Starting phenix.real_space_refine on Sat Mar 7 04:59:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oky_12973/03_2026/7oky_12973.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oky_12973/03_2026/7oky_12973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oky_12973/03_2026/7oky_12973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oky_12973/03_2026/7oky_12973.map" model { file = "/net/cci-nas-00/data/ceres_data/7oky_12973/03_2026/7oky_12973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oky_12973/03_2026/7oky_12973.cif" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.990 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 9 6.06 5 P 79 5.49 5 Mg 1 5.21 5 S 230 5.16 5 C 23946 2.51 5 N 6740 2.21 5 O 7336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38341 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11149 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1338} Chain breaks: 6 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9047 Classifications: {'peptide': 1131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1347 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 932 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} 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: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1106 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 549 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "O" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 279 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "T" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "Z" Number of atoms: 2979 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 2971 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 374, 2971 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 3011 Chain: "Y" Number of atoms: 920 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 116, 899 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 899 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" 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 472 SG CYS A 71 107.327 100.777 77.923 1.00 53.97 S ATOM 494 SG CYS A 74 106.063 104.031 79.616 1.00 50.43 S ATOM 541 SG CYS A 81 103.720 101.015 79.304 1.00 45.79 S ATOM 776 SG CYS A 111 89.795 108.014 34.549 1.00 65.63 S ATOM 804 SG CYS A 114 91.516 111.137 34.607 1.00 69.86 S ATOM 1117 SG CYS A 154 87.909 110.902 33.075 1.00 76.79 S ATOM 1144 SG CYS A 184 91.027 109.611 31.192 1.00 79.71 S ATOM 19765 SG CYS B1196 100.691 116.592 70.371 1.00 45.35 S ATOM 19787 SG CYS B1199 99.408 113.716 68.144 1.00 49.68 S ATOM 19902 SG CYS B1214 102.643 113.412 69.466 1.00 52.69 S ATOM 19923 SG CYS B1217 101.947 116.115 66.748 1.00 64.76 S ATOM 20890 SG CYS C 88 82.640 78.966 138.530 1.00 49.61 S ATOM 20903 SG CYS C 90 85.274 77.668 136.016 1.00 55.35 S ATOM 20938 SG CYS C 94 84.071 75.646 138.950 1.00 41.65 S ATOM 20960 SG CYS C 97 81.805 76.249 135.891 1.00 37.01 S ATOM 28729 SG CYS I 86 20.547 53.417 55.946 1.00 62.37 S ATOM 28753 SG CYS I 89 20.323 49.626 56.631 1.00 69.05 S ATOM 28957 SG CYS I 114 23.091 51.800 58.188 1.00 51.27 S ATOM 28992 SG CYS I 119 22.954 50.881 54.427 1.00 64.00 S ATOM 28177 SG CYS I 17 49.191 59.227 21.712 1.00 35.13 S ATOM 28201 SG CYS I 20 53.027 60.186 22.885 1.00 34.24 S ATOM 28352 SG CYS I 39 50.448 62.435 22.195 1.00 45.53 S ATOM 28377 SG CYS I 42 51.765 59.890 19.133 1.00 49.82 S ATOM 29102 SG CYS J 7 57.094 68.010 118.927 1.00 15.25 S ATOM 29126 SG CYS J 10 56.162 69.229 122.392 1.00 15.23 S ATOM 29390 SG CYS J 44 53.495 69.170 119.515 1.00 20.26 S ATOM 29396 SG CYS J 45 54.680 66.166 121.444 1.00 21.78 S ATOM 30533 SG CYS L 19 92.862 49.429 101.464 1.00 49.50 S ATOM 30552 SG CYS L 22 93.230 46.562 103.807 1.00 53.06 S ATOM 30663 SG CYS L 36 96.223 47.633 101.965 1.00 57.01 S ATOM 30689 SG CYS L 39 93.449 45.922 100.005 1.00 56.16 S ATOM 37530 SG CYS Y 16 127.725 65.380 30.388 1.00 13.45 S ATOM 37552 SG CYS Y 19 124.571 64.597 28.442 1.00 12.79 S ATOM 37664 SG CYS Y 33 126.661 61.860 29.266 1.00 14.97 S ATOM 37686 SG CYS Y 36 127.942 64.265 26.644 1.00 15.83 S Time building chain proxies: 9.51, per 1000 atoms: 0.25 Number of scatterers: 38341 At special positions: 0 Unit cell: (159.6, 172.2, 161.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 9 29.99 S 230 16.00 P 79 15.00 Mg 1 11.99 O 7336 8.00 N 6740 7.00 C 23946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 71 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 154 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1199 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1214 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1196 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1217 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " 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 22 " 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 39 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 36 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " Number of angles added : 51 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8640 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 57 sheets defined 34.9% alpha, 20.4% beta 27 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.683A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.594A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.600A pdb=" N VAL A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.571A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.579A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' 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: 3.503A 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 521 through 525 Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 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: 3.520A pdb=" N ASN A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 removed outlier: 3.581A pdb=" N SER A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.708A 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 869 removed outlier: 3.704A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.510A pdb=" N ARG A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 934 removed outlier: 4.222A pdb=" N ARG A 932 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 944 removed outlier: 3.728A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1017 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1052 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1102 removed outlier: 3.537A pdb=" N MET A1102 " --> pdb=" O ALA A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.594A pdb=" N SER A1147 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1162 Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1217 through 1223 removed outlier: 3.644A pdb=" N ASP A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1294 Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.670A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 4.504A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.900A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 3.636A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.843A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1479 through 1483 removed outlier: 3.837A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A1483 " --> pdb=" O CYS A1480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1479 through 1483' Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 98 through 114 removed outlier: 3.857A pdb=" N TRP B 104 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.804A pdb=" N SER B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 371 through 378 removed outlier: 4.087A pdb=" N MET B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 378 " --> pdb=" O MET B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 385 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 408 through 423 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.592A pdb=" N VAL B 428 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 454 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 472 through 502 removed outlier: 3.769A pdb=" N GLY B 483 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 501 " --> pdb=" O GLN B 497 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 528 removed outlier: 3.514A pdb=" N SER B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 615 through 625 removed outlier: 3.792A pdb=" N GLU B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.855A pdb=" N ILE B 638 " --> pdb=" O PRO B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 713 through 721 removed outlier: 3.512A pdb=" N ILE B 717 " --> pdb=" O LYS B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 727 removed outlier: 3.640A pdb=" N ASN B 727 " --> pdb=" O ARG B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 744 through 748 removed outlier: 3.588A pdb=" N GLU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 744 through 748' Processing helix chain 'B' and resid 755 through 760 Processing helix chain 'B' and resid 776 through 781 removed outlier: 3.757A pdb=" N ILE B 780 " --> pdb=" O PRO B 777 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 781 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 794 removed outlier: 3.580A pdb=" N ASN B 794 " --> pdb=" O PRO B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 806 Processing helix chain 'B' and resid 838 through 843 removed outlier: 3.754A pdb=" N GLU B 842 " --> pdb=" O ARG B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 880 Processing helix chain 'B' and resid 921 through 925 removed outlier: 4.004A pdb=" N LYS B 924 " --> pdb=" O ILE B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1054 through 1071 removed outlier: 3.911A pdb=" N LEU B1058 " --> pdb=" O THR B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1094 Processing helix chain 'B' and resid 1154 through 1158 removed outlier: 3.623A pdb=" N ARG B1157 " --> pdb=" O GLY B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1175 Processing helix chain 'B' and resid 1176 through 1185 Processing helix chain 'B' and resid 1229 through 1241 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.568A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 270 removed outlier: 3.594A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 84 through 92 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 118 through 132 removed outlier: 3.879A pdb=" N LYS D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.523A pdb=" N GLU D 161 " --> pdb=" O PRO D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.554A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) 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 121 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.698A 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 99 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.643A pdb=" N VAL G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.591A pdb=" N GLU G 118 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.690A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.573A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (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: 3.755A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.647A 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: 3.754A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.000A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 35 through 48 removed outlier: 3.601A pdb=" N HIS M 48 " --> pdb=" O THR M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 146 removed outlier: 3.900A pdb=" N GLN M 132 " --> pdb=" O ASN M 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 23 removed outlier: 3.543A pdb=" N PHE O 22 " --> pdb=" O GLY O 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 204 removed outlier: 4.081A pdb=" N ALA Z 193 " --> pdb=" O GLU Z 189 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE Z 194 " --> pdb=" O ARG Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 231 through 239 Processing helix chain 'Z' and resid 242 through 246 removed outlier: 3.581A pdb=" N LEU Z 245 " --> pdb=" O VAL Z 242 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG Z 246 " --> pdb=" O GLY Z 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 242 through 246' Processing helix chain 'Z' and resid 256 through 260 removed outlier: 3.845A pdb=" N MET Z 260 " --> pdb=" O ILE Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 630 through 633 removed outlier: 3.764A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 removed outlier: 4.041A pdb=" N VAL Y 49 " --> pdb=" O ASN Y 45 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR Y 50 " --> pdb=" O ARG Y 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 75 removed outlier: 3.783A pdb=" N LYS Y 73 " --> pdb=" O SER Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 104 removed outlier: 3.626A pdb=" N AARG Y 104 " --> pdb=" O GLU Y 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.704A pdb=" N ARG A 51 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.772A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.586A pdb=" N GLU A 201 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.585A pdb=" N LEU B1161 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1137 through 1139 removed outlier: 5.914A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.587A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (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: 6.347A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.656A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (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 872 through 873 Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.936A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 6.897A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1243 through 1248 removed outlier: 4.117A pdb=" N ASN A1248 " --> pdb=" O VAL A1256 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A1256 " --> pdb=" O ASN A1248 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ALA A1171 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LYS I 57 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR A1173 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL I 55 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A1175 " --> pdb=" O ILE I 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB9, first strand: chain 'A' and resid 1408 through 1409 removed outlier: 4.121A pdb=" N GLN E 174 " --> pdb=" O GLY A1409 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 72 through 73 removed outlier: 4.479A pdb=" N GLU D 72 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.108A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 142 through 144 removed outlier: 4.489A pdb=" N ASP B 204 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR B 202 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 170 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 199 " --> pdb=" O GLY B 227 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY B 227 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU B 201 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE B 225 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL B 203 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 174 through 176 Processing sheet with id=AC5, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AC6, first strand: chain 'B' and resid 468 through 471 removed outlier: 6.414A pdb=" N ALA B 273 " --> pdb=" O ASN B 563 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 282 through 285 removed outlier: 3.650A pdb=" N TYR B 294 " --> pdb=" O MET B 316 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP B 313 " --> pdb=" O THR B 336 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AC9, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD1, first strand: chain 'B' and resid 628 through 629 removed outlier: 5.494A pdb=" N TRP B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B 646 " --> pdb=" O TRP B 650 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 652 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS B 643 " --> pdb=" O ILE B 689 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE B 691 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE B 645 " --> pdb=" O ILE B 691 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 824 through 828 removed outlier: 4.103A pdb=" N LYS B 994 " --> pdb=" O GLU B 895 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL B1003 " --> pdb=" O THR B 978 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR B 978 " --> pdb=" O VAL B1003 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 824 through 828 removed outlier: 4.103A pdb=" N LYS B 994 " --> pdb=" O GLU B 895 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL B1003 " --> pdb=" O THR B 978 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR B 978 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL B 984 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 836 through 837 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1103 removed outlier: 7.081A pdb=" N VAL B 871 " --> pdb=" O GLY B1023 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLN B1025 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET B 873 " --> pdb=" O GLN B1025 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE B1119 " --> pdb=" O ILE B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 897 through 898 removed outlier: 4.942A pdb=" N GLU B 903 " --> pdb=" O THR B 949 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 949 " --> pdb=" O GLU B 903 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN B 915 " --> pdb=" O ASP B 968 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 942 through 944 removed outlier: 7.414A pdb=" N THR B 971 " --> pdb=" O ILE B 943 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1192 through 1196 Processing sheet with id=AD9, first strand: chain 'B' and resid 1204 through 1206 Processing sheet with id=AE1, first strand: chain 'C' and resid 8 through 15 removed outlier: 5.838A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 18 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ARG C 228 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR C 186 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.986A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 63 removed outlier: 4.048A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE6, first strand: chain 'G' and resid 84 through 92 removed outlier: 3.730A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 128 through 129 Processing sheet with id=AE8, first strand: chain 'I' and resid 24 through 29 Processing sheet with id=AE9, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AF2, first strand: chain 'M' and resid 57 through 58 removed outlier: 6.471A pdb=" N ARG O 17 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 112 through 117 removed outlier: 6.965A pdb=" N CYS M 99 " --> pdb=" O LEU M 115 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE M 117 " --> pdb=" O PHE M 97 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE M 97 " --> pdb=" O PHE M 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE O 33 " --> pdb=" O ASP M 98 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE O 30 " --> pdb=" O SER O 104 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ILE O 106 " --> pdb=" O PHE O 30 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR O 32 " --> pdb=" O ILE O 106 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL O 108 " --> pdb=" O THR O 32 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG O 34 " --> pdb=" O VAL O 108 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LYS O 110 " --> pdb=" O ARG O 34 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP O 36 " --> pdb=" O LYS O 110 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL O 74 " --> pdb=" O THR O 111 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 253 through 254 removed outlier: 3.542A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL Z 215 " --> pdb=" O ALA Y 62 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA Z 217 " --> pdb=" O ILE Y 60 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE Y 60 " --> pdb=" O ALA Z 217 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 267 through 268 removed outlier: 3.500A pdb=" N LYS Z 268 " --> pdb=" O ILE Y 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'Z' and resid 452 through 454 Processing sheet with id=AF7, first strand: chain 'Z' and resid 510 through 513 removed outlier: 7.180A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.175A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 586 through 587 removed outlier: 3.519A pdb=" N ALA Z 586 " --> pdb=" O ILE Z 594 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 635 through 639 removed outlier: 7.274A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.691A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 22 through 24 1474 hydrogen bonds defined for protein. 4076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 11.09 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6330 1.32 - 1.44: 10241 1.44 - 1.57: 22126 1.57 - 1.69: 156 1.69 - 1.82: 360 Bond restraints: 39213 Sorted by residual: bond pdb=" C PRO J 64 " pdb=" O PRO J 64 " ideal model delta sigma weight residual 1.234 1.192 0.041 1.14e-02 7.69e+03 1.30e+01 bond pdb=" CG LEU B 480 " pdb=" CD1 LEU B 480 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.85e+00 bond pdb=" N VAL A 538 " pdb=" CA VAL A 538 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.15e-02 7.56e+03 6.00e+00 bond pdb=" C GLN A 539 " pdb=" O GLN A 539 " ideal model delta sigma weight residual 1.241 1.214 0.026 1.08e-02 8.57e+03 5.88e+00 bond pdb=" N LEU J 65 " pdb=" CA LEU J 65 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.21e-02 6.83e+03 5.13e+00 ... (remaining 39208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 52672 2.78 - 5.55: 528 5.55 - 8.33: 85 8.33 - 11.10: 10 11.10 - 13.88: 1 Bond angle restraints: 53296 Sorted by residual: angle pdb=" C AARG Y 104 " pdb=" N GLY Y 105 " pdb=" CA GLY Y 105 " ideal model delta sigma weight residual 121.70 131.22 -9.52 1.80e+00 3.09e-01 2.80e+01 angle pdb=" C CYS I 20 " pdb=" N ASN I 21 " pdb=" CA ASN I 21 " ideal model delta sigma weight residual 122.74 130.25 -7.51 1.44e+00 4.82e-01 2.72e+01 angle pdb=" N GLN A 539 " pdb=" CA GLN A 539 " pdb=" C GLN A 539 " ideal model delta sigma weight residual 108.00 114.86 -6.86 1.48e+00 4.57e-01 2.15e+01 angle pdb=" CB MET Z 451 " pdb=" CG MET Z 451 " pdb=" SD MET Z 451 " ideal model delta sigma weight residual 112.70 126.58 -13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" C GLY A 536 " pdb=" N ILE A 537 " pdb=" CA ILE A 537 " ideal model delta sigma weight residual 121.80 115.75 6.05 1.40e+00 5.10e-01 1.87e+01 ... (remaining 53291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 23074 34.96 - 69.92: 711 69.92 - 104.88: 70 104.88 - 139.84: 0 139.84 - 174.80: 1 Dihedral angle restraints: 23856 sinusoidal: 10497 harmonic: 13359 Sorted by residual: dihedral pdb=" CA ASN G 124 " pdb=" C ASN G 124 " pdb=" N PRO G 125 " pdb=" CA PRO G 125 " ideal model delta harmonic sigma weight residual 180.00 140.82 39.18 0 5.00e+00 4.00e-02 6.14e+01 dihedral pdb=" CA MET G 117 " pdb=" C MET G 117 " pdb=" N GLU G 118 " pdb=" CA GLU G 118 " ideal model delta harmonic sigma weight residual 180.00 -148.92 -31.08 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA ASN G 122 " pdb=" C ASN G 122 " pdb=" N SER G 123 " pdb=" CA SER G 123 " ideal model delta harmonic sigma weight residual 180.00 150.11 29.89 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 23853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 5619 0.102 - 0.204: 342 0.204 - 0.306: 9 0.306 - 0.408: 2 0.408 - 0.510: 3 Chirality restraints: 5975 Sorted by residual: chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.51e+00 chirality pdb=" CB VAL Y 6 " pdb=" CA VAL Y 6 " pdb=" CG1 VAL Y 6 " pdb=" CG2 VAL Y 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CG LEU A 831 " pdb=" CB LEU A 831 " pdb=" CD1 LEU A 831 " pdb=" CD2 LEU A 831 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.31e+00 ... (remaining 5972 not shown) Planarity restraints: 6626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Y 93 " 0.102 5.00e-02 4.00e+02 1.53e-01 3.74e+01 pdb=" N PRO Y 94 " -0.264 5.00e-02 4.00e+02 pdb=" CA PRO Y 94 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO Y 94 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 536 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C GLY A 536 " -0.065 2.00e-02 2.50e+03 pdb=" O GLY A 536 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 537 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 829 " -0.025 2.00e-02 2.50e+03 2.13e-02 9.09e+00 pdb=" CG TYR B 829 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR B 829 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 829 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 829 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 829 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 829 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 829 " -0.002 2.00e-02 2.50e+03 ... (remaining 6623 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 577 2.65 - 3.22: 33004 3.22 - 3.78: 62040 3.78 - 4.34: 88434 4.34 - 4.90: 141885 Nonbonded interactions: 325940 Sorted by model distance: nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.093 2.170 nonbonded pdb=" ND1 HIS O 31 " pdb=" OG SER O 104 " model vdw 2.097 3.120 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 2.106 2.170 nonbonded pdb=" O3' A P 46 " pdb="MG MG A2001 " model vdw 2.107 2.170 nonbonded pdb=" OG SER B 938 " pdb=" OE2 GLU Z 735 " model vdw 2.123 3.040 ... (remaining 325935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.290 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: 0.050 Extract box with map and model: 0.550 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 47.040 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 39249 Z= 0.203 Angle : 0.778 16.526 53347 Z= 0.424 Chirality : 0.051 0.510 5975 Planarity : 0.006 0.153 6626 Dihedral : 16.233 174.796 15216 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.02 % Allowed : 0.47 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.12), residues: 4537 helix: -0.84 (0.12), residues: 1411 sheet: -1.02 (0.18), residues: 770 loop : -0.72 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG I 103 TYR 0.052 0.002 TYR B 829 PHE 0.050 0.002 PHE A 112 TRP 0.021 0.002 TRP B 530 HIS 0.013 0.001 HIS B 464 Details of bonding type rmsd covalent geometry : bond 0.00448 (39213) covalent geometry : angle 0.75778 (53296) hydrogen bonds : bond 0.16820 ( 1518) hydrogen bonds : angle 7.44317 ( 4204) metal coordination : bond 0.01109 ( 36) metal coordination : angle 5.74456 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 652 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.7302 (mtm) cc_final: 0.6809 (mtt) REVERT: A 339 LEU cc_start: 0.9021 (mt) cc_final: 0.8629 (mt) REVERT: A 355 MET cc_start: 0.8098 (mmm) cc_final: 0.7828 (mmp) REVERT: A 524 MET cc_start: 0.8183 (mmp) cc_final: 0.7898 (mmm) REVERT: A 1097 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7845 (tm-30) REVERT: A 1484 MET cc_start: 0.6149 (ptp) cc_final: 0.5583 (ptm) REVERT: B 206 THR cc_start: 0.6202 (p) cc_final: 0.5641 (p) REVERT: B 377 MET cc_start: 0.8334 (mtp) cc_final: 0.7696 (mtp) REVERT: B 653 ILE cc_start: 0.8969 (pt) cc_final: 0.8445 (pt) REVERT: D 174 ASP cc_start: 0.7018 (m-30) cc_final: 0.6730 (t70) REVERT: F 84 GLU cc_start: 0.7478 (mp0) cc_final: 0.6648 (mp0) REVERT: F 98 LYS cc_start: 0.8370 (mttt) cc_final: 0.8070 (mtpp) REVERT: F 125 ILE cc_start: 0.8828 (mm) cc_final: 0.8571 (mp) REVERT: H 9 ILE cc_start: 0.8962 (mm) cc_final: 0.8736 (pt) REVERT: H 37 MET cc_start: 0.7955 (mmt) cc_final: 0.7302 (mmt) REVERT: I 68 ILE cc_start: 0.8820 (mt) cc_final: 0.8095 (mt) REVERT: I 98 GLN cc_start: 0.7955 (mt0) cc_final: 0.7744 (mt0) REVERT: I 110 LEU cc_start: 0.8846 (mt) cc_final: 0.8477 (mt) REVERT: J 58 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8741 (mmtt) REVERT: K 25 THR cc_start: 0.7963 (p) cc_final: 0.7561 (t) REVERT: L 15 MET cc_start: 0.6769 (tpp) cc_final: 0.6354 (tpp) REVERT: M 80 ASN cc_start: 0.6131 (m-40) cc_final: 0.5847 (m-40) REVERT: M 133 MET cc_start: 0.7459 (ppp) cc_final: 0.5814 (ppp) REVERT: O 16 LEU cc_start: 0.5258 (tt) cc_final: 0.4703 (tt) REVERT: Z 254 MET cc_start: 0.5229 (tpt) cc_final: 0.5014 (tpt) REVERT: Z 460 MET cc_start: 0.4667 (tmm) cc_final: 0.4247 (tpp) REVERT: Z 474 MET cc_start: -0.1960 (mmp) cc_final: -0.2332 (mmp) REVERT: Z 481 ILE cc_start: 0.5446 (mt) cc_final: 0.5096 (mt) outliers start: 1 outliers final: 1 residues processed: 652 average time/residue: 0.2654 time to fit residues: 269.4047 Evaluate side-chains 328 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN A 671 ASN A 735 GLN A1244 ASN ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 GLN B 188 ASN B 537 HIS B1045 ASN B1171 GLN C 5 ASN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN D 90 ASN D 131 GLN D 171 GLN I 22 ASN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN K 89 ASN M 140 GLN O 14 HIS Z 232 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.045626 restraints weight = 218243.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.047531 restraints weight = 97135.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.048751 restraints weight = 58037.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.049536 restraints weight = 41943.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.049945 restraints weight = 34259.378| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 39249 Z= 0.186 Angle : 0.621 15.734 53347 Z= 0.318 Chirality : 0.045 0.236 5975 Planarity : 0.005 0.098 6626 Dihedral : 12.673 173.400 5942 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.12 % Allowed : 3.47 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.12), residues: 4537 helix: 0.24 (0.14), residues: 1439 sheet: -0.80 (0.18), residues: 783 loop : -0.43 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 134 TYR 0.033 0.001 TYR B 465 PHE 0.035 0.001 PHE A 458 TRP 0.021 0.002 TRP B 583 HIS 0.007 0.001 HIS G 111 Details of bonding type rmsd covalent geometry : bond 0.00417 (39213) covalent geometry : angle 0.60099 (53296) hydrogen bonds : bond 0.04347 ( 1518) hydrogen bonds : angle 5.45999 ( 4204) metal coordination : bond 0.00975 ( 36) metal coordination : angle 5.10510 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 412 time to evaluate : 1.456 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 19 LYS cc_start: 0.9055 (mmpt) cc_final: 0.8810 (mmmt) REVERT: A 58 MET cc_start: 0.8851 (ttm) cc_final: 0.8486 (tpp) REVERT: A 238 MET cc_start: 0.9104 (mtm) cc_final: 0.8408 (mpp) REVERT: A 565 MET cc_start: 0.8981 (mmm) cc_final: 0.8226 (mmm) REVERT: A 652 LEU cc_start: 0.9577 (tp) cc_final: 0.9307 (tt) REVERT: A 1097 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7985 (tm-30) REVERT: A 1262 MET cc_start: 0.7268 (tpt) cc_final: 0.7054 (tpt) REVERT: A 1344 MET cc_start: 0.7655 (tpt) cc_final: 0.7453 (tpt) REVERT: A 1447 GLU cc_start: 0.7393 (mp0) cc_final: 0.7140 (mp0) REVERT: A 1484 MET cc_start: 0.6820 (ptp) cc_final: 0.6236 (ptm) REVERT: B 606 MET cc_start: 0.9176 (mmm) cc_final: 0.8639 (mpp) REVERT: B 627 MET cc_start: 0.8923 (tmm) cc_final: 0.8455 (tmm) REVERT: D 87 LYS cc_start: 0.9267 (tttt) cc_final: 0.9045 (ttmt) REVERT: D 137 PHE cc_start: 0.3866 (t80) cc_final: 0.3390 (t80) REVERT: D 174 ASP cc_start: 0.8889 (m-30) cc_final: 0.8315 (t70) REVERT: E 167 GLU cc_start: 0.8451 (tp30) cc_final: 0.8177 (mm-30) REVERT: F 97 LEU cc_start: 0.9471 (tp) cc_final: 0.9269 (tt) REVERT: F 98 LYS cc_start: 0.9170 (mttt) cc_final: 0.8858 (mtpp) REVERT: G 33 GLU cc_start: 0.8395 (mp0) cc_final: 0.7779 (mp0) REVERT: G 42 TYR cc_start: 0.8476 (m-80) cc_final: 0.8267 (m-10) REVERT: G 71 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8410 (ttpp) REVERT: I 46 GLN cc_start: 0.7052 (pp30) cc_final: 0.6456 (pp30) REVERT: I 68 ILE cc_start: 0.9090 (mt) cc_final: 0.8249 (mt) REVERT: I 98 GLN cc_start: 0.6954 (tt0) cc_final: 0.6250 (mt0) REVERT: I 108 MET cc_start: 0.8603 (mmt) cc_final: 0.7194 (mmp) REVERT: I 110 LEU cc_start: 0.9078 (mt) cc_final: 0.8797 (mt) REVERT: J 31 GLU cc_start: 0.8102 (pm20) cc_final: 0.7860 (pm20) REVERT: K 25 THR cc_start: 0.8630 (p) cc_final: 0.8269 (t) REVERT: K 93 ASP cc_start: 0.8340 (m-30) cc_final: 0.8067 (m-30) REVERT: L 52 LEU cc_start: 0.9592 (tt) cc_final: 0.9356 (tt) REVERT: M 80 ASN cc_start: 0.8873 (m-40) cc_final: 0.8246 (t0) REVERT: M 91 ASP cc_start: 0.7590 (t0) cc_final: 0.7377 (t0) REVERT: M 119 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8712 (pm20) REVERT: M 120 ASP cc_start: 0.7967 (p0) cc_final: 0.7753 (p0) REVERT: M 133 MET cc_start: 0.6951 (ppp) cc_final: 0.5538 (ppp) REVERT: M 138 MET cc_start: 0.5422 (mmt) cc_final: 0.4601 (ttm) REVERT: O 36 ASP cc_start: 0.8491 (p0) cc_final: 0.7895 (p0) REVERT: O 72 MET cc_start: 0.8201 (tpp) cc_final: 0.7848 (tpp) REVERT: Z 226 TYR cc_start: 0.8951 (m-10) cc_final: 0.8510 (m-10) REVERT: Z 460 MET cc_start: 0.4613 (tmm) cc_final: 0.4237 (tpp) REVERT: Z 635 MET cc_start: 0.6556 (tpt) cc_final: 0.5813 (tpp) REVERT: Y 48 MET cc_start: 0.4412 (tmm) cc_final: 0.4202 (tmm) REVERT: Y 64 MET cc_start: 0.4867 (pmm) cc_final: 0.4413 (pmm) outliers start: 5 outliers final: 0 residues processed: 417 average time/residue: 0.2471 time to fit residues: 166.3715 Evaluate side-chains 301 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 118 optimal weight: 6.9990 chunk 282 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 412 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 280 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 204 HIS A 377 GLN A 982 ASN A1332 GLN A1384 HIS B 188 ASN B 537 HIS B1171 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN D 85 HIS D 90 ASN D 171 GLN E 210 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 GLN O 92 HIS Y 45 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.072116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.046317 restraints weight = 214416.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.048135 restraints weight = 99756.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.049307 restraints weight = 60850.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.050060 restraints weight = 44279.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.050454 restraints weight = 36423.813| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39249 Z= 0.134 Angle : 0.558 14.057 53347 Z= 0.288 Chirality : 0.043 0.192 5975 Planarity : 0.004 0.093 6626 Dihedral : 12.566 174.504 5942 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.12), residues: 4537 helix: 0.69 (0.14), residues: 1437 sheet: -0.61 (0.18), residues: 759 loop : -0.29 (0.13), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 928 TYR 0.020 0.001 TYR B1125 PHE 0.030 0.001 PHE A 458 TRP 0.015 0.001 TRP B 530 HIS 0.010 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00292 (39213) covalent geometry : angle 0.54264 (53296) hydrogen bonds : bond 0.03648 ( 1518) hydrogen bonds : angle 5.07038 ( 4204) metal coordination : bond 0.00730 ( 36) metal coordination : angle 4.29715 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 408 time to evaluate : 1.565 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: A 18 ILE cc_start: 0.9058 (mm) cc_final: 0.8787 (mm) REVERT: A 19 LYS cc_start: 0.9047 (mmpt) cc_final: 0.8757 (mmmt) REVERT: A 58 MET cc_start: 0.8756 (ttm) cc_final: 0.8338 (tpp) REVERT: A 652 LEU cc_start: 0.9539 (tp) cc_final: 0.9301 (tt) REVERT: A 1097 GLU cc_start: 0.8573 (tm-30) cc_final: 0.7917 (tm-30) REVERT: A 1447 GLU cc_start: 0.7502 (mp0) cc_final: 0.7207 (mp0) REVERT: A 1484 MET cc_start: 0.6767 (ptp) cc_final: 0.6129 (ptm) REVERT: B 627 MET cc_start: 0.8821 (tmm) cc_final: 0.8420 (tmm) REVERT: B 754 MET cc_start: 0.8956 (tpp) cc_final: 0.8730 (tpp) REVERT: B 868 GLU cc_start: 0.7487 (tp30) cc_final: 0.6635 (tp30) REVERT: B 985 MET cc_start: 0.8601 (tmm) cc_final: 0.8307 (tmm) REVERT: D 104 MET cc_start: 0.8469 (mmp) cc_final: 0.7588 (mmm) REVERT: D 137 PHE cc_start: 0.3570 (t80) cc_final: 0.2642 (t80) REVERT: D 174 ASP cc_start: 0.8882 (m-30) cc_final: 0.8377 (t70) REVERT: F 83 LEU cc_start: 0.8974 (pp) cc_final: 0.8749 (pp) REVERT: F 97 LEU cc_start: 0.9411 (tp) cc_final: 0.9185 (tt) REVERT: F 98 LYS cc_start: 0.9081 (mttt) cc_final: 0.8762 (mtpp) REVERT: F 116 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8048 (mt-10) REVERT: G 71 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8464 (ttpp) REVERT: H 37 MET cc_start: 0.8299 (mmm) cc_final: 0.7897 (mmt) REVERT: H 92 MET cc_start: 0.8708 (mtm) cc_final: 0.8488 (mtp) REVERT: I 21 ASN cc_start: 0.8612 (t0) cc_final: 0.8352 (m-40) REVERT: I 46 GLN cc_start: 0.6899 (pp30) cc_final: 0.6479 (pp30) REVERT: I 57 LYS cc_start: 0.7988 (mmtt) cc_final: 0.7701 (mmtp) REVERT: I 64 GLU cc_start: 0.7428 (tp30) cc_final: 0.7073 (tp30) REVERT: I 98 GLN cc_start: 0.6757 (tt0) cc_final: 0.6200 (mt0) REVERT: I 108 MET cc_start: 0.8454 (mmt) cc_final: 0.7120 (mmm) REVERT: I 110 LEU cc_start: 0.9027 (mt) cc_final: 0.8757 (mt) REVERT: J 31 GLU cc_start: 0.8068 (pm20) cc_final: 0.7665 (pm20) REVERT: K 25 THR cc_start: 0.8525 (p) cc_final: 0.8149 (t) REVERT: K 93 ASP cc_start: 0.8181 (m-30) cc_final: 0.7972 (m-30) REVERT: L 44 MET cc_start: 0.7890 (mtm) cc_final: 0.7656 (mtt) REVERT: M 48 HIS cc_start: 0.8193 (m-70) cc_final: 0.7960 (m-70) REVERT: M 80 ASN cc_start: 0.8706 (m-40) cc_final: 0.8176 (t0) REVERT: M 91 ASP cc_start: 0.7421 (t0) cc_final: 0.7189 (t0) REVERT: M 133 MET cc_start: 0.7119 (ppp) cc_final: 0.6510 (tmm) REVERT: M 138 MET cc_start: 0.5398 (mmt) cc_final: 0.4740 (ttt) REVERT: O 36 ASP cc_start: 0.8141 (p0) cc_final: 0.7795 (p0) REVERT: O 84 LYS cc_start: 0.7644 (mmmt) cc_final: 0.6922 (mmmt) REVERT: Z 226 TYR cc_start: 0.8925 (m-10) cc_final: 0.8488 (m-10) REVERT: Z 451 MET cc_start: 0.6064 (mmm) cc_final: 0.5828 (mmm) REVERT: Z 460 MET cc_start: 0.4777 (tmm) cc_final: 0.4140 (tpp) REVERT: Z 635 MET cc_start: 0.6662 (tpt) cc_final: 0.5919 (tpp) REVERT: Y 48 MET cc_start: 0.4107 (tmm) cc_final: 0.3816 (tmm) REVERT: Y 64 MET cc_start: 0.5161 (pmm) cc_final: 0.4708 (pmm) outliers start: 3 outliers final: 0 residues processed: 410 average time/residue: 0.2455 time to fit residues: 161.8820 Evaluate side-chains 293 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 111 optimal weight: 7.9990 chunk 436 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 378 optimal weight: 0.9980 chunk 448 optimal weight: 50.0000 chunk 252 optimal weight: 20.0000 chunk 236 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 222 HIS B 188 ASN B 537 HIS B 602 ASN B 894 GLN ** B1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN D 171 GLN E 107 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN M 82 ASN ** Y 45 ASN ** 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 = 0.3343 r_free = 0.3343 target = 0.070693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.045556 restraints weight = 222149.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.047801 restraints weight = 112361.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.048032 restraints weight = 61701.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.048483 restraints weight = 48365.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.048624 restraints weight = 43774.674| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39249 Z= 0.193 Angle : 0.582 13.105 53347 Z= 0.297 Chirality : 0.044 0.209 5975 Planarity : 0.004 0.086 6626 Dihedral : 12.529 176.685 5942 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.13), residues: 4537 helix: 0.93 (0.14), residues: 1437 sheet: -0.60 (0.18), residues: 759 loop : -0.20 (0.13), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 928 TYR 0.023 0.001 TYR D 109 PHE 0.030 0.001 PHE A 458 TRP 0.019 0.002 TRP B 104 HIS 0.015 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00435 (39213) covalent geometry : angle 0.56654 (53296) hydrogen bonds : bond 0.03603 ( 1518) hydrogen bonds : angle 4.96270 ( 4204) metal coordination : bond 0.01014 ( 36) metal coordination : angle 4.35899 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 355 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9123 (mm) cc_final: 0.8883 (mm) REVERT: A 19 LYS cc_start: 0.9100 (mmpt) cc_final: 0.8788 (mmmt) REVERT: A 58 MET cc_start: 0.8906 (ttm) cc_final: 0.8639 (ttm) REVERT: A 565 MET cc_start: 0.8780 (tpp) cc_final: 0.8181 (tpp) REVERT: A 1097 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8036 (tm-30) REVERT: A 1447 GLU cc_start: 0.7524 (mp0) cc_final: 0.7207 (mp0) REVERT: A 1484 MET cc_start: 0.6820 (ptp) cc_final: 0.6023 (ptm) REVERT: B 606 MET cc_start: 0.9182 (mmm) cc_final: 0.8654 (mpp) REVERT: B 627 MET cc_start: 0.8746 (tmm) cc_final: 0.8430 (tmm) REVERT: B 985 MET cc_start: 0.8562 (tmm) cc_final: 0.8254 (tmm) REVERT: D 104 MET cc_start: 0.8496 (mmp) cc_final: 0.8222 (mmm) REVERT: D 109 TYR cc_start: 0.6961 (t80) cc_final: 0.6594 (t80) REVERT: D 137 PHE cc_start: 0.3639 (t80) cc_final: 0.3214 (t80) REVERT: D 174 ASP cc_start: 0.8920 (m-30) cc_final: 0.8487 (t70) REVERT: F 98 LYS cc_start: 0.9076 (mttt) cc_final: 0.8824 (mtpp) REVERT: G 42 TYR cc_start: 0.8408 (m-80) cc_final: 0.8099 (m-80) REVERT: G 71 LYS cc_start: 0.9066 (ttpt) cc_final: 0.8398 (ttpp) REVERT: I 46 GLN cc_start: 0.7172 (pp30) cc_final: 0.6650 (pp30) REVERT: I 57 LYS cc_start: 0.7774 (mmtt) cc_final: 0.7533 (mmtt) REVERT: I 108 MET cc_start: 0.8119 (mmt) cc_final: 0.7026 (mmp) REVERT: J 31 GLU cc_start: 0.7969 (pm20) cc_final: 0.7723 (pm20) REVERT: K 25 THR cc_start: 0.8603 (p) cc_final: 0.8244 (t) REVERT: L 44 MET cc_start: 0.7851 (mtm) cc_final: 0.7552 (mtt) REVERT: M 54 PHE cc_start: 0.7187 (m-80) cc_final: 0.6921 (m-10) REVERT: M 80 ASN cc_start: 0.8937 (m-40) cc_final: 0.8486 (t0) REVERT: M 91 ASP cc_start: 0.7764 (t0) cc_final: 0.7496 (t0) REVERT: M 121 LYS cc_start: 0.8355 (tptt) cc_final: 0.7902 (tptt) REVERT: M 133 MET cc_start: 0.7159 (ppp) cc_final: 0.6755 (tmm) REVERT: M 138 MET cc_start: 0.5614 (mmt) cc_final: 0.4803 (ttt) REVERT: O 85 ASP cc_start: 0.6002 (m-30) cc_final: 0.5031 (m-30) REVERT: Z 226 TYR cc_start: 0.9120 (m-10) cc_final: 0.8592 (m-10) REVERT: Z 451 MET cc_start: 0.6760 (mmp) cc_final: 0.6500 (mmm) REVERT: Z 460 MET cc_start: 0.4875 (tmm) cc_final: 0.3716 (tpp) REVERT: Z 635 MET cc_start: 0.6775 (tpt) cc_final: 0.6108 (tpp) REVERT: Y 48 MET cc_start: 0.4141 (tmm) cc_final: 0.3766 (tmm) REVERT: Y 61 ILE cc_start: 0.7401 (mm) cc_final: 0.7169 (mp) REVERT: Y 64 MET cc_start: 0.5171 (pmm) cc_final: 0.4838 (pmm) outliers start: 2 outliers final: 0 residues processed: 355 average time/residue: 0.2395 time to fit residues: 138.9091 Evaluate side-chains 280 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 245 optimal weight: 0.4980 chunk 428 optimal weight: 50.0000 chunk 252 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 163 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 393 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN D 90 ASN D 171 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN M 140 GLN O 107 GLN ** Y 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.070233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.045373 restraints weight = 245433.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.047287 restraints weight = 116073.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.047607 restraints weight = 63000.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.047887 restraints weight = 52853.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.047960 restraints weight = 49825.097| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39249 Z= 0.180 Angle : 0.562 11.885 53347 Z= 0.288 Chirality : 0.044 0.260 5975 Planarity : 0.004 0.095 6626 Dihedral : 12.528 179.223 5942 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.05 % Allowed : 1.82 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 4537 helix: 1.00 (0.14), residues: 1448 sheet: -0.50 (0.18), residues: 760 loop : -0.16 (0.13), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 928 TYR 0.039 0.001 TYR B1125 PHE 0.030 0.001 PHE A 458 TRP 0.018 0.001 TRP B 104 HIS 0.006 0.001 HIS Y 12 Details of bonding type rmsd covalent geometry : bond 0.00405 (39213) covalent geometry : angle 0.54626 (53296) hydrogen bonds : bond 0.03427 ( 1518) hydrogen bonds : angle 4.84913 ( 4204) metal coordination : bond 0.00911 ( 36) metal coordination : angle 4.24492 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 351 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.9149 (mmpt) cc_final: 0.8803 (mmmt) REVERT: A 58 MET cc_start: 0.9015 (ttm) cc_final: 0.8712 (ttm) REVERT: A 306 ASP cc_start: 0.8647 (t70) cc_final: 0.8422 (m-30) REVERT: A 565 MET cc_start: 0.8887 (tpp) cc_final: 0.8151 (tpp) REVERT: A 1097 GLU cc_start: 0.8547 (tm-30) cc_final: 0.7929 (tm-30) REVERT: A 1296 MET cc_start: 0.7710 (tmm) cc_final: 0.7463 (tmm) REVERT: A 1447 GLU cc_start: 0.7521 (mp0) cc_final: 0.7198 (mp0) REVERT: A 1484 MET cc_start: 0.6858 (ptp) cc_final: 0.6145 (ptm) REVERT: B 606 MET cc_start: 0.9212 (mmm) cc_final: 0.8672 (mpp) REVERT: B 627 MET cc_start: 0.8749 (tmm) cc_final: 0.8517 (tmm) REVERT: B 985 MET cc_start: 0.8618 (tmm) cc_final: 0.8249 (tmm) REVERT: D 109 TYR cc_start: 0.7009 (t80) cc_final: 0.6656 (t80) REVERT: D 137 PHE cc_start: 0.3822 (t80) cc_final: 0.3475 (t80) REVERT: D 174 ASP cc_start: 0.8824 (m-30) cc_final: 0.8472 (t70) REVERT: F 98 LYS cc_start: 0.9178 (mttt) cc_final: 0.8864 (mtpp) REVERT: G 33 GLU cc_start: 0.8901 (mp0) cc_final: 0.8268 (mp0) REVERT: G 71 LYS cc_start: 0.9075 (ttpt) cc_final: 0.8565 (ttpp) REVERT: I 46 GLN cc_start: 0.7135 (pp30) cc_final: 0.6884 (pp30) REVERT: I 57 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7544 (mttt) REVERT: I 108 MET cc_start: 0.8438 (mmt) cc_final: 0.7520 (mmp) REVERT: J 31 GLU cc_start: 0.8017 (pm20) cc_final: 0.7777 (pm20) REVERT: K 25 THR cc_start: 0.8606 (p) cc_final: 0.8266 (t) REVERT: L 44 MET cc_start: 0.7881 (mtm) cc_final: 0.7600 (mtt) REVERT: M 33 LYS cc_start: 0.8838 (tppt) cc_final: 0.8483 (tptt) REVERT: M 80 ASN cc_start: 0.8878 (m-40) cc_final: 0.8521 (t0) REVERT: M 121 LYS cc_start: 0.8583 (tttp) cc_final: 0.8159 (tptm) REVERT: M 133 MET cc_start: 0.6889 (ppp) cc_final: 0.6611 (tmm) REVERT: M 138 MET cc_start: 0.5581 (mmt) cc_final: 0.4895 (ttt) REVERT: O 72 MET cc_start: 0.8253 (tpp) cc_final: 0.7387 (pmm) REVERT: O 85 ASP cc_start: 0.5275 (m-30) cc_final: 0.4511 (m-30) REVERT: O 107 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: Z 226 TYR cc_start: 0.9151 (m-10) cc_final: 0.8547 (m-10) REVERT: Z 451 MET cc_start: 0.6736 (mmp) cc_final: 0.6501 (mmm) REVERT: Z 460 MET cc_start: 0.4748 (tmm) cc_final: 0.3656 (tpp) REVERT: Z 635 MET cc_start: 0.6954 (tpt) cc_final: 0.6184 (tpp) REVERT: Y 48 MET cc_start: 0.4199 (tmm) cc_final: 0.3908 (tmm) REVERT: Y 64 MET cc_start: 0.5584 (pmm) cc_final: 0.5263 (pmm) outliers start: 2 outliers final: 0 residues processed: 351 average time/residue: 0.2486 time to fit residues: 139.2885 Evaluate side-chains 277 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 384 optimal weight: 30.0000 chunk 345 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 205 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 chunk 343 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 HIS B 188 ASN D 90 ASN D 135 HIS D 171 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN M 140 GLN Y 12 HIS ** Y 45 ASN ** 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 = 0.3321 r_free = 0.3321 target = 0.069697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.044123 restraints weight = 243474.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.045977 restraints weight = 120854.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.046781 restraints weight = 77316.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.047531 restraints weight = 51127.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.047697 restraints weight = 43929.903| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39249 Z= 0.191 Angle : 0.575 12.256 53347 Z= 0.292 Chirality : 0.044 0.262 5975 Planarity : 0.004 0.095 6626 Dihedral : 12.547 179.053 5942 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.02 % Allowed : 1.50 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.13), residues: 4537 helix: 1.09 (0.14), residues: 1440 sheet: -0.53 (0.18), residues: 765 loop : -0.13 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 119 TYR 0.024 0.001 TYR B 829 PHE 0.020 0.001 PHE A 458 TRP 0.017 0.001 TRP B 104 HIS 0.006 0.001 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00430 (39213) covalent geometry : angle 0.55871 (53296) hydrogen bonds : bond 0.03449 ( 1518) hydrogen bonds : angle 4.80549 ( 4204) metal coordination : bond 0.00971 ( 36) metal coordination : angle 4.38250 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 1.419 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 19 LYS cc_start: 0.9145 (mmpt) cc_final: 0.8762 (mmmt) REVERT: A 58 MET cc_start: 0.9040 (ttm) cc_final: 0.8417 (tpp) REVERT: A 565 MET cc_start: 0.8870 (tpp) cc_final: 0.8126 (tpp) REVERT: A 1097 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 1228 MET cc_start: 0.8615 (mtp) cc_final: 0.8364 (mtp) REVERT: A 1296 MET cc_start: 0.7702 (tmm) cc_final: 0.7408 (tmm) REVERT: A 1447 GLU cc_start: 0.7482 (mp0) cc_final: 0.7147 (mp0) REVERT: A 1484 MET cc_start: 0.6785 (ptp) cc_final: 0.6028 (ptm) REVERT: B 627 MET cc_start: 0.8716 (tmm) cc_final: 0.8514 (tmm) REVERT: B 754 MET cc_start: 0.8883 (tpp) cc_final: 0.8294 (mpp) REVERT: B 985 MET cc_start: 0.8604 (tmm) cc_final: 0.8256 (tmm) REVERT: B 1243 SER cc_start: 0.9348 (m) cc_final: 0.9048 (p) REVERT: D 104 MET cc_start: 0.8465 (mmp) cc_final: 0.7880 (mmm) REVERT: D 109 TYR cc_start: 0.7147 (t80) cc_final: 0.6821 (t80) REVERT: D 137 PHE cc_start: 0.3896 (t80) cc_final: 0.3543 (t80) REVERT: D 174 ASP cc_start: 0.8850 (m-30) cc_final: 0.8523 (t70) REVERT: F 98 LYS cc_start: 0.9182 (mttt) cc_final: 0.8882 (mtpp) REVERT: G 71 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8286 (ttpp) REVERT: I 46 GLN cc_start: 0.7220 (pp30) cc_final: 0.6912 (pp30) REVERT: I 57 LYS cc_start: 0.7785 (mmtt) cc_final: 0.7489 (mttt) REVERT: I 98 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7344 (mm-40) REVERT: I 108 MET cc_start: 0.8398 (mmt) cc_final: 0.7662 (mmm) REVERT: J 31 GLU cc_start: 0.8009 (pm20) cc_final: 0.7790 (pm20) REVERT: L 27 GLU cc_start: 0.7967 (tp30) cc_final: 0.7676 (tm-30) REVERT: L 44 MET cc_start: 0.7940 (mtm) cc_final: 0.7700 (mtt) REVERT: M 80 ASN cc_start: 0.8880 (m-40) cc_final: 0.8513 (t0) REVERT: M 98 ASP cc_start: 0.7866 (m-30) cc_final: 0.7385 (m-30) REVERT: M 121 LYS cc_start: 0.8454 (tttp) cc_final: 0.8062 (tptt) REVERT: M 138 MET cc_start: 0.5767 (mmt) cc_final: 0.5138 (ttt) REVERT: O 36 ASP cc_start: 0.8474 (p0) cc_final: 0.7913 (p0) REVERT: O 84 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7859 (mmmt) REVERT: O 109 LYS cc_start: 0.8404 (mtpp) cc_final: 0.8117 (mtpp) REVERT: Z 226 TYR cc_start: 0.9136 (m-10) cc_final: 0.8535 (m-10) REVERT: Z 451 MET cc_start: 0.6806 (mmp) cc_final: 0.6588 (mmm) REVERT: Z 460 MET cc_start: 0.4745 (tmm) cc_final: 0.3724 (tpp) REVERT: Z 635 MET cc_start: 0.6886 (tpt) cc_final: 0.5504 (tmm) REVERT: Y 48 MET cc_start: 0.4444 (tmm) cc_final: 0.3923 (tmm) REVERT: Y 64 MET cc_start: 0.6002 (pmm) cc_final: 0.5717 (pmm) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.2489 time to fit residues: 135.0031 Evaluate side-chains 273 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 73 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 313 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 232 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 171 optimal weight: 0.6980 chunk 447 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 432 optimal weight: 40.0000 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 HIS B 188 ASN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN D 171 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 GLN ** Y 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.070435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.045432 restraints weight = 226179.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.047634 restraints weight = 115067.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.048156 restraints weight = 64622.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.048427 restraints weight = 46105.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.048647 restraints weight = 44279.614| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39249 Z= 0.129 Angle : 0.544 10.887 53347 Z= 0.278 Chirality : 0.043 0.223 5975 Planarity : 0.004 0.096 6626 Dihedral : 12.507 178.231 5942 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.02 % Allowed : 1.08 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.13), residues: 4537 helix: 1.13 (0.14), residues: 1441 sheet: -0.47 (0.18), residues: 768 loop : -0.10 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Y 14 TYR 0.025 0.001 TYR B1125 PHE 0.025 0.001 PHE B 882 TRP 0.013 0.001 TRP B 104 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd covalent geometry : bond 0.00293 (39213) covalent geometry : angle 0.53008 (53296) hydrogen bonds : bond 0.03216 ( 1518) hydrogen bonds : angle 4.70355 ( 4204) metal coordination : bond 0.00773 ( 36) metal coordination : angle 4.03283 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 347 time to evaluate : 1.432 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 19 LYS cc_start: 0.9160 (mmpt) cc_final: 0.8803 (mmmt) REVERT: A 58 MET cc_start: 0.9044 (ttm) cc_final: 0.8427 (tpp) REVERT: A 92 LYS cc_start: 0.9402 (mmpt) cc_final: 0.9201 (mmmt) REVERT: A 565 MET cc_start: 0.8892 (tpp) cc_final: 0.8124 (tpp) REVERT: A 1097 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 1228 MET cc_start: 0.8734 (mtp) cc_final: 0.8482 (mtp) REVERT: A 1296 MET cc_start: 0.7702 (tmm) cc_final: 0.7421 (tmm) REVERT: A 1447 GLU cc_start: 0.7512 (mp0) cc_final: 0.7128 (mp0) REVERT: A 1484 MET cc_start: 0.6784 (ptp) cc_final: 0.5999 (ptm) REVERT: B 1243 SER cc_start: 0.9304 (m) cc_final: 0.8996 (p) REVERT: D 73 THR cc_start: 0.8006 (m) cc_final: 0.7131 (p) REVERT: D 104 MET cc_start: 0.8520 (mmp) cc_final: 0.7938 (mmm) REVERT: D 109 TYR cc_start: 0.6942 (t80) cc_final: 0.6576 (t80) REVERT: D 137 PHE cc_start: 0.4003 (t80) cc_final: 0.3543 (t80) REVERT: E 18 MET cc_start: 0.8608 (tpp) cc_final: 0.8354 (tpp) REVERT: E 94 MET cc_start: 0.8216 (mmm) cc_final: 0.7935 (mmm) REVERT: F 98 LYS cc_start: 0.9191 (mttt) cc_final: 0.8873 (mtpp) REVERT: G 33 GLU cc_start: 0.8916 (mp0) cc_final: 0.8362 (mp0) REVERT: G 71 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8389 (ttpp) REVERT: H 87 GLN cc_start: 0.9092 (mp10) cc_final: 0.8782 (mp10) REVERT: I 46 GLN cc_start: 0.7070 (pp30) cc_final: 0.6789 (pp30) REVERT: I 57 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7509 (mttt) REVERT: J 31 GLU cc_start: 0.8107 (pm20) cc_final: 0.7767 (pm20) REVERT: L 27 GLU cc_start: 0.7915 (tp30) cc_final: 0.7594 (tm-30) REVERT: L 44 MET cc_start: 0.7897 (mtm) cc_final: 0.7679 (mtt) REVERT: M 33 LYS cc_start: 0.8708 (tppt) cc_final: 0.8404 (tptt) REVERT: M 98 ASP cc_start: 0.7918 (m-30) cc_final: 0.7409 (m-30) REVERT: M 121 LYS cc_start: 0.8460 (tttp) cc_final: 0.8125 (tptt) REVERT: M 138 MET cc_start: 0.5723 (mmt) cc_final: 0.5089 (ttt) REVERT: O 36 ASP cc_start: 0.8511 (p0) cc_final: 0.7817 (p0) REVERT: O 72 MET cc_start: 0.8284 (tpp) cc_final: 0.7349 (pmm) REVERT: O 84 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7435 (mmmt) REVERT: O 109 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8139 (mtpp) REVERT: Z 226 TYR cc_start: 0.9092 (m-10) cc_final: 0.8507 (m-10) REVERT: Z 460 MET cc_start: 0.4744 (tmm) cc_final: 0.3806 (tpp) REVERT: Z 635 MET cc_start: 0.6947 (tpt) cc_final: 0.5925 (tmm) REVERT: Y 64 MET cc_start: 0.6021 (pmm) cc_final: 0.5655 (pmm) outliers start: 1 outliers final: 0 residues processed: 347 average time/residue: 0.2503 time to fit residues: 139.1080 Evaluate side-chains 275 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 199 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 356 optimal weight: 1.9990 chunk 396 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 297 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 258 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 HIS A1032 GLN A1194 ASN B 188 ASN D 90 ASN D 171 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 GLN O 107 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.068835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.043978 restraints weight = 209787.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.046021 restraints weight = 109457.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.046531 restraints weight = 65229.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.046934 restraints weight = 48608.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.047037 restraints weight = 45163.469| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 39249 Z= 0.257 Angle : 0.620 14.837 53347 Z= 0.313 Chirality : 0.045 0.197 5975 Planarity : 0.004 0.099 6626 Dihedral : 12.517 176.895 5942 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.05 % Allowed : 0.89 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.13), residues: 4537 helix: 1.08 (0.14), residues: 1444 sheet: -0.51 (0.18), residues: 775 loop : -0.19 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 928 TYR 0.027 0.002 TYR B 829 PHE 0.036 0.002 PHE B 499 TRP 0.020 0.002 TRP B 104 HIS 0.006 0.001 HIS I 100 Details of bonding type rmsd covalent geometry : bond 0.00577 (39213) covalent geometry : angle 0.60213 (53296) hydrogen bonds : bond 0.03652 ( 1518) hydrogen bonds : angle 4.83174 ( 4204) metal coordination : bond 0.01302 ( 36) metal coordination : angle 4.79619 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 316 time to evaluate : 1.456 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 19 LYS cc_start: 0.9189 (mmpt) cc_final: 0.8789 (mmmt) REVERT: A 58 MET cc_start: 0.9073 (ttm) cc_final: 0.8467 (tpp) REVERT: A 78 MET cc_start: 0.8940 (ttt) cc_final: 0.8630 (tpp) REVERT: A 92 LYS cc_start: 0.9425 (mmpt) cc_final: 0.9169 (mmmt) REVERT: A 524 MET cc_start: 0.8151 (mmm) cc_final: 0.7926 (mmm) REVERT: A 1228 MET cc_start: 0.8808 (mtp) cc_final: 0.8594 (mtp) REVERT: A 1296 MET cc_start: 0.7890 (tmm) cc_final: 0.7570 (tmm) REVERT: A 1447 GLU cc_start: 0.7550 (mp0) cc_final: 0.7122 (mp0) REVERT: A 1484 MET cc_start: 0.6907 (ptp) cc_final: 0.6182 (ptm) REVERT: B 232 MET cc_start: 0.8881 (ttm) cc_final: 0.8642 (ttp) REVERT: B 985 MET cc_start: 0.8584 (tmm) cc_final: 0.8227 (tmm) REVERT: B 1243 SER cc_start: 0.9322 (m) cc_final: 0.9097 (p) REVERT: D 73 THR cc_start: 0.8164 (m) cc_final: 0.7420 (p) REVERT: D 104 MET cc_start: 0.8410 (mmp) cc_final: 0.7987 (mmm) REVERT: D 109 TYR cc_start: 0.7284 (t80) cc_final: 0.7012 (t80) REVERT: D 137 PHE cc_start: 0.4040 (t80) cc_final: 0.3630 (t80) REVERT: E 18 MET cc_start: 0.8596 (tpp) cc_final: 0.8280 (tpp) REVERT: F 98 LYS cc_start: 0.9103 (mttt) cc_final: 0.8863 (mtpp) REVERT: G 33 GLU cc_start: 0.8921 (mp0) cc_final: 0.8344 (mp0) REVERT: G 71 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8308 (ttpp) REVERT: I 46 GLN cc_start: 0.7368 (pp30) cc_final: 0.7058 (pp30) REVERT: I 57 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7636 (mttt) REVERT: I 108 MET cc_start: 0.8845 (mmm) cc_final: 0.8490 (mmm) REVERT: J 31 GLU cc_start: 0.8162 (pm20) cc_final: 0.7846 (pm20) REVERT: L 27 GLU cc_start: 0.7888 (tp30) cc_final: 0.7609 (tm-30) REVERT: L 44 MET cc_start: 0.8040 (mtm) cc_final: 0.7839 (mtt) REVERT: M 33 LYS cc_start: 0.8555 (tppt) cc_final: 0.8183 (tptt) REVERT: M 98 ASP cc_start: 0.7969 (m-30) cc_final: 0.7494 (m-30) REVERT: M 121 LYS cc_start: 0.8413 (tttp) cc_final: 0.7840 (tptt) REVERT: M 138 MET cc_start: 0.6001 (mmt) cc_final: 0.5352 (ttt) REVERT: O 36 ASP cc_start: 0.8501 (p0) cc_final: 0.8256 (p0) REVERT: O 72 MET cc_start: 0.8318 (tpp) cc_final: 0.7593 (tpp) REVERT: O 84 LYS cc_start: 0.7967 (mmmt) cc_final: 0.7531 (mmmt) REVERT: O 85 ASP cc_start: 0.5546 (m-30) cc_final: 0.4550 (m-30) REVERT: Z 226 TYR cc_start: 0.9152 (m-10) cc_final: 0.8584 (m-10) REVERT: Z 460 MET cc_start: 0.4678 (tmm) cc_final: 0.3840 (tpp) REVERT: Z 635 MET cc_start: 0.6925 (tpt) cc_final: 0.6049 (tmm) REVERT: Y 64 MET cc_start: 0.6252 (pmm) cc_final: 0.5904 (pmm) outliers start: 2 outliers final: 0 residues processed: 316 average time/residue: 0.2439 time to fit residues: 125.3574 Evaluate side-chains 255 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 207 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 245 optimal weight: 0.5980 chunk 315 optimal weight: 0.9980 chunk 340 optimal weight: 0.7980 chunk 276 optimal weight: 0.7980 chunk 251 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 438 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 595 HIS ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 GLN Z 573 GLN ** Y 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.070464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.045166 restraints weight = 240082.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.047308 restraints weight = 116263.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.048016 restraints weight = 71128.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.048721 restraints weight = 47661.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.048842 restraints weight = 40971.450| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39249 Z= 0.114 Angle : 0.552 12.177 53347 Z= 0.281 Chirality : 0.043 0.202 5975 Planarity : 0.004 0.099 6626 Dihedral : 12.435 176.619 5942 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.05 % Allowed : 0.49 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.13), residues: 4537 helix: 1.22 (0.14), residues: 1436 sheet: -0.35 (0.18), residues: 766 loop : -0.13 (0.13), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 928 TYR 0.023 0.001 TYR B 829 PHE 0.024 0.001 PHE B 386 TRP 0.014 0.001 TRP A1192 HIS 0.004 0.001 HIS K 69 Details of bonding type rmsd covalent geometry : bond 0.00254 (39213) covalent geometry : angle 0.53809 (53296) hydrogen bonds : bond 0.03182 ( 1518) hydrogen bonds : angle 4.62348 ( 4204) metal coordination : bond 0.00661 ( 36) metal coordination : angle 3.97578 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.9155 (mmpt) cc_final: 0.8808 (mmmt) REVERT: A 58 MET cc_start: 0.9020 (ttm) cc_final: 0.8428 (tpp) REVERT: A 92 LYS cc_start: 0.9389 (mmpt) cc_final: 0.9126 (mmmt) REVERT: A 565 MET cc_start: 0.8756 (tpp) cc_final: 0.8048 (tpp) REVERT: A 1097 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 1447 GLU cc_start: 0.7485 (mp0) cc_final: 0.7175 (mp0) REVERT: A 1484 MET cc_start: 0.6999 (ptp) cc_final: 0.6256 (ptm) REVERT: B 1243 SER cc_start: 0.9312 (m) cc_final: 0.9013 (p) REVERT: D 73 THR cc_start: 0.8129 (m) cc_final: 0.7319 (p) REVERT: D 104 MET cc_start: 0.8424 (mmp) cc_final: 0.7970 (mmm) REVERT: D 109 TYR cc_start: 0.7063 (t80) cc_final: 0.6808 (t80) REVERT: D 137 PHE cc_start: 0.4031 (t80) cc_final: 0.3587 (t80) REVERT: E 18 MET cc_start: 0.8574 (tpp) cc_final: 0.8248 (tpp) REVERT: F 98 LYS cc_start: 0.9108 (mttt) cc_final: 0.8805 (mtpp) REVERT: G 33 GLU cc_start: 0.8855 (mp0) cc_final: 0.8248 (mp0) REVERT: G 71 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8275 (ttpp) REVERT: H 37 MET cc_start: 0.8930 (tpp) cc_final: 0.8327 (mmm) REVERT: H 87 GLN cc_start: 0.9046 (mp10) cc_final: 0.8751 (mp10) REVERT: I 46 GLN cc_start: 0.7031 (pp30) cc_final: 0.6751 (pp30) REVERT: I 57 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7434 (mttt) REVERT: I 108 MET cc_start: 0.8839 (mmm) cc_final: 0.7809 (mmm) REVERT: J 31 GLU cc_start: 0.8150 (pm20) cc_final: 0.7801 (pm20) REVERT: L 27 GLU cc_start: 0.7806 (tp30) cc_final: 0.7396 (tm-30) REVERT: L 44 MET cc_start: 0.7917 (mtm) cc_final: 0.7717 (mtt) REVERT: M 31 HIS cc_start: 0.8825 (t-170) cc_final: 0.7934 (t70) REVERT: M 33 LYS cc_start: 0.8569 (tppt) cc_final: 0.8255 (tptt) REVERT: M 98 ASP cc_start: 0.8064 (m-30) cc_final: 0.7686 (m-30) REVERT: M 121 LYS cc_start: 0.8404 (tttp) cc_final: 0.7692 (tptt) REVERT: M 138 MET cc_start: 0.5932 (mmt) cc_final: 0.5307 (ttt) REVERT: O 36 ASP cc_start: 0.8426 (p0) cc_final: 0.7654 (p0) REVERT: O 72 MET cc_start: 0.8198 (tpp) cc_final: 0.7250 (pmm) REVERT: O 84 LYS cc_start: 0.7747 (mmmt) cc_final: 0.7419 (mmmt) REVERT: O 85 ASP cc_start: 0.5291 (m-30) cc_final: 0.4204 (m-30) REVERT: O 109 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7716 (mtpp) REVERT: Z 226 TYR cc_start: 0.9014 (m-10) cc_final: 0.8438 (m-10) REVERT: Z 451 MET cc_start: 0.6755 (mmp) cc_final: 0.6479 (mmm) REVERT: Z 460 MET cc_start: 0.4742 (tmm) cc_final: 0.3626 (tpp) REVERT: Z 635 MET cc_start: 0.6853 (tpt) cc_final: 0.5163 (tmm) REVERT: Y 64 MET cc_start: 0.6296 (pmm) cc_final: 0.5974 (pmm) outliers start: 1 outliers final: 0 residues processed: 329 average time/residue: 0.2319 time to fit residues: 125.0459 Evaluate side-chains 267 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 107 optimal weight: 2.9990 chunk 253 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.3980 chunk 238 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 193 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN D 171 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 GLN ** Y 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.070536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.045772 restraints weight = 210477.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.048005 restraints weight = 107162.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.048342 restraints weight = 59112.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.048599 restraints weight = 47258.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.048790 restraints weight = 44538.408| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39249 Z= 0.119 Angle : 0.555 11.532 53347 Z= 0.282 Chirality : 0.043 0.196 5975 Planarity : 0.004 0.097 6626 Dihedral : 12.344 175.994 5942 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.05 % Allowed : 0.30 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.13), residues: 4537 helix: 1.23 (0.14), residues: 1435 sheet: -0.35 (0.18), residues: 774 loop : -0.10 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 11 TYR 0.052 0.001 TYR B1125 PHE 0.018 0.001 PHE B 499 TRP 0.015 0.001 TRP A1192 HIS 0.005 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00271 (39213) covalent geometry : angle 0.54172 (53296) hydrogen bonds : bond 0.03152 ( 1518) hydrogen bonds : angle 4.56844 ( 4204) metal coordination : bond 0.00673 ( 36) metal coordination : angle 3.92157 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 1.419 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 19 LYS cc_start: 0.9166 (mmpt) cc_final: 0.8827 (mmmt) REVERT: A 58 MET cc_start: 0.9033 (ttm) cc_final: 0.8469 (tpp) REVERT: A 92 LYS cc_start: 0.9395 (mmpt) cc_final: 0.9120 (mmmt) REVERT: A 565 MET cc_start: 0.8798 (tpp) cc_final: 0.8038 (tpp) REVERT: A 1097 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8094 (tm-30) REVERT: A 1228 MET cc_start: 0.8346 (mtp) cc_final: 0.7777 (ttp) REVERT: A 1447 GLU cc_start: 0.7487 (mp0) cc_final: 0.7142 (mp0) REVERT: A 1484 MET cc_start: 0.6927 (ptp) cc_final: 0.6185 (ptm) REVERT: B 465 TYR cc_start: 0.8695 (m-80) cc_final: 0.8495 (m-80) REVERT: B 1243 SER cc_start: 0.9310 (m) cc_final: 0.9005 (p) REVERT: D 73 THR cc_start: 0.8130 (m) cc_final: 0.7309 (p) REVERT: D 104 MET cc_start: 0.8421 (mmp) cc_final: 0.8020 (mmm) REVERT: D 109 TYR cc_start: 0.7097 (t80) cc_final: 0.6852 (t80) REVERT: E 18 MET cc_start: 0.8588 (tpp) cc_final: 0.8246 (tpp) REVERT: F 98 LYS cc_start: 0.9123 (mttt) cc_final: 0.8830 (mtpp) REVERT: F 116 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7909 (mt-10) REVERT: G 33 GLU cc_start: 0.8872 (mp0) cc_final: 0.8281 (mp0) REVERT: H 87 GLN cc_start: 0.9071 (mp10) cc_final: 0.8757 (mp10) REVERT: I 46 GLN cc_start: 0.7045 (pp30) cc_final: 0.6815 (pp30) REVERT: I 57 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7426 (mttt) REVERT: I 108 MET cc_start: 0.8801 (mmm) cc_final: 0.7772 (mmm) REVERT: J 31 GLU cc_start: 0.8120 (pm20) cc_final: 0.7774 (pm20) REVERT: L 27 GLU cc_start: 0.7840 (tp30) cc_final: 0.7425 (tm-30) REVERT: M 31 HIS cc_start: 0.8885 (t-170) cc_final: 0.7911 (t70) REVERT: M 33 LYS cc_start: 0.8589 (tppt) cc_final: 0.8194 (tptt) REVERT: M 98 ASP cc_start: 0.8047 (m-30) cc_final: 0.7687 (m-30) REVERT: M 121 LYS cc_start: 0.8355 (tttp) cc_final: 0.7467 (tptt) REVERT: M 137 ARG cc_start: 0.6684 (mmp80) cc_final: 0.6310 (mmp-170) REVERT: M 138 MET cc_start: 0.5915 (mmt) cc_final: 0.5317 (ttt) REVERT: O 36 ASP cc_start: 0.8490 (p0) cc_final: 0.7725 (p0) REVERT: O 72 MET cc_start: 0.8376 (tpp) cc_final: 0.7678 (tpp) REVERT: O 84 LYS cc_start: 0.7849 (mmmt) cc_final: 0.7639 (mmmt) REVERT: O 85 ASP cc_start: 0.5645 (m-30) cc_final: 0.4508 (m-30) REVERT: O 109 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7807 (mtpp) REVERT: Z 226 TYR cc_start: 0.9068 (m-10) cc_final: 0.8501 (m-10) REVERT: Z 451 MET cc_start: 0.6641 (mmp) cc_final: 0.6339 (mmm) REVERT: Z 460 MET cc_start: 0.4548 (tmm) cc_final: 0.3501 (tpp) REVERT: Z 635 MET cc_start: 0.7090 (tpt) cc_final: 0.5165 (tmm) REVERT: Y 64 MET cc_start: 0.6291 (pmm) cc_final: 0.5971 (pmm) outliers start: 1 outliers final: 0 residues processed: 329 average time/residue: 0.2330 time to fit residues: 127.0640 Evaluate side-chains 270 residues out of total 4068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 443 optimal weight: 6.9990 chunk 417 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 330 optimal weight: 50.0000 chunk 66 optimal weight: 9.9990 chunk 228 optimal weight: 0.6980 chunk 189 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN D 171 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 GLN ** Y 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.069264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.044078 restraints weight = 233825.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.046145 restraints weight = 116159.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.046804 restraints weight = 71939.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.047419 restraints weight = 48390.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.047622 restraints weight = 42315.524| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 39249 Z= 0.202 Angle : 0.593 12.587 53347 Z= 0.299 Chirality : 0.044 0.192 5975 Planarity : 0.004 0.098 6626 Dihedral : 12.340 175.099 5942 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.05 % Allowed : 0.37 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.13), residues: 4537 helix: 1.21 (0.14), residues: 1434 sheet: -0.36 (0.19), residues: 751 loop : -0.09 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 34 TYR 0.038 0.001 TYR B 829 PHE 0.018 0.001 PHE B 499 TRP 0.019 0.001 TRP B 104 HIS 0.004 0.001 HIS O 31 Details of bonding type rmsd covalent geometry : bond 0.00457 (39213) covalent geometry : angle 0.57724 (53296) hydrogen bonds : bond 0.03394 ( 1518) hydrogen bonds : angle 4.65057 ( 4204) metal coordination : bond 0.01006 ( 36) metal coordination : angle 4.45583 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6316.36 seconds wall clock time: 110 minutes 15.75 seconds (6615.75 seconds total)