Starting phenix.real_space_refine on Sat Mar 7 10:22:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2z_14468/03_2026/7z2z_14468.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2z_14468/03_2026/7z2z_14468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z2z_14468/03_2026/7z2z_14468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2z_14468/03_2026/7z2z_14468.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2z_14468/03_2026/7z2z_14468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2z_14468/03_2026/7z2z_14468.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 7 6.06 5 P 44 5.49 5 Mg 2 5.21 5 S 217 5.16 5 C 26270 2.51 5 N 7189 2.21 5 O 7941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 41670 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 11192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1431, 11192 Classifications: {'peptide': 1431} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 1365} Chain breaks: 3 Chain: "B" Number of atoms: 8715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8715 Classifications: {'peptide': 1104} Link IDs: {'PTRANS': 41, 'TRANS': 1062} Chain breaks: 1 Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1140 Classifications: {'peptide': 145} Incomplete info: {'backbone_only': 11} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1544 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain breaks: 2 Chain: "H" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain breaks: 1 Chain: "I" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 864 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 381 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1492 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 1 Chain: "N" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1171 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 142} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4558 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 20, 'TRANS': 547} Chain breaks: 1 Chain: "P" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1126 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 829 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain breaks: 1 Chain: "R" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "S" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 383 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "T" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 453 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "W" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 134 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 2, 'TRANS': 13} Chain: "X" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '4QM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "I" 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: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 492 SG CYS A 67 76.415 61.958 78.255 1.00 41.35 S ATOM 510 SG CYS A 70 78.336 64.311 75.997 1.00 56.56 S ATOM 557 SG CYS A 77 79.050 62.947 79.720 1.00 31.80 S ATOM 795 SG CYS A 107 59.605 105.876 95.974 1.00 25.56 S ATOM 818 SG CYS A 110 58.747 106.454 92.247 1.00 35.40 S ATOM 1184 SG CYS A 154 60.308 109.069 93.893 1.00 51.01 S ATOM 1208 SG CYS A 157 56.688 108.163 95.099 1.00 41.49 S ATOM 19480 SG CYS B1095 79.669 79.903 71.477 1.00 35.95 S ATOM 19503 SG CYS B1098 78.246 80.998 74.865 1.00 27.81 S ATOM 19569 SG CYS B1107 77.189 77.924 72.352 1.00 42.19 S ATOM 19589 SG CYS B1110 75.965 80.282 71.514 1.00 34.73 S ATOM 28818 SG CYS I 5 71.647 105.371 160.873 1.00 30.74 S ATOM 28837 SG CYS I 8 71.085 102.814 159.589 1.00 46.17 S ATOM 28965 SG CYS I 26 69.689 106.006 157.689 1.00 46.65 S ATOM 28988 SG CYS I 29 68.471 105.037 161.313 1.00 56.95 S ATOM 29315 SG CYS I 69 132.678 94.447 113.243 1.00 76.37 S ATOM 29363 SG CYS I 75 134.380 97.761 114.437 1.00 75.13 S ATOM 29565 SG CYS I 100 132.752 95.661 117.179 1.00 76.08 S ATOM 29586 SG CYS I 103 131.003 97.682 115.013 1.00 73.09 S ATOM 29697 SG CYS J 7 133.965 40.077 117.911 1.00 19.79 S ATOM 29720 SG CYS J 10 138.021 40.542 117.382 1.00 39.72 S ATOM 30000 SG CYS J 45 136.879 42.291 119.183 1.00 31.23 S ATOM 30006 SG CYS J 46 136.947 38.563 119.833 1.00 24.26 S ATOM 31057 SG CYS L 31 93.400 22.883 120.435 1.00 47.09 S ATOM 31077 SG CYS L 34 94.056 19.964 122.052 1.00 56.56 S ATOM 31181 SG CYS L 48 91.572 20.286 119.520 1.00 54.77 S ATOM 31204 SG CYS L 51 91.554 21.807 123.409 1.00 74.53 S Time building chain proxies: 7.71, per 1000 atoms: 0.19 Number of scatterers: 41670 At special positions: 0 Unit cell: (190.96, 157.325, 203.98, 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 7 29.99 S 217 16.00 P 44 15.00 Mg 2 11.99 O 7941 8.00 N 7189 7.00 C 26270 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: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 157 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 154 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 26 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN I 203 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 100 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 69 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 75 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb=" ZN L2001 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 31 " Number of angles added : 39 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9668 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 54 sheets defined 40.1% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 133 through 151 Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.587A pdb=" N ARG A 184 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TRP A 185 " --> pdb=" O THR A 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 181 through 185' Processing helix chain 'A' and resid 191 through 208 removed outlier: 3.921A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 4.313A pdb=" N LYS A 216 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 283 through 306 removed outlier: 3.947A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 3.532A pdb=" N GLU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.900A pdb=" N MET A 336 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 448 through 456 removed outlier: 3.852A pdb=" N LEU A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.367A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 Processing helix chain 'A' and resid 537 through 541 removed outlier: 4.221A pdb=" N LEU A 541 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 566 removed outlier: 3.980A pdb=" N SER A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 642 through 646 removed outlier: 3.516A pdb=" N MET A 645 " --> pdb=" O PRO A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.697A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 705 " --> pdb=" O CYS A 701 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 720 through 748 removed outlier: 3.883A pdb=" N LYS A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 785 removed outlier: 3.681A pdb=" N LEU A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 857 through 894 removed outlier: 4.162A pdb=" N GLY A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 877 " --> pdb=" O VAL A 873 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 934 through 946 Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.919A pdb=" N MET A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 973 Processing helix chain 'A' and resid 998 through 1025 Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1063 through 1081 Processing helix chain 'A' and resid 1088 through 1102 Proline residue: A1100 - end of helix Processing helix chain 'A' and resid 1122 through 1132 Processing helix chain 'A' and resid 1154 through 1159 Processing helix chain 'A' and resid 1165 through 1171 removed outlier: 4.539A pdb=" N PHE A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1196 Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1254 through 1267 Processing helix chain 'A' and resid 1268 through 1270 No H-bonds generated for 'chain 'A' and resid 1268 through 1270' Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1345 Processing helix chain 'A' and resid 1351 through 1363 removed outlier: 3.950A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1390 Processing helix chain 'A' and resid 1391 through 1403 Processing helix chain 'A' and resid 1410 through 1417 Processing helix chain 'A' and resid 1423 through 1426 Processing helix chain 'A' and resid 1438 through 1442 removed outlier: 4.070A pdb=" N VAL A1442 " --> pdb=" O LYS A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1457 removed outlier: 3.850A pdb=" N ALA A1456 " --> pdb=" O ASN A1453 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.555A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 80 removed outlier: 5.480A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LYS B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 276 through 284 removed outlier: 3.980A pdb=" N ILE B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 removed outlier: 4.095A pdb=" N LEU B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.525A pdb=" N ILE B 319 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 330 through 333 removed outlier: 4.295A pdb=" N ALA B 333 " --> pdb=" O THR B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 342 through 362 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 408 removed outlier: 3.572A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 426 removed outlier: 4.076A pdb=" N SER B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 440 removed outlier: 4.010A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.855A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.878A pdb=" N ALA B 488 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 527 through 537 removed outlier: 3.701A pdb=" N LYS B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 581 Processing helix chain 'B' and resid 624 through 633 Processing helix chain 'B' and resid 637 through 643 removed outlier: 3.885A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 657 removed outlier: 4.007A pdb=" N ASP B 656 " --> pdb=" O ASN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.532A pdb=" N ILE B 666 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 688 removed outlier: 3.690A pdb=" N LEU B 687 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 688 " --> pdb=" O ALA B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 694 removed outlier: 3.605A pdb=" N ASN B 694 " --> pdb=" O PRO B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 706 Processing helix chain 'B' and resid 738 through 744 removed outlier: 3.830A pdb=" N GLU B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 743 " --> pdb=" O LYS B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 Processing helix chain 'B' and resid 927 through 931 Processing helix chain 'B' and resid 945 through 949 removed outlier: 3.552A pdb=" N GLY B 948 " --> pdb=" O ASN B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 971 Processing helix chain 'B' and resid 983 through 993 Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1063 through 1073 Processing helix chain 'B' and resid 1075 through 1084 removed outlier: 3.560A pdb=" N LEU B1079 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.998A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.269A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.585A pdb=" N SER C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 removed outlier: 4.088A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.686A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 14 through 27 removed outlier: 3.638A pdb=" N LYS D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 36 Processing helix chain 'D' and resid 52 through 68 removed outlier: 3.502A pdb=" N GLN D 56 " --> pdb=" O HIS D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 106 Processing helix chain 'D' and resid 106 through 113 removed outlier: 3.930A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.518A pdb=" N ILE D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 119 through 124' Processing helix chain 'D' and resid 130 through 138 removed outlier: 4.059A pdb=" N VAL D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 150 through 158 Processing helix chain 'E' and resid 2 through 28 removed outlier: 3.730A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.536A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 58 removed outlier: 3.640A pdb=" N MET E 57 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.510A pdb=" N HIS E 146 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.502A pdb=" N TYR E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 20 removed outlier: 4.321A pdb=" N HIS G 19 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.732A pdb=" N HIS G 28 " --> pdb=" O SER G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 173 Processing helix chain 'G' and resid 207 through 211 removed outlier: 3.659A pdb=" N TRP G 211 " --> pdb=" O VAL G 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.710A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.990A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 132 through 140 Processing helix chain 'M' and resid 183 through 194 removed outlier: 3.923A pdb=" N ASP M 187 " --> pdb=" O PHE M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 240 Processing helix chain 'M' and resid 255 through 263 Processing helix chain 'M' and resid 273 through 281 removed outlier: 3.673A pdb=" N ILE M 278 " --> pdb=" O GLN M 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 200 removed outlier: 3.977A pdb=" N PHE N 200 " --> pdb=" O GLU N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 220 removed outlier: 3.994A pdb=" N ARG N 217 " --> pdb=" O GLU N 213 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU N 218 " --> pdb=" O THR N 214 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN N 220 " --> pdb=" O LYS N 216 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 297 removed outlier: 3.755A pdb=" N GLU N 279 " --> pdb=" O GLU N 275 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 35 removed outlier: 3.696A pdb=" N THR O 33 " --> pdb=" O GLU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 57 Processing helix chain 'O' and resid 58 through 72 Processing helix chain 'O' and resid 75 through 83 Processing helix chain 'O' and resid 87 through 101 Processing helix chain 'O' and resid 123 through 132 removed outlier: 3.647A pdb=" N ILE O 129 " --> pdb=" O GLU O 125 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.583A pdb=" N MET O 144 " --> pdb=" O ILE O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 167 removed outlier: 3.587A pdb=" N LYS O 153 " --> pdb=" O GLU O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 177 Processing helix chain 'O' and resid 188 through 197 Processing helix chain 'O' and resid 210 through 220 Processing helix chain 'O' and resid 233 through 258 removed outlier: 4.214A pdb=" N THR O 247 " --> pdb=" O MET O 243 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP O 248 " --> pdb=" O ASN O 244 " (cutoff:3.500A) Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 260 through 265 Processing helix chain 'O' and resid 283 through 301 removed outlier: 3.527A pdb=" N PHE O 287 " --> pdb=" O ASN O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 305 through 319 removed outlier: 3.639A pdb=" N ILE O 314 " --> pdb=" O GLN O 310 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG O 317 " --> pdb=" O LYS O 313 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR O 319 " --> pdb=" O ALA O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 356 removed outlier: 3.957A pdb=" N GLU O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 364 through 369 removed outlier: 4.374A pdb=" N ARG O 368 " --> pdb=" O ILE O 364 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N HIS O 369 " --> pdb=" O ASP O 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 364 through 369' Processing helix chain 'O' and resid 449 through 463 removed outlier: 3.674A pdb=" N SER O 455 " --> pdb=" O SER O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 479 through 500 Proline residue: O 485 - end of helix Processing helix chain 'O' and resid 501 through 514 Processing helix chain 'O' and resid 518 through 527 Processing helix chain 'O' and resid 529 through 542 Processing helix chain 'O' and resid 569 through 609 removed outlier: 5.442A pdb=" N THR O 601 " --> pdb=" O GLN O 597 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU O 602 " --> pdb=" O GLU O 598 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU O 603 " --> pdb=" O ASN O 599 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS O 605 " --> pdb=" O THR O 601 " (cutoff:3.500A) Processing helix chain 'O' and resid 610 through 615 removed outlier: 3.926A pdb=" N ARG O 614 " --> pdb=" O ASP O 610 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU O 615 " --> pdb=" O VAL O 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 610 through 615' Processing helix chain 'O' and resid 616 through 619 Processing helix chain 'O' and resid 620 through 653 removed outlier: 4.573A pdb=" N VAL O 650 " --> pdb=" O SER O 646 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 191 removed outlier: 3.751A pdb=" N ILE P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG P 184 " --> pdb=" O THR P 180 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE P 186 " --> pdb=" O VAL P 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 199 Processing helix chain 'P' and resid 217 through 229 Processing helix chain 'P' and resid 236 through 248 Processing helix chain 'P' and resid 265 through 271 Processing helix chain 'P' and resid 295 through 299 removed outlier: 3.784A pdb=" N LYS P 298 " --> pdb=" O ASN P 295 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 61 Processing helix chain 'Q' and resid 128 through 132 Processing helix chain 'Q' and resid 133 through 138 removed outlier: 4.372A pdb=" N ASN Q 138 " --> pdb=" O GLU Q 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 612 through 617 removed outlier: 4.251A pdb=" N THR W 616 " --> pdb=" O ASP W 612 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 17 removed outlier: 6.650A pdb=" N ARG B1142 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU A 16 " --> pdb=" O ARG B1140 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG B1140 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 33 removed outlier: 7.688A pdb=" N HIS A 83 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU A 33 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LYS A 85 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ARG A 259 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.663A pdb=" N LEU A 88 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N ILE A 257 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 167 removed outlier: 4.628A pdb=" N LYS A 177 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 178 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.514A pdb=" N LYS A 371 " --> pdb=" O LEU B1062 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B1060 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 383 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 376 through 383 current: chain 'A' and resid 485 through 489 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 404 through 407 removed outlier: 7.054A pdb=" N VAL A 461 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU A 433 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU A 463 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG A 441 " --> pdb=" O UNK X1017 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA8, first strand: chain 'A' and resid 597 through 599 removed outlier: 5.721A pdb=" N VAL H 96 " --> pdb=" O MET A 598 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 626 through 629 removed outlier: 6.287A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 817 through 818 Processing sheet with id=AB2, first strand: chain 'A' and resid 897 through 898 Processing sheet with id=AB3, first strand: chain 'A' and resid 1278 through 1285 removed outlier: 3.832A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A1282 " --> pdb=" O LEU A1294 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ARG A1291 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU A1145 " --> pdb=" O ARG A1291 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A1293 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A1143 " --> pdb=" O LEU A1293 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A1144 " --> pdb=" O ARG A1313 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG A1313 " --> pdb=" O VAL A1144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1222 through 1223 removed outlier: 3.625A pdb=" N ARG A1187 " --> pdb=" O TYR A1172 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR A1172 " --> pdb=" O ARG A1187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AB6, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.630A pdb=" N ASP B 132 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE B 98 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR B 130 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B 100 " --> pdb=" O PRO B 128 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB8, first strand: chain 'B' and resid 375 through 378 removed outlier: 3.648A pdb=" N VAL B 196 " --> pdb=" O ARG B 472 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 206 through 210 removed outlier: 3.630A pdb=" N GLU B 208 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 220 through 222 Processing sheet with id=AC2, first strand: chain 'B' and resid 241 through 242 Processing sheet with id=AC3, first strand: chain 'B' and resid 442 through 443 Processing sheet with id=AC4, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.762A pdb=" N SER B 564 " --> pdb=" O GLU B 539 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 560 through 561 Processing sheet with id=AC7, first strand: chain 'B' and resid 611 through 616 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 619 through 620 current: chain 'B' and resid 672 through 673 Processing sheet with id=AC8, first strand: chain 'B' and resid 724 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 785 through 794 current: chain 'B' and resid 879 through 888 removed outlier: 8.241A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 894 through 904 current: chain 'L' and resid 37 through 38 Processing sheet with id=AC9, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AD1, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 6.868A pdb=" N LEU B 771 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE B 925 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 773 " --> pdb=" O ILE B 925 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 841 through 843 removed outlier: 3.920A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 846 through 847 Processing sheet with id=AD4, first strand: chain 'B' and resid 1043 through 1044 Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1095 Processing sheet with id=AD6, first strand: chain 'C' and resid 4 through 7 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 12 through 13 current: chain 'C' and resid 51 through 57 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 57 current: chain 'C' and resid 289 through 304 Processing sheet with id=AD7, first strand: chain 'C' and resid 168 through 169 removed outlier: 6.339A pdb=" N GLU C 201 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASN C 87 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.539A pdb=" N THR C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AE1, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AE2, first strand: chain 'D' and resid 3 through 5 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 3 through 5 current: chain 'G' and resid 43 through 54 removed outlier: 3.614A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ARG G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASP G 50 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR G 71 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N LEU G 52 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 11.351A pdb=" N ASN G 69 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N VAL G 54 " --> pdb=" O TYR G 67 " (cutoff:3.500A) removed outlier: 11.299A pdb=" N TYR G 67 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.589A pdb=" N ALA E 62 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 78 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP E 79 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E 109 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.866A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 96 through 100 removed outlier: 7.875A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER G 90 " --> pdb=" O LYS G 98 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP G 88 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL G 85 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE G 148 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 152 through 155 Processing sheet with id=AE8, first strand: chain 'I' and resid 13 through 14 Processing sheet with id=AE9, first strand: chain 'I' and resid 64 through 65 removed outlier: 5.821A pdb=" N PHE I 82 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LYS I 99 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLN I 84 " --> pdb=" O PHE I 97 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE I 97 " --> pdb=" O GLN I 84 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN I 86 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR I 96 " --> pdb=" O GLU I 109 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 47 through 50 removed outlier: 4.620A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 73 through 74 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 73 through 74 current: chain 'M' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 145 through 149 current: chain 'M' and resid 168 through 172 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 168 through 172 current: chain 'N' and resid 371 through 374 removed outlier: 6.741A pdb=" N LEU N 371 " --> pdb=" O ILE N 382 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE N 382 " --> pdb=" O LEU N 371 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL N 373 " --> pdb=" O MET N 380 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 379 through 384 current: chain 'N' and resid 405 through 420 Processing sheet with id=AF3, first strand: chain 'M' and resid 269 through 270 removed outlier: 4.294A pdb=" N VAL M 269 " --> pdb=" O GLU N 317 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 104 through 110 removed outlier: 3.667A pdb=" N GLU O 109 " --> pdb=" O THR O 117 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 201 through 202 Processing sheet with id=AF6, first strand: chain 'O' and resid 361 through 362 Processing sheet with id=AF7, first strand: chain 'O' and resid 380 through 381 Processing sheet with id=AF8, first strand: chain 'O' and resid 547 through 551 Processing sheet with id=AF9, first strand: chain 'P' and resid 254 through 256 1509 hydrogen bonds defined for protein. 4197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.12 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11426 1.33 - 1.45: 7410 1.45 - 1.58: 23236 1.58 - 1.70: 87 1.70 - 1.82: 352 Bond restraints: 42511 Sorted by residual: bond pdb=" N ASP A 511 " pdb=" CA ASP A 511 " ideal model delta sigma weight residual 1.459 1.491 -0.031 9.10e-03 1.21e+04 1.20e+01 bond pdb=" N HIS A 427 " pdb=" CA HIS A 427 " ideal model delta sigma weight residual 1.462 1.491 -0.029 8.50e-03 1.38e+04 1.20e+01 bond pdb=" N VAL A 426 " pdb=" CA VAL A 426 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.12e-02 7.97e+03 1.11e+01 bond pdb=" N VAL A 90 " pdb=" CA VAL A 90 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.08e+01 bond pdb=" C TYR P 208 " pdb=" N ALA P 209 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.07e-02 2.33e+03 1.05e+01 ... (remaining 42506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 56853 2.56 - 5.11: 682 5.11 - 7.67: 44 7.67 - 10.23: 8 10.23 - 12.78: 2 Bond angle restraints: 57589 Sorted by residual: angle pdb=" CA PRO P 301 " pdb=" N PRO P 301 " pdb=" CD PRO P 301 " ideal model delta sigma weight residual 112.00 104.59 7.41 1.40e+00 5.10e-01 2.80e+01 angle pdb=" N ASP P 171 " pdb=" CA ASP P 171 " pdb=" C ASP P 171 " ideal model delta sigma weight residual 113.88 107.99 5.89 1.23e+00 6.61e-01 2.29e+01 angle pdb=" N PRO N 301 " pdb=" CD PRO N 301 " pdb=" CG PRO N 301 " ideal model delta sigma weight residual 103.20 96.04 7.16 1.50e+00 4.44e-01 2.28e+01 angle pdb=" CA GLY I 57 " pdb=" C GLY I 57 " pdb=" O GLY I 57 " ideal model delta sigma weight residual 121.77 118.01 3.76 8.60e-01 1.35e+00 1.91e+01 angle pdb=" N GLY A 514 " pdb=" CA GLY A 514 " pdb=" C GLY A 514 " ideal model delta sigma weight residual 114.95 109.12 5.83 1.41e+00 5.03e-01 1.71e+01 ... (remaining 57584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.26: 24190 29.26 - 58.51: 1648 58.51 - 87.77: 134 87.77 - 117.03: 9 117.03 - 146.28: 3 Dihedral angle restraints: 25984 sinusoidal: 11033 harmonic: 14951 Sorted by residual: dihedral pdb=" CA GLU B 249 " pdb=" C GLU B 249 " pdb=" N GLU B 250 " pdb=" CA GLU B 250 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ASN M 242 " pdb=" C ASN M 242 " pdb=" N ILE M 243 " pdb=" CA ILE M 243 " ideal model delta harmonic sigma weight residual 180.00 153.78 26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA PHE A1171 " pdb=" C PHE A1171 " pdb=" N TYR A1172 " pdb=" CA TYR A1172 " ideal model delta harmonic sigma weight residual 180.00 154.03 25.97 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 25981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4390 0.042 - 0.083: 1504 0.083 - 0.125: 507 0.125 - 0.167: 72 0.167 - 0.209: 18 Chirality restraints: 6491 Sorted by residual: chirality pdb=" CA ILE B 841 " pdb=" N ILE B 841 " pdb=" C ILE B 841 " pdb=" CB ILE B 841 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA THR B1108 " pdb=" N THR B1108 " pdb=" C THR B1108 " pdb=" CB THR B1108 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA LEU I 55 " pdb=" N LEU I 55 " pdb=" C LEU I 55 " pdb=" CB LEU I 55 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 6488 not shown) Planarity restraints: 7261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 127 " 0.080 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO D 128 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 300 " -0.075 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO N 301 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO N 301 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO N 301 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 74 " 0.058 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO M 75 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO M 75 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO M 75 " 0.049 5.00e-02 4.00e+02 ... (remaining 7258 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1661 2.71 - 3.26: 40876 3.26 - 3.80: 66124 3.80 - 4.35: 85413 4.35 - 4.90: 141538 Nonbonded interactions: 335612 Sorted by model distance: nonbonded pdb=" OG SER A 388 " pdb=" O ILE A 389 " model vdw 2.161 3.040 nonbonded pdb=" O THR A 409 " pdb=" OG1 THR A 409 " model vdw 2.192 3.040 nonbonded pdb=" OG SER A1025 " pdb=" NZ LYS H 109 " model vdw 2.196 3.120 nonbonded pdb=" OH TYR M 131 " pdb=" O VAL M 143 " model vdw 2.197 3.040 nonbonded pdb=" OD2 ASP I 91 " pdb="MG MG I 201 " model vdw 2.211 2.170 ... (remaining 335607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.040 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 40.360 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.377 42539 Z= 0.279 Angle : 0.816 34.544 57628 Z= 0.399 Chirality : 0.047 0.209 6491 Planarity : 0.006 0.121 7261 Dihedral : 18.273 146.283 16316 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 1.29 % Allowed : 22.35 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.12), residues: 5052 helix: 0.22 (0.12), residues: 1807 sheet: -0.81 (0.20), residues: 633 loop : -1.97 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 93 TYR 0.023 0.002 TYR A1172 PHE 0.037 0.002 PHE N 390 TRP 0.014 0.002 TRP M 119 HIS 0.010 0.001 HIS B 692 Details of bonding type rmsd covalent geometry : bond 0.00550 (42511) covalent geometry : angle 0.69830 (57589) hydrogen bonds : bond 0.17526 ( 1509) hydrogen bonds : angle 6.38366 ( 4197) metal coordination : bond 0.10459 ( 28) metal coordination : angle 16.20896 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 495 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 121 MET cc_start: 0.7937 (mmm) cc_final: 0.7598 (mmm) REVERT: P 208 TYR cc_start: 0.4695 (p90) cc_final: 0.4481 (p90) outliers start: 58 outliers final: 23 residues processed: 521 average time/residue: 0.2501 time to fit residues: 210.6819 Evaluate side-chains 492 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 469 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 1080 LYS Chi-restraints excluded: chain A residue 1183 PHE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 804 ASP Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 264 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 0.5980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 GLN A 808 GLN A 941 HIS A1254 ASN A1346 HIS B 286 ASN B 708 GLN C 14 ASN C 29 ASN D 8 ASN D 130 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN G 201 GLN H 11 GLN H 137 GLN I 64 GLN I 84 GLN M 86 HIS ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 HIS M 146 GLN N 289 HIS N 298 ASN N 366 HIS N 421 GLN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN O 454 ASN P 193 ASN P 205 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.153379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120863 restraints weight = 58875.055| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.24 r_work: 0.3324 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 42539 Z= 0.120 Angle : 0.586 20.282 57628 Z= 0.299 Chirality : 0.042 0.185 6491 Planarity : 0.004 0.083 7261 Dihedral : 10.883 143.780 6161 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.75 % Allowed : 20.86 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.12), residues: 5052 helix: 0.58 (0.12), residues: 1860 sheet: -0.77 (0.20), residues: 665 loop : -1.81 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 60 TYR 0.018 0.001 TYR A1172 PHE 0.023 0.001 PHE B 678 TRP 0.013 0.001 TRP I 107 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00267 (42511) covalent geometry : angle 0.56650 (57589) hydrogen bonds : bond 0.04371 ( 1509) hydrogen bonds : angle 5.00414 ( 4197) metal coordination : bond 0.00936 ( 28) metal coordination : angle 5.83053 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 514 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1278 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8204 (mt) REVERT: A 1398 ASP cc_start: 0.8759 (m-30) cc_final: 0.8490 (m-30) REVERT: B 152 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.6726 (tpt) REVERT: B 332 ILE cc_start: 0.5977 (OUTLIER) cc_final: 0.5591 (tp) REVERT: B 365 MET cc_start: 0.7935 (mmm) cc_final: 0.7691 (mmp) REVERT: B 624 ASP cc_start: 0.6353 (OUTLIER) cc_final: 0.6027 (p0) REVERT: B 901 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8425 (ptt90) REVERT: D 107 MET cc_start: 0.4112 (ppp) cc_final: 0.3660 (ppp) REVERT: E 1 MET cc_start: 0.3384 (tmm) cc_final: 0.1948 (tpt) REVERT: K 142 MET cc_start: 0.7972 (tpp) cc_final: 0.7759 (tpt) REVERT: N 313 LEU cc_start: 0.6846 (pp) cc_final: 0.6620 (pt) REVERT: N 391 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7634 (mt) REVERT: O 206 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7843 (pt) outliers start: 124 outliers final: 66 residues processed: 605 average time/residue: 0.2338 time to fit residues: 231.3542 Evaluate side-chains 553 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 480 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 701 TYR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain P residue 235 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain Q residue 16 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 31 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 460 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 453 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 286 ASN B 490 GLN B 708 GLN B1036 HIS C 159 ASN C 237 GLN D 8 ASN G 41 ASN I 84 GLN I 86 GLN L 53 HIS ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 146 GLN N 289 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 321 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.149879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117951 restraints weight = 59149.564| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.17 r_work: 0.3257 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 42539 Z= 0.232 Angle : 0.688 20.689 57628 Z= 0.349 Chirality : 0.046 0.211 6491 Planarity : 0.005 0.061 7261 Dihedral : 10.987 146.741 6130 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.30 % Allowed : 21.18 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.12), residues: 5052 helix: 0.39 (0.12), residues: 1836 sheet: -0.87 (0.20), residues: 633 loop : -1.90 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 144 TYR 0.024 0.002 TYR A1172 PHE 0.018 0.002 PHE A 610 TRP 0.013 0.002 TRP C 31 HIS 0.011 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00560 (42511) covalent geometry : angle 0.66859 (57589) hydrogen bonds : bond 0.05265 ( 1509) hydrogen bonds : angle 5.06391 ( 4197) metal coordination : bond 0.01331 ( 28) metal coordination : angle 6.24248 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 489 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6087 (mp0) REVERT: A 390 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6762 (t0) REVERT: A 477 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.6471 (mt0) REVERT: A 591 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7756 (p0) REVERT: A 749 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5837 (pm20) REVERT: A 1215 LEU cc_start: 0.3946 (OUTLIER) cc_final: 0.3623 (mt) REVERT: A 1398 ASP cc_start: 0.8754 (m-30) cc_final: 0.8492 (m-30) REVERT: B 135 TYR cc_start: 0.5287 (OUTLIER) cc_final: 0.5008 (p90) REVERT: B 152 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.6564 (tpt) REVERT: B 159 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.8019 (m110) REVERT: B 332 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5659 (tp) REVERT: B 539 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.5553 (mp0) REVERT: B 624 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6250 (p0) REVERT: D 107 MET cc_start: 0.3732 (ppp) cc_final: 0.3348 (ppp) REVERT: E 121 MET cc_start: 0.8096 (mmm) cc_final: 0.7851 (mmm) REVERT: G 138 LEU cc_start: 0.2579 (OUTLIER) cc_final: 0.2356 (tt) REVERT: M 238 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.7022 (p0) REVERT: N 313 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6735 (pt) REVERT: N 391 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7688 (mt) REVERT: N 411 ARG cc_start: 0.7126 (ptt90) cc_final: 0.6857 (ptt90) REVERT: O 86 MET cc_start: 0.5916 (tmm) cc_final: 0.5690 (tmm) REVERT: O 206 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7906 (pt) outliers start: 194 outliers final: 132 residues processed: 635 average time/residue: 0.2331 time to fit residues: 243.1357 Evaluate side-chains 621 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 472 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1021 ASN Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 701 TYR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1012 CYS Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 211 ILE Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 303 ARG Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 360 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain O residue 653 MET Chi-restraints excluded: chain P residue 235 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 105 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 8 optimal weight: 0.5980 chunk 447 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 443 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 368 optimal weight: 20.0000 chunk 500 optimal weight: 20.0000 chunk 305 optimal weight: 5.9990 chunk 310 optimal weight: 20.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN B 286 ASN B 708 GLN C 237 GLN D 8 ASN G 41 ASN L 53 HIS M 146 GLN N 289 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.150475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118642 restraints weight = 58741.156| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.14 r_work: 0.3272 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 42539 Z= 0.189 Angle : 0.646 19.440 57628 Z= 0.329 Chirality : 0.045 0.201 6491 Planarity : 0.005 0.060 7261 Dihedral : 10.937 145.595 6130 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.35 % Allowed : 22.04 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.12), residues: 5052 helix: 0.43 (0.12), residues: 1831 sheet: -0.84 (0.20), residues: 636 loop : -1.91 (0.12), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 144 TYR 0.022 0.002 TYR A1172 PHE 0.022 0.002 PHE B 678 TRP 0.011 0.002 TRP A 258 HIS 0.010 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00453 (42511) covalent geometry : angle 0.62986 (57589) hydrogen bonds : bond 0.04804 ( 1509) hydrogen bonds : angle 4.96198 ( 4197) metal coordination : bond 0.01080 ( 28) metal coordination : angle 5.61292 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 486 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6136 (mp0) REVERT: A 390 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6642 (t0) REVERT: A 414 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7173 (p-80) REVERT: A 736 HIS cc_start: 0.7596 (t70) cc_final: 0.7187 (t70) REVERT: A 1398 ASP cc_start: 0.8754 (m-30) cc_final: 0.8502 (m-30) REVERT: B 135 TYR cc_start: 0.5245 (OUTLIER) cc_final: 0.4964 (p90) REVERT: B 152 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.6689 (tpt) REVERT: B 168 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7033 (tp30) REVERT: B 199 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6428 (mm-40) REVERT: B 332 ILE cc_start: 0.6295 (OUTLIER) cc_final: 0.5806 (tp) REVERT: B 448 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.5619 (mtmt) REVERT: B 539 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.5471 (mp0) REVERT: B 614 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8228 (mt) REVERT: B 624 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.6281 (p0) REVERT: B 673 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7470 (tp) REVERT: B 929 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: C 172 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7851 (mt0) REVERT: C 284 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7096 (pt0) REVERT: D 97 LYS cc_start: 0.4030 (pttp) cc_final: 0.3513 (mtmm) REVERT: D 107 MET cc_start: 0.3690 (ppp) cc_final: 0.3332 (ppp) REVERT: G 138 LEU cc_start: 0.2586 (OUTLIER) cc_final: 0.2357 (tt) REVERT: M 133 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6309 (mtmt) REVERT: M 238 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6959 (p0) REVERT: N 391 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7728 (mt) REVERT: N 411 ARG cc_start: 0.7138 (ptt90) cc_final: 0.6874 (ptt90) REVERT: O 153 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6868 (mttp) REVERT: O 206 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7901 (pt) REVERT: O 525 THR cc_start: 0.7158 (t) cc_final: 0.6822 (m) REVERT: P 314 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7445 (tp30) outliers start: 196 outliers final: 138 residues processed: 643 average time/residue: 0.2398 time to fit residues: 253.1278 Evaluate side-chains 632 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 473 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1021 ASN Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1183 PHE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 701 TYR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 929 GLU Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1012 CYS Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain N residue 374 LYS Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 155 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 211 ILE Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 303 ARG Chi-restraints excluded: chain O residue 318 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 360 THR Chi-restraints excluded: chain O residue 548 ILE Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain P residue 235 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 314 GLU Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 379 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 96 optimal weight: 0.2980 chunk 140 optimal weight: 9.9990 chunk 262 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 446 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 chunk 324 optimal weight: 5.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN B 708 GLN C 237 GLN D 8 ASN G 41 ASN I 71 ASN I 84 GLN L 53 HIS N 289 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.150106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117881 restraints weight = 58785.464| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.15 r_work: 0.3272 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 42539 Z= 0.202 Angle : 0.658 20.585 57628 Z= 0.335 Chirality : 0.045 0.212 6491 Planarity : 0.005 0.059 7261 Dihedral : 10.946 145.983 6130 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 5.14 % Allowed : 21.95 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.12), residues: 5052 helix: 0.40 (0.12), residues: 1830 sheet: -0.83 (0.20), residues: 644 loop : -1.94 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 144 TYR 0.022 0.002 TYR A1172 PHE 0.021 0.002 PHE B 678 TRP 0.013 0.002 TRP C 31 HIS 0.010 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00486 (42511) covalent geometry : angle 0.64265 (57589) hydrogen bonds : bond 0.04864 ( 1509) hydrogen bonds : angle 4.95905 ( 4197) metal coordination : bond 0.01145 ( 28) metal coordination : angle 5.53878 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 488 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: A 390 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6715 (t0) REVERT: A 414 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7120 (p-80) REVERT: A 477 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.6460 (mt0) REVERT: A 591 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8135 (p0) REVERT: A 736 HIS cc_start: 0.7526 (t70) cc_final: 0.7127 (t70) REVERT: A 749 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5808 (pm20) REVERT: A 1398 ASP cc_start: 0.8757 (m-30) cc_final: 0.8478 (m-30) REVERT: B 135 TYR cc_start: 0.5212 (OUTLIER) cc_final: 0.4981 (p90) REVERT: B 152 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.6687 (tpt) REVERT: B 168 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7086 (tp30) REVERT: B 199 GLN cc_start: 0.6698 (mm-40) cc_final: 0.6461 (mm-40) REVERT: B 332 ILE cc_start: 0.6189 (OUTLIER) cc_final: 0.5708 (tp) REVERT: B 448 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.5667 (mtmt) REVERT: B 539 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.5458 (mp0) REVERT: B 614 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8250 (mt) REVERT: B 624 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.5803 (p0) REVERT: B 673 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7479 (tp) REVERT: B 929 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: C 172 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: C 284 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7172 (pt0) REVERT: D 97 LYS cc_start: 0.4109 (pttp) cc_final: 0.3660 (mtmm) REVERT: D 98 MET cc_start: 0.4628 (ttm) cc_final: 0.4417 (ttm) REVERT: D 107 MET cc_start: 0.3336 (ppp) cc_final: 0.2947 (ppp) REVERT: E 200 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8212 (ptt180) REVERT: G 138 LEU cc_start: 0.2640 (OUTLIER) cc_final: 0.2414 (tt) REVERT: I 2 LEU cc_start: 0.6333 (OUTLIER) cc_final: 0.5885 (mp) REVERT: M 133 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6225 (mtmt) REVERT: M 238 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6954 (p0) REVERT: N 297 MET cc_start: 0.6401 (ttm) cc_final: 0.6078 (ttt) REVERT: N 313 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6986 (pt) REVERT: N 391 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7675 (mt) REVERT: N 411 ARG cc_start: 0.7111 (ptt90) cc_final: 0.6831 (ptt90) REVERT: O 152 HIS cc_start: 0.5007 (OUTLIER) cc_final: 0.3729 (t-90) REVERT: O 153 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6810 (mttp) REVERT: O 206 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7926 (pt) REVERT: P 205 ASN cc_start: 0.6723 (OUTLIER) cc_final: 0.6083 (t0) REVERT: P 314 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7478 (tp30) REVERT: Q 30 LYS cc_start: 0.7147 (tmtt) cc_final: 0.6939 (tmtt) outliers start: 232 outliers final: 170 residues processed: 680 average time/residue: 0.2349 time to fit residues: 263.4259 Evaluate side-chains 668 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 469 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1021 ASN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 701 TYR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 929 GLU Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1012 CYS Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain N residue 374 LYS Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 155 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 211 ILE Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 303 ARG Chi-restraints excluded: chain O residue 318 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 360 THR Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 548 ILE Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain P residue 235 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 314 GLU Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 378 optimal weight: 5.9990 chunk 391 optimal weight: 6.9990 chunk 410 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 chunk 423 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 465 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 489 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN C 237 GLN D 8 ASN G 41 ASN L 53 HIS N 289 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.150650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118292 restraints weight = 58731.548| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.19 r_work: 0.3281 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 42539 Z= 0.174 Angle : 0.633 20.421 57628 Z= 0.322 Chirality : 0.044 0.199 6491 Planarity : 0.005 0.060 7261 Dihedral : 10.886 145.172 6130 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.99 % Allowed : 22.39 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.12), residues: 5052 helix: 0.47 (0.12), residues: 1842 sheet: -0.81 (0.20), residues: 642 loop : -1.92 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 144 TYR 0.021 0.002 TYR A1172 PHE 0.022 0.002 PHE B 678 TRP 0.011 0.002 TRP A 258 HIS 0.009 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00416 (42511) covalent geometry : angle 0.61791 (57589) hydrogen bonds : bond 0.04604 ( 1509) hydrogen bonds : angle 4.90248 ( 4197) metal coordination : bond 0.01006 ( 28) metal coordination : angle 5.33088 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 486 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: A 414 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.7140 (p-80) REVERT: A 477 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.6529 (mt0) REVERT: A 749 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5805 (pm20) REVERT: A 1398 ASP cc_start: 0.8749 (m-30) cc_final: 0.8493 (m-30) REVERT: B 135 TYR cc_start: 0.5244 (OUTLIER) cc_final: 0.4610 (p90) REVERT: B 152 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.6669 (tpt) REVERT: B 159 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7870 (m110) REVERT: B 168 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7251 (tp30) REVERT: B 199 GLN cc_start: 0.6615 (mm-40) cc_final: 0.6376 (mm-40) REVERT: B 213 LYS cc_start: 0.6498 (OUTLIER) cc_final: 0.5367 (tmmt) REVERT: B 332 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.5846 (tp) REVERT: B 448 LYS cc_start: 0.6618 (OUTLIER) cc_final: 0.5617 (mtmt) REVERT: B 539 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.5255 (mp0) REVERT: B 614 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8240 (mt) REVERT: B 624 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.5795 (p0) REVERT: B 673 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7435 (tp) REVERT: B 816 ASP cc_start: 0.6885 (p0) cc_final: 0.6609 (m-30) REVERT: B 929 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: C 172 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: C 284 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: D 97 LYS cc_start: 0.4176 (pttp) cc_final: 0.3715 (mtmm) REVERT: E 200 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8216 (ptt180) REVERT: G 138 LEU cc_start: 0.2639 (OUTLIER) cc_final: 0.2423 (tt) REVERT: I 2 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.5889 (mp) REVERT: M 133 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6213 (mtmt) REVERT: M 141 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6419 (p0) REVERT: M 166 MET cc_start: 0.6225 (mmp) cc_final: 0.5214 (ptt) REVERT: M 238 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6953 (p0) REVERT: N 297 MET cc_start: 0.6441 (ttm) cc_final: 0.6149 (ttt) REVERT: N 313 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6995 (pt) REVERT: N 391 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7674 (mt) REVERT: O 152 HIS cc_start: 0.5025 (OUTLIER) cc_final: 0.3732 (t-90) REVERT: O 153 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6910 (mttp) REVERT: O 206 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7901 (pt) REVERT: O 254 ASN cc_start: 0.7637 (m-40) cc_final: 0.7253 (t0) REVERT: O 520 LYS cc_start: 0.5345 (ttmm) cc_final: 0.5087 (tmtt) REVERT: P 205 ASN cc_start: 0.6502 (OUTLIER) cc_final: 0.6155 (t0) REVERT: P 314 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: Q 30 LYS cc_start: 0.7197 (tmtt) cc_final: 0.6979 (tmtt) outliers start: 225 outliers final: 169 residues processed: 672 average time/residue: 0.2338 time to fit residues: 258.8799 Evaluate side-chains 670 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 471 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1021 ASN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 701 TYR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 929 GLU Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1012 CYS Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 155 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 211 ILE Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 303 ARG Chi-restraints excluded: chain O residue 318 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 340 GLU Chi-restraints excluded: chain O residue 360 THR Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 548 ILE Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain P residue 235 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 314 GLU Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 412 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 354 optimal weight: 0.0980 chunk 411 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 238 optimal weight: 0.0770 chunk 436 optimal weight: 5.9990 chunk 282 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 overall best weight: 2.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN C 237 GLN D 8 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN N 289 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.151371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119094 restraints weight = 58739.059| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.15 r_work: 0.3293 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 42539 Z= 0.149 Angle : 0.607 20.049 57628 Z= 0.310 Chirality : 0.043 0.198 6491 Planarity : 0.004 0.082 7261 Dihedral : 10.792 144.129 6130 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.77 % Allowed : 22.71 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.12), residues: 5052 helix: 0.59 (0.12), residues: 1841 sheet: -0.81 (0.20), residues: 643 loop : -1.85 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 54 TYR 0.019 0.002 TYR A1172 PHE 0.038 0.001 PHE M 252 TRP 0.012 0.001 TRP C 31 HIS 0.008 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00350 (42511) covalent geometry : angle 0.59349 (57589) hydrogen bonds : bond 0.04315 ( 1509) hydrogen bonds : angle 4.82486 ( 4197) metal coordination : bond 0.00858 ( 28) metal coordination : angle 4.96154 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 484 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: A 361 GLN cc_start: 0.8200 (mt0) cc_final: 0.7985 (mt0) REVERT: A 414 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.7077 (p-80) REVERT: A 477 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.6487 (mt0) REVERT: A 1398 ASP cc_start: 0.8758 (m-30) cc_final: 0.8448 (m-30) REVERT: B 152 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.6646 (tpt) REVERT: B 159 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7857 (m110) REVERT: B 168 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6948 (mm-30) REVERT: B 199 GLN cc_start: 0.6750 (mm-40) cc_final: 0.6498 (mm-40) REVERT: B 213 LYS cc_start: 0.6444 (OUTLIER) cc_final: 0.5219 (tmmt) REVERT: B 332 ILE cc_start: 0.6177 (OUTLIER) cc_final: 0.5693 (tp) REVERT: B 469 MET cc_start: 0.8823 (tpp) cc_final: 0.8435 (tpp) REVERT: B 539 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.5169 (mp0) REVERT: B 614 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8187 (mt) REVERT: B 624 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.5799 (p0) REVERT: B 673 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7424 (tp) REVERT: B 816 ASP cc_start: 0.6838 (p0) cc_final: 0.6591 (m-30) REVERT: B 929 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7319 (pm20) REVERT: C 172 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: C 284 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7105 (pt0) REVERT: D 97 LYS cc_start: 0.4164 (pttp) cc_final: 0.3735 (mtmm) REVERT: E 200 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8236 (ptt180) REVERT: I 2 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5856 (mp) REVERT: I 83 PHE cc_start: 0.6402 (p90) cc_final: 0.6145 (p90) REVERT: M 133 LYS cc_start: 0.6700 (OUTLIER) cc_final: 0.6318 (mtmt) REVERT: M 141 ASN cc_start: 0.7267 (OUTLIER) cc_final: 0.6492 (p0) REVERT: M 166 MET cc_start: 0.6127 (mmp) cc_final: 0.5121 (ptt) REVERT: N 297 MET cc_start: 0.6477 (ttm) cc_final: 0.6165 (ttt) REVERT: N 313 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6988 (pt) REVERT: O 152 HIS cc_start: 0.5035 (OUTLIER) cc_final: 0.3731 (t-90) REVERT: O 153 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6895 (mttp) REVERT: O 206 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7910 (pt) REVERT: O 254 ASN cc_start: 0.7788 (m-40) cc_final: 0.7268 (t0) REVERT: O 520 LYS cc_start: 0.5319 (ttmm) cc_final: 0.5067 (tmtt) REVERT: P 205 ASN cc_start: 0.6443 (OUTLIER) cc_final: 0.6052 (t0) REVERT: P 314 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7368 (tp30) REVERT: Q 30 LYS cc_start: 0.7182 (tmtt) cc_final: 0.6927 (tmtt) outliers start: 215 outliers final: 173 residues processed: 660 average time/residue: 0.2321 time to fit residues: 251.7065 Evaluate side-chains 671 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 474 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1080 LYS Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 701 TYR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 929 GLU Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1012 CYS Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain N residue 374 LYS Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 155 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 303 ARG Chi-restraints excluded: chain O residue 318 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 340 GLU Chi-restraints excluded: chain O residue 360 THR Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 548 ILE Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain P residue 235 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 314 GLU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 417 optimal weight: 0.9990 chunk 350 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 424 optimal weight: 2.9990 chunk 331 optimal weight: 8.9990 chunk 290 optimal weight: 0.0070 chunk 176 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 189 optimal weight: 0.4980 chunk 268 optimal weight: 6.9990 overall best weight: 2.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN C 237 GLN D 8 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN H 137 GLN N 289 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.151824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119288 restraints weight = 58729.477| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.18 r_work: 0.3302 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42539 Z= 0.137 Angle : 0.593 19.823 57628 Z= 0.302 Chirality : 0.043 0.191 6491 Planarity : 0.004 0.078 7261 Dihedral : 10.704 143.277 6130 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.81 % Allowed : 22.79 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.12), residues: 5052 helix: 0.69 (0.12), residues: 1846 sheet: -0.81 (0.20), residues: 662 loop : -1.81 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 54 TYR 0.018 0.001 TYR A1172 PHE 0.023 0.001 PHE M 252 TRP 0.013 0.001 TRP C 31 HIS 0.008 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00320 (42511) covalent geometry : angle 0.58094 (57589) hydrogen bonds : bond 0.04109 ( 1509) hydrogen bonds : angle 4.74322 ( 4197) metal coordination : bond 0.00776 ( 28) metal coordination : angle 4.66439 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 488 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: A 361 GLN cc_start: 0.8208 (mt0) cc_final: 0.7983 (mt0) REVERT: A 414 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.7092 (p-80) REVERT: A 477 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.6494 (mt0) REVERT: A 749 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5783 (pm20) REVERT: A 1008 LEU cc_start: 0.8468 (tp) cc_final: 0.8220 (tp) REVERT: A 1398 ASP cc_start: 0.8760 (m-30) cc_final: 0.8474 (m-30) REVERT: B 152 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.6651 (tpt) REVERT: B 159 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7940 (m110) REVERT: B 168 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6866 (mm-30) REVERT: B 213 LYS cc_start: 0.6547 (OUTLIER) cc_final: 0.5277 (tmmt) REVERT: B 332 ILE cc_start: 0.6189 (OUTLIER) cc_final: 0.5708 (tp) REVERT: B 448 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.5567 (mtmt) REVERT: B 469 MET cc_start: 0.8801 (tpp) cc_final: 0.8417 (tpp) REVERT: B 539 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.5199 (mp0) REVERT: B 614 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8139 (mt) REVERT: B 624 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.5945 (p0) REVERT: B 673 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7371 (tp) REVERT: B 816 ASP cc_start: 0.6847 (p0) cc_final: 0.6610 (m-30) REVERT: B 901 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8481 (ptt90) REVERT: B 929 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7287 (pm20) REVERT: C 172 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: C 284 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: D 97 LYS cc_start: 0.4177 (pttp) cc_final: 0.3756 (mtmm) REVERT: E 200 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8220 (ptt180) REVERT: I 83 PHE cc_start: 0.6491 (p90) cc_final: 0.6271 (p90) REVERT: K 139 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7807 (tp) REVERT: M 133 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6318 (mtmt) REVERT: M 141 ASN cc_start: 0.7278 (OUTLIER) cc_final: 0.6855 (p0) REVERT: M 166 MET cc_start: 0.6039 (mmp) cc_final: 0.5062 (ptt) REVERT: M 238 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6922 (p0) REVERT: N 297 MET cc_start: 0.6553 (ttm) cc_final: 0.6243 (ttt) REVERT: N 313 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7062 (pt) REVERT: N 411 ARG cc_start: 0.7193 (ptt90) cc_final: 0.6922 (ptt90) REVERT: O 152 HIS cc_start: 0.5333 (OUTLIER) cc_final: 0.4010 (t70) REVERT: O 206 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7882 (pt) REVERT: O 254 ASN cc_start: 0.7788 (m-40) cc_final: 0.7267 (t0) REVERT: O 520 LYS cc_start: 0.5305 (ttmm) cc_final: 0.5077 (tmtt) REVERT: P 314 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: Q 30 LYS cc_start: 0.7136 (tmtt) cc_final: 0.6916 (tmtt) outliers start: 217 outliers final: 171 residues processed: 670 average time/residue: 0.2401 time to fit residues: 263.1925 Evaluate side-chains 674 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 477 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1080 LYS Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 701 TYR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 929 GLU Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1012 CYS Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain N residue 374 LYS Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 152 HIS Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 303 ARG Chi-restraints excluded: chain O residue 318 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 340 GLU Chi-restraints excluded: chain O residue 360 THR Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 548 ILE Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain O residue 648 TRP Chi-restraints excluded: chain P residue 235 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 314 GLU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 324 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 232 optimal weight: 0.6980 chunk 464 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 497 optimal weight: 6.9990 chunk 354 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 367 ASN A1346 HIS B 708 GLN C 237 GLN D 8 ASN G 36 ASN G 41 ASN H 137 GLN N 289 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.153379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121405 restraints weight = 58572.747| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.02 r_work: 0.3333 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 42539 Z= 0.109 Angle : 0.563 18.038 57628 Z= 0.287 Chirality : 0.042 0.181 6491 Planarity : 0.004 0.076 7261 Dihedral : 10.557 142.471 6130 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.92 % Allowed : 23.55 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.12), residues: 5052 helix: 0.90 (0.13), residues: 1840 sheet: -0.72 (0.20), residues: 669 loop : -1.72 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 54 TYR 0.017 0.001 TYR Q 127 PHE 0.026 0.001 PHE M 252 TRP 0.012 0.001 TRP C 31 HIS 0.027 0.001 HIS O 152 Details of bonding type rmsd covalent geometry : bond 0.00245 (42511) covalent geometry : angle 0.55319 (57589) hydrogen bonds : bond 0.03701 ( 1509) hydrogen bonds : angle 4.61668 ( 4197) metal coordination : bond 0.00575 ( 28) metal coordination : angle 4.02281 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 498 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6249 (mp0) REVERT: A 361 GLN cc_start: 0.8133 (mt0) cc_final: 0.7900 (mt0) REVERT: A 414 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.6963 (p-80) REVERT: A 477 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.6440 (mt0) REVERT: A 649 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7152 (m-30) REVERT: A 1008 LEU cc_start: 0.8376 (tp) cc_final: 0.8099 (tp) REVERT: A 1398 ASP cc_start: 0.8755 (m-30) cc_final: 0.8460 (m-30) REVERT: B 152 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.6628 (tpt) REVERT: B 168 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6922 (mm-30) REVERT: B 213 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.5095 (tmmt) REVERT: B 332 ILE cc_start: 0.5966 (OUTLIER) cc_final: 0.5532 (tp) REVERT: B 365 MET cc_start: 0.7885 (mmm) cc_final: 0.7649 (mmp) REVERT: B 448 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.5526 (mtmt) REVERT: B 469 MET cc_start: 0.8789 (tpp) cc_final: 0.8423 (tpp) REVERT: B 539 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.4990 (mp0) REVERT: B 624 ASP cc_start: 0.6749 (OUTLIER) cc_final: 0.5931 (p0) REVERT: B 673 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7275 (tp) REVERT: B 929 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: C 278 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: D 97 LYS cc_start: 0.4153 (pttp) cc_final: 0.3744 (mtmm) REVERT: E 57 MET cc_start: 0.7308 (mtt) cc_final: 0.6977 (tpt) REVERT: E 200 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7990 (ptt180) REVERT: G 152 ARG cc_start: 0.6264 (ptp-170) cc_final: 0.6001 (ptm-80) REVERT: K 139 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7732 (tp) REVERT: M 133 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6386 (mtmt) REVERT: M 141 ASN cc_start: 0.7309 (OUTLIER) cc_final: 0.6877 (p0) REVERT: M 166 MET cc_start: 0.5906 (mmp) cc_final: 0.4913 (ptt) REVERT: M 238 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6890 (p0) REVERT: N 297 MET cc_start: 0.6532 (ttm) cc_final: 0.6257 (ttt) REVERT: N 313 LEU cc_start: 0.7264 (pp) cc_final: 0.6986 (pt) REVERT: N 411 ARG cc_start: 0.7117 (ptt90) cc_final: 0.6828 (ptt90) REVERT: O 206 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7893 (pt) REVERT: O 254 ASN cc_start: 0.7751 (m-40) cc_final: 0.7217 (t0) REVERT: O 520 LYS cc_start: 0.5271 (ttmm) cc_final: 0.5051 (tmtt) REVERT: O 608 ARG cc_start: 0.3646 (mmt-90) cc_final: 0.3400 (ttp-170) REVERT: P 314 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7392 (tp30) outliers start: 177 outliers final: 135 residues processed: 634 average time/residue: 0.2352 time to fit residues: 244.8590 Evaluate side-chains 634 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 479 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1080 LYS Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 701 TYR Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 929 GLU Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1012 CYS Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 303 ARG Chi-restraints excluded: chain O residue 318 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 340 GLU Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 548 ILE Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain P residue 235 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 314 GLU Chi-restraints excluded: chain Q residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 457 optimal weight: 8.9990 chunk 216 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 150 optimal weight: 0.4980 chunk 356 optimal weight: 4.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN C 237 GLN D 8 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN N 289 HIS ** O 43 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 = 0.3933 r_free = 0.3933 target = 0.149913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117384 restraints weight = 58691.193| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.19 r_work: 0.3270 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 42539 Z= 0.235 Angle : 0.703 23.629 57628 Z= 0.354 Chirality : 0.047 0.205 6491 Planarity : 0.005 0.072 7261 Dihedral : 10.841 146.590 6130 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.24 % Allowed : 23.44 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.12), residues: 5052 helix: 0.49 (0.12), residues: 1847 sheet: -0.79 (0.20), residues: 639 loop : -1.89 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 95 TYR 0.026 0.002 TYR A1172 PHE 0.023 0.002 PHE B 678 TRP 0.012 0.002 TRP M 119 HIS 0.043 0.002 HIS A1346 Details of bonding type rmsd covalent geometry : bond 0.00568 (42511) covalent geometry : angle 0.68695 (57589) hydrogen bonds : bond 0.04987 ( 1509) hydrogen bonds : angle 4.91262 ( 4197) metal coordination : bond 0.01330 ( 28) metal coordination : angle 5.71021 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 486 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6403 (mp0) REVERT: A 235 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7921 (mttp) REVERT: A 361 GLN cc_start: 0.8243 (mt0) cc_final: 0.7991 (mt0) REVERT: A 414 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7185 (p-80) REVERT: A 477 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.6440 (mt0) REVERT: A 736 HIS cc_start: 0.7480 (t70) cc_final: 0.7189 (t70) REVERT: A 749 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.5797 (pm20) REVERT: A 1398 ASP cc_start: 0.8755 (m-30) cc_final: 0.8481 (m-30) REVERT: B 152 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.6610 (tpt) REVERT: B 168 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7233 (mm-30) REVERT: B 213 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.5271 (tmmt) REVERT: B 217 GLN cc_start: 0.6687 (pp30) cc_final: 0.6486 (pp30) REVERT: B 332 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5647 (tp) REVERT: B 448 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.5602 (mtmt) REVERT: B 539 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.5372 (mp0) REVERT: B 673 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7446 (tp) REVERT: B 901 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8500 (ptt90) REVERT: C 172 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7893 (mt0) REVERT: C 278 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: D 97 LYS cc_start: 0.4175 (pttp) cc_final: 0.3758 (mtmm) REVERT: E 200 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8224 (ptt180) REVERT: I 2 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5945 (mp) REVERT: K 142 MET cc_start: 0.7635 (tpt) cc_final: 0.7329 (tpp) REVERT: M 133 LYS cc_start: 0.6653 (OUTLIER) cc_final: 0.6238 (mtmt) REVERT: M 141 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.6949 (p0) REVERT: M 166 MET cc_start: 0.6151 (mmp) cc_final: 0.5169 (ptt) REVERT: M 238 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6994 (p0) REVERT: M 278 ILE cc_start: 0.7117 (mm) cc_final: 0.6840 (mm) REVERT: N 287 HIS cc_start: 0.6882 (OUTLIER) cc_final: 0.6472 (m-70) REVERT: N 297 MET cc_start: 0.6500 (ttm) cc_final: 0.6244 (ttt) REVERT: N 313 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7132 (pt) REVERT: N 411 ARG cc_start: 0.7234 (ptt90) cc_final: 0.6891 (ptt90) REVERT: O 206 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7916 (pt) REVERT: O 254 ASN cc_start: 0.7859 (m-40) cc_final: 0.7298 (t0) REVERT: O 520 LYS cc_start: 0.5430 (ttmm) cc_final: 0.5196 (tmtt) REVERT: P 314 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7372 (tp30) outliers start: 191 outliers final: 159 residues processed: 644 average time/residue: 0.2346 time to fit residues: 247.1786 Evaluate side-chains 662 residues out of total 4521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 480 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 414 HIS Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 995 VAL Chi-restraints excluded: chain A residue 1021 ASN Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 701 TYR Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1012 CYS Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 287 HIS Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain N residue 374 LYS Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 195 CYS Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 211 ILE Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 303 ARG Chi-restraints excluded: chain O residue 318 LEU Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 340 GLU Chi-restraints excluded: chain O residue 365 ASP Chi-restraints excluded: chain O residue 548 ILE Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 646 SER Chi-restraints excluded: chain P residue 235 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 314 GLU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 308 optimal weight: 0.9990 chunk 476 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 381 optimal weight: 1.9990 chunk 281 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 349 optimal weight: 0.6980 chunk 316 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 209 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 708 GLN C 237 GLN D 8 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN N 289 HIS ** O 43 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 = 0.3977 r_free = 0.3977 target = 0.153574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121713 restraints weight = 58920.277| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.07 r_work: 0.3333 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42539 Z= 0.111 Angle : 0.576 17.571 57628 Z= 0.292 Chirality : 0.042 0.282 6491 Planarity : 0.004 0.075 7261 Dihedral : 10.532 141.050 6128 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.90 % Allowed : 24.81 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.12), residues: 5052 helix: 0.87 (0.13), residues: 1843 sheet: -0.68 (0.20), residues: 673 loop : -1.72 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 54 TYR 0.019 0.001 TYR O 476 PHE 0.027 0.001 PHE M 252 TRP 0.013 0.001 TRP C 31 HIS 0.010 0.001 HIS A1346 Details of bonding type rmsd covalent geometry : bond 0.00251 (42511) covalent geometry : angle 0.56565 (57589) hydrogen bonds : bond 0.03670 ( 1509) hydrogen bonds : angle 4.64159 ( 4197) metal coordination : bond 0.00601 ( 28) metal coordination : angle 4.19905 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13137.44 seconds wall clock time: 224 minutes 38.44 seconds (13478.44 seconds total)