tpp80) cc_final: 0.6291 (tpt90) REVERT: B 1172 MET cc_start: 0.7907 (mmt) cc_final: 0.7544 (mpp) REVERT: C 18 ASN cc_start: 0.8236 (t0) cc_final: 0.7973 (t0) REVERT: E 187 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7836 (ttm-80) REVERT: H 37 MET cc_start: 0.7956 (mtt) cc_final: 0.7727 (mtt) REVERT: I 32 ASN cc_start: 0.8219 (m-40) cc_final: 0.7846 (m-40) REVERT: D 38 HIS cc_start: 0.4065 (t70) cc_final: 0.3834 (t70) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.4535 time to fit residues: 323.1121 Evaluate side-chains 378 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 40 optimal weight: 0.7980 chunk 357 optimal weight: 20.0000 chunk 257 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 326 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 366 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 chunk 310 optimal weight: 5.9990 chunk 292 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114507 restraints weight = 57886.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.098191 restraints weight = 121077.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.096778 restraints weight = 128068.489| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32398 Z= 0.141 Angle : 0.468 10.070 43948 Z= 0.245 Chirality : 0.041 0.144 4960 Planarity : 0.003 0.043 5558 Dihedral : 9.492 165.411 4696 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 27.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3849 helix: 1.96 (0.14), residues: 1379 sheet: -0.18 (0.22), residues: 574 loop : -0.79 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1192 HIS 0.005 0.001 HIS B1097 PHE 0.016 0.001 PHE A 458 TYR 0.025 0.001 TYR B1153 ARG 0.006 0.000 ARG A 483 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 1322) hydrogen bonds : angle 4.36255 ( 3804) metal coordination : bond 0.00562 ( 25) metal coordination : angle 3.26611 ( 27) covalent geometry : bond 0.00334 (32373) covalent geometry : angle 0.46079 (43921) *********************** 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 450 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 3.437 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: 0.7945 (mmm) cc_final: 0.7601 (tpt) REVERT: A 105 LYS cc_start: 0.7487 (tppp) cc_final: 0.6685 (mtmt) REVERT: A 145 TYR cc_start: 0.5969 (t80) cc_final: 0.5682 (t80) REVERT: A 225 PHE cc_start: 0.6900 (m-80) cc_final: 0.6267 (m-80) REVERT: A 388 MET cc_start: 0.8045 (mtp) cc_final: 0.7774 (mtp) REVERT: A 465 HIS cc_start: 0.6886 (p-80) cc_final: 0.6615 (p-80) REVERT: A 467 MET cc_start: 0.7244 (mmt) cc_final: 0.6953 (mmm) REVERT: A 625 ASP cc_start: 0.8712 (t0) cc_final: 0.8266 (t0) REVERT: A 758 LYS cc_start: 0.8622 (mmmt) cc_final: 0.7836 (mttm) REVERT: A 769 MET cc_start: 0.8186 (mtm) cc_final: 0.7850 (mtm) REVERT: A 962 ASP cc_start: 0.7560 (m-30) cc_final: 0.7341 (m-30) REVERT: A 1125 LYS cc_start: 0.6610 (mmtt) cc_final: 0.6240 (mttt) REVERT: A 1405 MET cc_start: 0.8269 (mtm) cc_final: 0.8020 (mtp) REVERT: A 1428 MET cc_start: 0.8140 (mmm) cc_final: 0.7488 (mmm) REVERT: B 61 ASP cc_start: 0.7611 (m-30) cc_final: 0.7300 (t70) REVERT: B 270 ILE cc_start: 0.8757 (mm) cc_final: 0.8551 (mm) REVERT: B 413 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7280 (mttt) REVERT: B 442 ASP cc_start: 0.7103 (m-30) cc_final: 0.6881 (m-30) REVERT: B 463 ARG cc_start: 0.7562 (mtp180) cc_final: 0.5781 (ptt-90) REVERT: B 667 THR cc_start: 0.8762 (m) cc_final: 0.8487 (t) REVERT: B 897 ARG cc_start: 0.6831 (mmm160) cc_final: 0.6547 (mmm160) REVERT: B 1076 GLU cc_start: 0.6759 (tt0) cc_final: 0.5613 (mp0) REVERT: B 1125 MET cc_start: 0.7813 (tmm) cc_final: 0.6453 (mtp) REVERT: B 1150 ARG cc_start: 0.7100 (tpp80) cc_final: 0.6118 (tpt90) REVERT: B 1172 MET cc_start: 0.7832 (mmt) cc_final: 0.7412 (mpp) REVERT: E 187 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7833 (ttm-80) REVERT: H 37 MET cc_start: 0.7916 (mtt) cc_final: 0.7674 (mtt) REVERT: I 32 ASN cc_start: 0.8314 (m-40) cc_final: 0.7961 (m-40) REVERT: L 29 LYS cc_start: 0.7715 (ttmt) cc_final: 0.7433 (ttmt) REVERT: D 38 HIS cc_start: 0.4176 (t70) cc_final: 0.3950 (t70) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.4681 time to fit residues: 331.1021 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 : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 301 optimal weight: 0.6980 chunk 247 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 chunk 272 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 323 optimal weight: 0.7980 chunk 217 optimal weight: 8.9990 chunk 324 optimal weight: 0.5980 chunk 328 optimal weight: 0.7980 chunk 172 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 144 HIS B 525 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 28 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115755 restraints weight = 57432.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.099708 restraints weight = 122414.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.097955 restraints weight = 121050.380| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32398 Z= 0.093 Angle : 0.427 9.573 43948 Z= 0.225 Chirality : 0.040 0.153 4960 Planarity : 0.003 0.048 5558 Dihedral : 9.350 165.145 4696 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 26.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3849 helix: 2.18 (0.15), residues: 1384 sheet: -0.06 (0.22), residues: 593 loop : -0.66 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1192 HIS 0.004 0.001 HIS G 14 PHE 0.010 0.001 PHE B 356 TYR 0.016 0.001 TYR R 597 ARG 0.008 0.000 ARG L 42 Details of bonding type rmsd hydrogen bonds : bond 0.02939 ( 1322) hydrogen bonds : angle 4.18553 ( 3804) metal coordination : bond 0.00342 ( 25) metal coordination : angle 2.79020 ( 27) covalent geometry : bond 0.00212 (32373) covalent geometry : angle 0.42185 (43921) *********************** 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 453 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7939 (mmm) cc_final: 0.7448 (tpt) REVERT: A 105 LYS cc_start: 0.7485 (tppp) cc_final: 0.6663 (mttt) REVERT: A 145 TYR cc_start: 0.5925 (t80) cc_final: 0.5624 (t80) REVERT: A 225 PHE cc_start: 0.6818 (m-80) cc_final: 0.6065 (m-80) REVERT: A 248 MET cc_start: 0.6635 (ttp) cc_final: 0.6163 (tmm) REVERT: A 388 MET cc_start: 0.8158 (mtp) cc_final: 0.7946 (mtp) REVERT: A 465 HIS cc_start: 0.6957 (p-80) cc_final: 0.6601 (p-80) REVERT: A 625 ASP cc_start: 0.8648 (t0) cc_final: 0.8213 (t0) REVERT: A 758 LYS cc_start: 0.8549 (mmmt) cc_final: 0.7747 (mttm) REVERT: A 986 MET cc_start: 0.8156 (mtt) cc_final: 0.7732 (mtm) REVERT: A 1057 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7146 (tt0) REVERT: A 1125 LYS cc_start: 0.6469 (mmtt) cc_final: 0.6141 (mttt) REVERT: A 1405 MET cc_start: 0.8300 (mtm) cc_final: 0.8056 (mtp) REVERT: A 1428 MET cc_start: 0.8157 (mmm) cc_final: 0.7565 (mmm) REVERT: A 1432 PHE cc_start: 0.6242 (t80) cc_final: 0.5951 (t80) REVERT: B 61 ASP cc_start: 0.7612 (m-30) cc_final: 0.7332 (t70) REVERT: B 270 ILE cc_start: 0.8683 (mm) cc_final: 0.8406 (mm) REVERT: B 413 LYS cc_start: 0.7717 (ttpt) cc_final: 0.7273 (mttt) REVERT: B 442 ASP cc_start: 0.7010 (m-30) cc_final: 0.6786 (m-30) REVERT: B 463 ARG cc_start: 0.7610 (mtp180) cc_final: 0.5837 (ptt-90) REVERT: B 667 THR cc_start: 0.8792 (m) cc_final: 0.8470 (t) REVERT: B 897 ARG cc_start: 0.6926 (mmm160) cc_final: 0.6619 (mmm160) REVERT: B 1125 MET cc_start: 0.7745 (tmm) cc_final: 0.6455 (mtp) REVERT: B 1150 ARG cc_start: 0.7078 (tpp80) cc_final: 0.6119 (tpt90) REVERT: B 1172 MET cc_start: 0.7807 (mmt) cc_final: 0.7331 (mpp) REVERT: C 18 ASN cc_start: 0.8083 (t0) cc_final: 0.7697 (t0) REVERT: E 187 ARG cc_start: 0.8107 (mtp180) cc_final: 0.7827 (ttm-80) REVERT: H 37 MET cc_start: 0.7908 (mtt) cc_final: 0.7655 (mtt) REVERT: L 29 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7323 (ttmt) REVERT: D 38 HIS cc_start: 0.4132 (t70) cc_final: 0.3915 (t70) REVERT: G 104 MET cc_start: 0.5973 (ptt) cc_final: 0.5680 (ptm) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.4483 time to fit residues: 323.0683 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 : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 0 optimal weight: 20.0000 chunk 327 optimal weight: 7.9990 chunk 276 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 4 optimal weight: 0.0170 chunk 330 optimal weight: 3.9990 chunk 372 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A1034 GLN A1384 HIS ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 ASN K 2 ASN ** L 26 ASN ** 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 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.119702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112226 restraints weight = 58098.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.096338 restraints weight = 129873.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.094561 restraints weight = 142606.912| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 32398 Z= 0.244 Angle : 0.580 10.179 43948 Z= 0.302 Chirality : 0.044 0.163 4960 Planarity : 0.004 0.074 5558 Dihedral : 9.647 167.188 4696 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 28.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3849 helix: 1.74 (0.14), residues: 1379 sheet: -0.31 (0.22), residues: 584 loop : -0.86 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1210 HIS 0.006 0.001 HIS A1163 PHE 0.024 0.002 PHE A 668 TYR 0.050 0.002 TYR B 752 ARG 0.010 0.001 ARG A 483 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 1322) hydrogen bonds : angle 4.60362 ( 3804) metal coordination : bond 0.00939 ( 25) metal coordination : angle 3.83503 ( 27) covalent geometry : bond 0.00584 (32373) covalent geometry : angle 0.57249 (43921) ********************** 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 434 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 433 time to evaluate : 3.569 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: 0.7761 (mmm) cc_final: 0.7485 (tpt) REVERT: A 101 VAL cc_start: 0.8387 (m) cc_final: 0.7854 (p) REVERT: A 105 LYS cc_start: 0.7482 (tppp) cc_final: 0.6785 (mtmt) REVERT: A 145 TYR cc_start: 0.5923 (t80) cc_final: 0.5554 (t80) REVERT: A 225 PHE cc_start: 0.6856 (m-80) cc_final: 0.6255 (m-80) REVERT: A 248 MET cc_start: 0.6498 (ttp) cc_final: 0.6040 (tmm) REVERT: A 528 PRO cc_start: 0.7850 (Cg_exo) cc_final: 0.7642 (Cg_endo) REVERT: A 625 ASP cc_start: 0.8749 (t0) cc_final: 0.8284 (t0) REVERT: A 758 LYS cc_start: 0.8665 (mmmt) cc_final: 0.7869 (mttm) REVERT: A 868 MET cc_start: 0.8122 (mtm) cc_final: 0.7697 (mtt) REVERT: A 962 ASP cc_start: 0.7658 (m-30) cc_final: 0.7215 (m-30) REVERT: A 1125 LYS cc_start: 0.6630 (mmtt) cc_final: 0.6246 (mttt) REVERT: A 1405 MET cc_start: 0.8249 (mtm) cc_final: 0.7982 (mtp) REVERT: A 1428 MET cc_start: 0.8118 (mmm) cc_final: 0.7372 (mmm) REVERT: B 61 ASP cc_start: 0.7845 (m-30) cc_final: 0.7502 (t70) REVERT: B 413 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7325 (mttt) REVERT: B 463 ARG cc_start: 0.7554 (mtp180) cc_final: 0.5811 (ptt-90) REVERT: B 667 THR cc_start: 0.8781 (m) cc_final: 0.8387 (t) REVERT: B 897 ARG cc_start: 0.6977 (mmm160) cc_final: 0.6745 (mmm160) REVERT: B 1076 GLU cc_start: 0.6847 (tt0) cc_final: 0.5703 (mp0) REVERT: B 1125 MET cc_start: 0.7729 (tmm) cc_final: 0.6598 (mtp) REVERT: B 1150 ARG cc_start: 0.7151 (tpp80) cc_final: 0.6229 (tpt90) REVERT: B 1172 MET cc_start: 0.7816 (mmt) cc_final: 0.7429 (mpp) REVERT: E 187 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7775 (ttm-80) REVERT: H 37 MET cc_start: 0.8012 (mtt) cc_final: 0.7776 (mtt) REVERT: L 29 LYS cc_start: 0.7785 (ttmt) cc_final: 0.7339 (ttmt) REVERT: D 38 HIS cc_start: 0.4167 (t70) cc_final: 0.3928 (t70) outliers start: 1 outliers final: 0 residues processed: 434 average time/residue: 0.4708 time to fit residues: 325.0243 Evaluate side-chains 369 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 166 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** 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 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.121283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113752 restraints weight = 57371.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.097706 restraints weight = 137902.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.095978 restraints weight = 153787.671| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32398 Z= 0.138 Angle : 0.467 10.011 43948 Z= 0.245 Chirality : 0.041 0.152 4960 Planarity : 0.003 0.060 5558 Dihedral : 9.485 166.620 4696 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 27.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3849 helix: 2.03 (0.15), residues: 1375 sheet: -0.21 (0.22), residues: 588 loop : -0.77 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1192 HIS 0.004 0.001 HIS K 69 PHE 0.014 0.001 PHE A 668 TYR 0.025 0.001 TYR B 752 ARG 0.006 0.000 ARG A 483 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 1322) hydrogen bonds : angle 4.36025 ( 3804) metal coordination : bond 0.00582 ( 25) metal coordination : angle 3.25758 ( 27) covalent geometry : bond 0.00324 (32373) covalent geometry : angle 0.45985 (43921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10050.72 seconds wall clock time: 177 minutes 20.55 seconds (10640.55 seconds total)