Starting phenix.real_space_refine on Tue Sep 15 19:47:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rie_4890/09_2026/6rie_4890.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rie_4890/09_2026/6rie_4890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rie_4890/09_2026/6rie_4890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rie_4890/09_2026/6rie_4890.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rie_4890/09_2026/6rie_4890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rie_4890/09_2026/6rie_4890.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rie_4890/09_2026/6rie_4890.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rie_4890/09_2026/6rie_4890.cif" } resolution = 3.1 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8814 atoms to isotropic. 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 4 6.06 5 P 42 5.49 5 Mg 2 5.21 5 S 161 5.16 5 C 23319 2.51 5 N 6104 2.21 5 O 6951 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36583 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 10330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10330 Classifications: {'peptide': 1285} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1240} Chain: "B" Number of atoms: 9089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9089 Classifications: {'peptide': 1129} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1076} Chain breaks: 3 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2475 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1024 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "L" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2345 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 9, 'TRANS': 277} Chain: "N" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "O" Number of atoms: 6661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 6661 Classifications: {'peptide': 822} Link IDs: {'PTRANS': 30, 'TRANS': 791} Chain breaks: 3 Chain: "P" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 350 Unusual residues: {'GDP': 1} Classifications: {'RNAv2': 15, 'undetermined': 1} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna3p': 14, None: 1} Not linked: pdbres="GDP P 1 " pdbres=" A P 2 " Chain breaks: 1 Chain: "S" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 929 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Chain: "T" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 360 SG CYS A 49 46.599 90.788 91.537 1.00 46.07 S ATOM 382 SG CYS A 52 47.166 94.376 91.096 1.00 43.17 S ATOM 434 SG CYS A 59 50.256 91.904 91.542 1.00 35.72 S ATOM 694 SG CYS A 90 55.449 79.269 138.557 1.00 74.88 S ATOM 718 SG CYS A 93 53.704 81.396 139.996 1.00 76.26 S ATOM 1016 SG CYS A 130 55.980 80.765 141.620 1.00 79.81 S ATOM 1059 SG CYS A 135 52.147 78.381 141.745 1.00 85.90 S ATOM 18828 SG CYS B1087 50.073 102.080 104.692 1.00 33.26 S ATOM 18851 SG CYS B1090 50.138 98.552 106.128 1.00 33.48 S ATOM 18940 SG CYS B1103 48.206 99.170 103.052 1.00 36.59 S ATOM 18965 SG CYS B1106 47.455 100.482 106.899 1.00 38.67 S ATOM 25310 SG CYS J 7 111.266 77.088 57.165 1.00 16.99 S ATOM 25329 SG CYS J 10 112.892 79.280 54.749 1.00 19.49 S ATOM 25566 SG CYS J 39 114.497 78.750 58.418 1.00 21.87 S ATOM 25572 SG CYS J 40 114.158 76.737 55.147 1.00 20.15 S Time building chain proxies: 7.53, per 1000 atoms: 0.21 Number of scatterers: 36583 At special positions: 0 Unit cell: (148.05, 163.8, 174.3, 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 4 29.99 S 161 16.00 P 42 15.00 Mg 2 11.99 O 6951 8.00 N 6104 7.00 C 23319 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 40 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 39 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " Number of angles added : 21 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8440 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 50 sheets defined 38.2% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.726A pdb=" N ARG A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 118 " --> pdb=" O HIS A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 118' Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 218 through 230 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 250 through 253 removed outlier: 3.754A pdb=" N ILE A 253 " --> pdb=" O ILE A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 253' Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.575A pdb=" N TYR A 264 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.610A pdb=" N SER A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 321 through 330 removed outlier: 3.669A pdb=" N VAL A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 409 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 458 through 471 removed outlier: 4.467A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 572 Processing helix chain 'A' and resid 585 through 615 removed outlier: 3.694A pdb=" N TYR A 609 " --> pdb=" O ALA A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 656 removed outlier: 3.844A pdb=" N LEU A 637 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 653 " --> pdb=" O MET A 649 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'A' and resid 672 through 681 removed outlier: 3.678A pdb=" N TYR A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 700 removed outlier: 3.560A pdb=" N ARG A 700 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 764 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 809 through 821 removed outlier: 3.612A pdb=" N LYS A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 removed outlier: 3.817A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 875 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.685A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.834A pdb=" N TYR A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 944 Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.588A pdb=" N PHE A 964 " --> pdb=" O GLY A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 996 removed outlier: 3.556A pdb=" N SER A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 994 " --> pdb=" O SER A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1004 removed outlier: 3.542A pdb=" N ASN A1004 " --> pdb=" O GLY A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1047 removed outlier: 3.663A pdb=" N VAL A1037 " --> pdb=" O THR A1033 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1093 removed outlier: 3.768A pdb=" N SER A1083 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Proline residue: A1090 - end of helix removed outlier: 3.626A pdb=" N ALA A1093 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1136 removed outlier: 4.560A pdb=" N GLU A1132 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A1136 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 Processing helix chain 'A' and resid 1155 through 1170 removed outlier: 3.611A pdb=" N THR A1170 " --> pdb=" O ALA A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1218 through 1227 removed outlier: 3.646A pdb=" N ASN A1222 " --> pdb=" O LYS A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1241 Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'A' and resid 1264 through 1282 Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.695A pdb=" N PHE B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 88 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.535A pdb=" N VAL B 261 " --> pdb=" O PRO B 257 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 303 through 313 Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.543A pdb=" N ASN B 320 " --> pdb=" O PRO B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.701A pdb=" N LYS B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 392 removed outlier: 3.874A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 413 removed outlier: 3.906A pdb=" N ALA B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 498 through 516 removed outlier: 3.585A pdb=" N TYR B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 removed outlier: 4.113A pdb=" N ILE B 521 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 544 removed outlier: 3.543A pdb=" N MET B 544 " --> pdb=" O ASN B 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 541 through 544' Processing helix chain 'B' and resid 545 through 557 removed outlier: 3.973A pdb=" N ASP B 551 " --> pdb=" O ASP B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 610 removed outlier: 3.712A pdb=" N GLU B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.584A pdb=" N PHE B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.769A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.642A pdb=" N ASN B 682 " --> pdb=" O ILE B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 695 removed outlier: 4.098A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 731 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.796A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.732A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 941 removed outlier: 3.512A pdb=" N ILE B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 977 removed outlier: 3.579A pdb=" N TYR B 965 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 990 removed outlier: 3.532A pdb=" N LEU B 985 " --> pdb=" O SER B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1065 removed outlier: 3.575A pdb=" N GLY B1065 " --> pdb=" O LEU B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1075 Processing helix chain 'B' and resid 1103 through 1109 Processing helix chain 'B' and resid 1121 through 1133 removed outlier: 3.527A pdb=" N LYS B1125 " --> pdb=" O THR B1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.604A pdb=" N TRP C 52 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.603A pdb=" N VAL C 155 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 157' Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.602A pdb=" N VAL C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 207 through 229 removed outlier: 4.131A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 283 through 303 Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.696A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS E 11 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE E 12 " --> pdb=" O TYR E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 146 through 152 Processing helix chain 'F' and resid 63 through 75 removed outlier: 4.024A pdb=" N ARG F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 112 through 124 removed outlier: 3.570A pdb=" N VAL F 116 " --> pdb=" O ASN F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 161 removed outlier: 3.669A pdb=" N TYR F 153 " --> pdb=" O PHE F 149 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN F 161 " --> pdb=" O ILE F 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 36 removed outlier: 3.614A pdb=" N LEU G 36 " --> pdb=" O TYR G 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 23 Processing helix chain 'J' and resid 27 through 32 Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'L' and resid 2 through 10 Processing helix chain 'L' and resid 36 through 40 Processing helix chain 'L' and resid 42 through 47 Processing helix chain 'L' and resid 47 through 56 removed outlier: 3.841A pdb=" N MET L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 65 Processing helix chain 'L' and resid 73 through 82 Processing helix chain 'L' and resid 132 through 136 removed outlier: 3.698A pdb=" N LEU L 136 " --> pdb=" O TYR L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 142 removed outlier: 3.770A pdb=" N VAL L 140 " --> pdb=" O THR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 175 removed outlier: 3.617A pdb=" N SER L 174 " --> pdb=" O ARG L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 218 Processing helix chain 'L' and resid 238 through 268 removed outlier: 4.165A pdb=" N PHE L 248 " --> pdb=" O LYS L 244 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG L 251 " --> pdb=" O GLU L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 287 removed outlier: 3.938A pdb=" N ARG L 280 " --> pdb=" O ASN L 276 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG L 281 " --> pdb=" O LYS L 277 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 25 removed outlier: 3.638A pdb=" N TYR O 14 " --> pdb=" O THR O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 55 removed outlier: 3.997A pdb=" N LEU O 50 " --> pdb=" O PRO O 46 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR O 51 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 85 No H-bonds generated for 'chain 'O' and resid 83 through 85' Processing helix chain 'O' and resid 91 through 97 Processing helix chain 'O' and resid 137 through 140 Processing helix chain 'O' and resid 174 through 182 Processing helix chain 'O' and resid 204 through 220 Processing helix chain 'O' and resid 243 through 248 removed outlier: 3.949A pdb=" N ILE O 247 " --> pdb=" O LYS O 244 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL O 248 " --> pdb=" O GLN O 245 " (cutoff:3.500A) Processing helix chain 'O' and resid 327 through 337 Processing helix chain 'O' and resid 359 through 370 removed outlier: 3.626A pdb=" N VAL O 363 " --> pdb=" O THR O 359 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR O 368 " --> pdb=" O ASP O 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 503 Processing helix chain 'O' and resid 510 through 523 removed outlier: 3.516A pdb=" N ILE O 514 " --> pdb=" O GLN O 510 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU O 516 " --> pdb=" O ASN O 512 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE O 523 " --> pdb=" O ARG O 519 " (cutoff:3.500A) Processing helix chain 'O' and resid 562 through 581 removed outlier: 3.529A pdb=" N GLY O 566 " --> pdb=" O ARG O 562 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR O 580 " --> pdb=" O LEU O 576 " (cutoff:3.500A) Processing helix chain 'O' and resid 604 through 611 Processing helix chain 'O' and resid 623 through 638 Processing helix chain 'O' and resid 658 through 668 removed outlier: 3.828A pdb=" N SER O 662 " --> pdb=" O THR O 658 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL O 666 " --> pdb=" O SER O 662 " (cutoff:3.500A) Processing helix chain 'O' and resid 680 through 684 removed outlier: 3.633A pdb=" N TYR O 683 " --> pdb=" O ALA O 680 " (cutoff:3.500A) Processing helix chain 'O' and resid 686 through 688 No H-bonds generated for 'chain 'O' and resid 686 through 688' Processing helix chain 'O' and resid 689 through 697 Processing helix chain 'O' and resid 713 through 718 Processing helix chain 'O' and resid 733 through 736 Processing helix chain 'O' and resid 767 through 778 removed outlier: 3.677A pdb=" N TYR O 778 " --> pdb=" O VAL O 774 " (cutoff:3.500A) Processing helix chain 'O' and resid 788 through 801 removed outlier: 4.734A pdb=" N LYS O 797 " --> pdb=" O GLU O 793 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N PHE O 798 " --> pdb=" O ARG O 794 " (cutoff:3.500A) Processing helix chain 'O' and resid 802 through 806 removed outlier: 3.933A pdb=" N MET O 805 " --> pdb=" O ALA O 802 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU O 806 " --> pdb=" O SER O 803 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 802 through 806' Processing helix chain 'O' and resid 808 through 823 removed outlier: 3.751A pdb=" N LYS O 823 " --> pdb=" O ARG O 819 " (cutoff:3.500A) Processing helix chain 'O' and resid 828 through 833 Processing helix chain 'S' and resid 37 through 51 removed outlier: 3.806A pdb=" N SER S 49 " --> pdb=" O MET S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 79 removed outlier: 4.702A pdb=" N GLY S 75 " --> pdb=" O LYS S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 105 Processing helix chain 'S' and resid 113 through 131 removed outlier: 3.864A pdb=" N PHE S 117 " --> pdb=" O THR S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 147 removed outlier: 3.757A pdb=" N ASP S 146 " --> pdb=" O SER S 143 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR S 147 " --> pdb=" O TYR S 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 143 through 147' Processing sheet with id=AA1, first strand: chain 'A' and resid 1228 through 1231 removed outlier: 6.021A pdb=" N ILE A 4 " --> pdb=" O GLU B1143 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLU B1143 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 6 " --> pdb=" O ASP B1141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.699A pdb=" N GLY A 64 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.054A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 210 removed outlier: 3.797A pdb=" N PHE A 208 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 282 removed outlier: 3.982A pdb=" N ILE B1051 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.618A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.295A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AB2, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB3, first strand: chain 'A' and resid 766 through 768 removed outlier: 6.458A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB5, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB6, first strand: chain 'A' and resid 1106 through 1111 Processing sheet with id=AB7, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 3.674A pdb=" N LYS A1015 " --> pdb=" O GLU A1012 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 135 through 137 removed outlier: 3.827A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 135 through 137 removed outlier: 3.827A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TYR A1254 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE G 50 " --> pdb=" O PRO G 71 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE G 48 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR G 75 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.603A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYS B 104 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS B 116 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL B 106 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE B 114 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.603A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AC4, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.759A pdb=" N ASN B 169 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.518A pdb=" N ARG B 181 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 231 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC7, first strand: chain 'B' and resid 598 through 599 removed outlier: 3.881A pdb=" N GLU B 598 " --> pdb=" O ASP B 595 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 535 through 540 removed outlier: 5.503A pdb=" N LEU B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B 532 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 538 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 removed outlier: 6.660A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 870 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 852 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 715 removed outlier: 6.660A pdb=" N LYS B 864 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU B 861 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS B 866 " --> pdb=" O VAL B 859 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 859 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 868 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 857 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 870 " --> pdb=" O GLU B 855 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD3, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.838A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1084 through 1086 removed outlier: 4.224A pdb=" N VAL B1084 " --> pdb=" O ILE B1118 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD6, first strand: chain 'C' and resid 5 through 13 removed outlier: 3.700A pdb=" N ILE C 188 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD8, first strand: chain 'C' and resid 37 through 43 removed outlier: 6.434A pdb=" N GLU C 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASN C 43 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR C 138 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.521A pdb=" N HIS C 126 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 233 through 234 removed outlier: 6.365A pdb=" N LYS C 233 " --> pdb=" O TYR C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 35 through 40 removed outlier: 8.541A pdb=" N VAL E 60 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE E 82 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLN E 62 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE E 84 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE E 64 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE E 95 " --> pdb=" O PRO E 81 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE E 83 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.008A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 84 through 90 removed outlier: 6.522A pdb=" N ILE G 105 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA G 156 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS G 107 " --> pdb=" O ALA G 156 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE G 158 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 12 through 16 removed outlier: 4.424A pdb=" N VAL L 179 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE L 176 " --> pdb=" O VAL L 201 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL L 201 " --> pdb=" O PHE L 176 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL L 99 " --> pdb=" O ILE L 154 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS L 156 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA L 101 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS L 88 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ASP L 102 " --> pdb=" O LYS L 88 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 25 through 29 removed outlier: 4.071A pdb=" N ILE L 232 " --> pdb=" O ASN L 26 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER L 28 " --> pdb=" O PHE L 230 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE L 230 " --> pdb=" O SER L 28 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 34 through 42 removed outlier: 7.890A pdb=" N CYS O 119 " --> pdb=" O ARG O 114 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG O 114 " --> pdb=" O CYS O 119 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU O 121 " --> pdb=" O GLU O 112 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU O 112 " --> pdb=" O LEU O 121 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU O 123 " --> pdb=" O VAL O 110 " (cutoff:3.500A) removed outlier: 9.750A pdb=" N VAL O 103 " --> pdb=" O LYS O 79 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LYS O 79 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU O 143 " --> pdb=" O LEU O 166 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU O 38 " --> pdb=" O PHE O 195 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 227 through 228 removed outlier: 6.948A pdb=" N PHE O 301 " --> pdb=" O ILE O 315 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP O 310 " --> pdb=" O VAL O 346 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LYS O 348 " --> pdb=" O TRP O 310 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL O 312 " --> pdb=" O LYS O 348 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 238 through 241 removed outlier: 7.323A pdb=" N ILE O 389 " --> pdb=" O TYR O 381 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N TYR O 381 " --> pdb=" O ILE O 389 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 436 through 441 removed outlier: 6.722A pdb=" N LYS O 428 " --> pdb=" O TYR O 439 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER O 441 " --> pdb=" O TYR O 426 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR O 426 " --> pdb=" O SER O 441 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASN O 431 " --> pdb=" O ASP O 400 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N ASP O 400 " --> pdb=" O ASN O 431 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE O 480 " --> pdb=" O PRO O 492 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU O 482 " --> pdb=" O LEU O 490 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 415 through 417 Processing sheet with id=AF3, first strand: chain 'O' and resid 450 through 453 removed outlier: 8.458A pdb=" N LYS O 471 " --> pdb=" O ASN O 463 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 646 through 651 removed outlier: 6.405A pdb=" N VAL O 594 " --> pdb=" O VAL O 617 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR O 619 " --> pdb=" O VAL O 594 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA O 596 " --> pdb=" O THR O 619 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS O 593 " --> pdb=" O ILE O 674 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ASP O 676 " --> pdb=" O LYS O 593 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU O 595 " --> pdb=" O ASP O 676 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLN O 678 " --> pdb=" O LEU O 595 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE O 597 " --> pdb=" O GLN O 678 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN O 673 " --> pdb=" O LYS O 706 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU O 708 " --> pdb=" O ASN O 673 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE O 675 " --> pdb=" O LEU O 708 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR O 710 " --> pdb=" O ILE O 675 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TRP O 677 " --> pdb=" O THR O 710 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N MET O 712 " --> pdb=" O TRP O 677 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS O 843 " --> pdb=" O GLY O 704 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS O 706 " --> pdb=" O PHE O 841 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE O 841 " --> pdb=" O LYS O 706 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU O 708 " --> pdb=" O TYR O 839 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR O 839 " --> pdb=" O LEU O 708 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR O 710 " --> pdb=" O VAL O 837 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL O 837 " --> pdb=" O THR O 710 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER O 842 " --> pdb=" O LEU O 782 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU O 782 " --> pdb=" O SER O 842 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 724 through 727 1507 hydrogen bonds defined for protein. 4200 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: 10.28 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11003 1.34 - 1.46: 7582 1.46 - 1.58: 18462 1.58 - 1.70: 79 1.70 - 1.82: 260 Bond restraints: 37386 Sorted by residual: bond pdb=" C4' DA T 28 " pdb=" C3' DA T 28 " ideal model delta sigma weight residual 1.529 1.497 0.032 1.00e-02 1.00e+04 1.02e+01 bond pdb=" C3' DA T 28 " pdb=" O3' DA T 28 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.78e+00 bond pdb=" C4' DT T 30 " pdb=" C3' DT T 30 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.00e-02 1.00e+04 9.02e+00 bond pdb=" C4' DA T 29 " pdb=" C3' DA T 29 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.00e-02 1.00e+04 8.86e+00 bond pdb=" C3' DC T 33 " pdb=" C2' DC T 33 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.39e+00 ... (remaining 37381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 50203 2.95 - 5.89: 447 5.89 - 8.84: 41 8.84 - 11.78: 8 11.78 - 14.73: 3 Bond angle restraints: 50702 Sorted by residual: angle pdb=" C ASP O 307 " pdb=" N LYS O 308 " pdb=" CA LYS O 308 " ideal model delta sigma weight residual 121.54 134.43 -12.89 1.91e+00 2.74e-01 4.56e+01 angle pdb=" C VAL G 62 " pdb=" N ASN G 63 " pdb=" CA ASN G 63 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" O4' DA T 28 " pdb=" C4' DA T 28 " pdb=" C3' DA T 28 " ideal model delta sigma weight residual 106.00 102.50 3.50 6.00e-01 2.78e+00 3.41e+01 angle pdb=" O4' DC T 27 " pdb=" C4' DC T 27 " pdb=" C3' DC T 27 " ideal model delta sigma weight residual 106.00 102.50 3.50 6.00e-01 2.78e+00 3.41e+01 angle pdb=" C3' A P 19 " pdb=" O3' A P 19 " pdb=" P A P 20 " ideal model delta sigma weight residual 119.70 125.53 -5.83 1.20e+00 6.94e-01 2.36e+01 ... (remaining 50697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.36: 21683 29.36 - 58.73: 867 58.73 - 88.09: 60 88.09 - 117.45: 4 117.45 - 146.81: 1 Dihedral angle restraints: 22615 sinusoidal: 9555 harmonic: 13060 Sorted by residual: dihedral pdb=" O5' U P 24 " pdb=" C5' U P 24 " pdb=" C4' U P 24 " pdb=" C3' U P 24 " ideal model delta sinusoidal sigma weight residual 180.00 134.18 45.82 3 6.40e+00 2.44e-02 4.52e+01 dihedral pdb=" O5' U P 22 " pdb=" C5' U P 22 " pdb=" C4' U P 22 " pdb=" C3' U P 22 " ideal model delta sinusoidal sigma weight residual -60.00 -21.81 -38.19 3 6.40e+00 2.44e-02 3.69e+01 dihedral pdb=" CA ASN O 512 " pdb=" C ASN O 512 " pdb=" N ILE O 513 " pdb=" CA ILE O 513 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 22612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4987 0.076 - 0.152: 719 0.152 - 0.228: 63 0.228 - 0.303: 7 0.303 - 0.379: 4 Chirality restraints: 5780 Sorted by residual: chirality pdb=" CB VAL O 475 " pdb=" CA VAL O 475 " pdb=" CG1 VAL O 475 " pdb=" CG2 VAL O 475 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C3' A P 19 " pdb=" C4' A P 19 " pdb=" O3' A P 19 " pdb=" C2' A P 19 " both_signs ideal model delta sigma weight residual False -2.50 -2.17 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB VAL B 677 " pdb=" CA VAL B 677 " pdb=" CG1 VAL B 677 " pdb=" CG2 VAL B 677 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 5777 not shown) Planarity restraints: 6261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS O 686 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO O 687 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO O 687 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO O 687 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL O 475 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO O 476 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO O 476 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO O 476 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 100 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO A 101 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.039 5.00e-02 4.00e+02 ... (remaining 6258 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 443 2.63 - 3.20: 29828 3.20 - 3.77: 56571 3.77 - 4.33: 82884 4.33 - 4.90: 134928 Nonbonded interactions: 304654 Sorted by model distance: nonbonded pdb=" OD1 ASP A 417 " pdb="MG MG A1301 " model vdw 2.067 2.170 nonbonded pdb=" OD1 ASP A 419 " pdb="MG MG A1301 " model vdw 2.088 2.170 nonbonded pdb=" O3' G P 30 " pdb="MG MG A1301 " model vdw 2.128 2.170 nonbonded pdb=" OH TYR B 38 " pdb=" O PRO B 131 " model vdw 2.266 3.040 nonbonded pdb=" O TYR A 486 " pdb=" OH TYR A 506 " model vdw 2.273 3.040 ... (remaining 304649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 41.980 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 0.199 37403 Z= 0.261 Angle : 0.843 34.798 50723 Z= 0.441 Chirality : 0.054 0.379 5780 Planarity : 0.006 0.076 6261 Dihedral : 15.084 146.813 14175 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.07 % Allowed : 7.78 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -3.21 (0.10), residues: 4382 helix: -2.42 (0.09), residues: 1503 sheet: -1.18 (0.18), residues: 717 loop : -2.19 (0.11), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 115 TYR 0.040 0.002 TYR O 649 PHE 0.046 0.002 PHE A 938 TRP 0.030 0.002 TRP O 677 HIS 0.011 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.25 (37386) covalent geometry : angle 0.77194 / 0.44 (50702) hydrogen bonds : bond 0.15382 / 10.23 ( 1467) hydrogen bonds : angle 6.78347 / 4.63 ( 4200) metal coordination : bond 0.08169 / 5.61 ( 16) metal coordination : angle 16.68839 / 10.84 ( 21) Misc. bond : bond 0.03113 / 1.64 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 505 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8216 (tt0) cc_final: 0.7761 (tp40) REVERT: A 413 ASN cc_start: 0.8568 (t0) cc_final: 0.8096 (t0) REVERT: A 520 ASP cc_start: 0.7861 (m-30) cc_final: 0.7617 (t0) REVERT: A 677 MET cc_start: 0.8370 (ttp) cc_final: 0.8104 (ttt) REVERT: A 1047 PHE cc_start: 0.8926 (m-80) cc_final: 0.8719 (m-80) REVERT: A 1057 GLU cc_start: 0.7897 (tt0) cc_final: 0.7693 (mt-10) REVERT: A 1084 LYS cc_start: 0.8235 (tttt) cc_final: 0.7651 (mttp) REVERT: A 1152 ASP cc_start: 0.8156 (t70) cc_final: 0.7528 (t0) REVERT: B 205 TYR cc_start: 0.8018 (m-80) cc_final: 0.7585 (m-80) REVERT: B 216 GLN cc_start: 0.7423 (pm20) cc_final: 0.7219 (pm20) REVERT: B 256 MET cc_start: 0.8984 (mmt) cc_final: 0.8521 (mmt) REVERT: B 313 HIS cc_start: 0.7057 (t-90) cc_final: 0.6672 (t70) REVERT: B 994 ILE cc_start: 0.9022 (mt) cc_final: 0.8624 (mp) REVERT: C 195 LYS cc_start: 0.7917 (tttt) cc_final: 0.7650 (tttt) REVERT: J 26 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8675 (mmtm) REVERT: O 32 TYR cc_start: 0.8306 (m-10) cc_final: 0.8041 (m-10) REVERT: O 308 LYS cc_start: 0.7618 (pttm) cc_final: 0.7087 (ttpp) REVERT: O 348 LYS cc_start: 0.7389 (mmtt) cc_final: 0.6837 (tttt) REVERT: O 490 LEU cc_start: 0.8468 (mm) cc_final: 0.8260 (mt) REVERT: O 739 MET cc_start: 0.7735 (ttt) cc_final: 0.7505 (ttt) REVERT: O 814 PHE cc_start: 0.8178 (t80) cc_final: 0.7931 (t80) outliers start: 3 outliers final: 1 residues processed: 507 average time/residue: 0.2651 time to fit residues: 213.5410 Evaluate side-chains 393 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 74 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.1980 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN A 114 HIS A 162 ASN A 167 GLN A 218 ASN A 356 ASN A 412 GLN A 435 GLN A 459 GLN A 548 HIS A 720 ASN A 822 GLN A 894 ASN A 941 GLN A 994 ASN A1081 ASN A1239 HIS B 61 ASN B 101 ASN B 169 ASN B 305 ASN B 318 HIS B 371 HIS B 376 ASN B 391 ASN B 408 ASN B 481 GLN B 487 GLN B 576 ASN B 682 ASN B 693 GLN B 740 GLN B 778 HIS B 779 GLN B 789 ASN B 858 GLN B 971 GLN B1040 GLN C 8 ASN C 109 ASN C 137 GLN C 230 HIS E 129 GLN F 119 GLN G 7 ASN G 29 ASN G 100 GLN G 157 ASN J 16 HIS J 53 ASN L 7 ASN L 51 ASN L 234 ASN ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 182 HIS O 218 HIS O 466 ASN O 486 ASN ** O 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 550 ASN O 673 ASN O 818 ASN S 58 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105334 restraints weight = 50237.554| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.47 r_work: 0.3041 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 37403 Z= 0.132 Angle : 0.569 17.613 50723 Z= 0.296 Chirality : 0.044 0.271 5780 Planarity : 0.004 0.059 6261 Dihedral : 9.436 145.006 5276 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.86 % Allowed : 10.47 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.83 (0.12), residues: 4382 helix: -0.64 (0.12), residues: 1526 sheet: -0.85 (0.19), residues: 713 loop : -1.73 (0.12), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 114 TYR 0.016 0.001 TYR A 466 PHE 0.033 0.001 PHE A 938 TRP 0.016 0.001 TRP O 677 HIS 0.005 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (37386) covalent geometry : angle 0.55306 / 0.29 (50702) hydrogen bonds : bond 0.04381 / 2.91 ( 1467) hydrogen bonds : angle 4.97049 / 3.38 ( 4200) metal coordination : bond 0.01543 / 0.97 ( 16) metal coordination : angle 6.55285 / 4.28 ( 21) Misc. bond : bond 0.00576 / 0.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 429 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8622 (tt0) cc_final: 0.8196 (tp40) REVERT: A 413 ASN cc_start: 0.8908 (t0) cc_final: 0.8447 (t0) REVERT: A 520 ASP cc_start: 0.8462 (m-30) cc_final: 0.7947 (t0) REVERT: A 619 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7454 (p) REVERT: A 677 MET cc_start: 0.8844 (ttp) cc_final: 0.8547 (ttt) REVERT: A 1031 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7129 (tm-30) REVERT: A 1047 PHE cc_start: 0.9075 (m-80) cc_final: 0.8811 (m-80) REVERT: A 1057 GLU cc_start: 0.8261 (tt0) cc_final: 0.8040 (mt-10) REVERT: A 1086 MET cc_start: 0.8823 (mmm) cc_final: 0.8592 (mmp) REVERT: A 1152 ASP cc_start: 0.8762 (t70) cc_final: 0.8175 (t0) REVERT: B 205 TYR cc_start: 0.8349 (m-80) cc_final: 0.8068 (m-80) REVERT: B 226 LYS cc_start: 0.8190 (ptpt) cc_final: 0.7606 (tttp) REVERT: B 256 MET cc_start: 0.9311 (mmt) cc_final: 0.8906 (mmt) REVERT: B 286 TYR cc_start: 0.7465 (t80) cc_final: 0.7221 (t80) REVERT: B 313 HIS cc_start: 0.7415 (t-90) cc_final: 0.6892 (t70) REVERT: B 354 MET cc_start: 0.9062 (mmm) cc_final: 0.8594 (mmm) REVERT: B 374 LEU cc_start: 0.8185 (tp) cc_final: 0.7810 (tt) REVERT: B 409 HIS cc_start: 0.7134 (t-90) cc_final: 0.6827 (t-90) REVERT: B 478 ARG cc_start: 0.8172 (mtp180) cc_final: 0.7885 (mtp180) REVERT: B 945 ASN cc_start: 0.8201 (p0) cc_final: 0.7900 (p0) REVERT: C 105 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: C 276 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8313 (mtm-85) REVERT: G 84 ILE cc_start: 0.5345 (OUTLIER) cc_final: 0.4685 (mp) REVERT: J 26 LYS cc_start: 0.9229 (mmmm) cc_final: 0.8858 (mmtm) REVERT: L 267 MET cc_start: 0.7685 (mtt) cc_final: 0.7243 (mtt) REVERT: L 279 GLN cc_start: 0.8245 (tp-100) cc_final: 0.8026 (tp-100) REVERT: O 348 LYS cc_start: 0.7408 (mmtt) cc_final: 0.6646 (tttt) REVERT: O 490 LEU cc_start: 0.8475 (mm) cc_final: 0.8247 (mt) REVERT: O 676 ASP cc_start: 0.7966 (t70) cc_final: 0.7647 (t70) REVERT: O 814 PHE cc_start: 0.8104 (t80) cc_final: 0.7871 (t80) REVERT: S 84 ASN cc_start: 0.8282 (m-40) cc_final: 0.8053 (m110) REVERT: S 90 ASN cc_start: 0.7376 (t0) cc_final: 0.7046 (t0) REVERT: S 135 ASN cc_start: 0.8047 (t0) cc_final: 0.7772 (t0) REVERT: S 149 ASN cc_start: 0.7506 (m-40) cc_final: 0.7177 (m-40) outliers start: 35 outliers final: 18 residues processed: 448 average time/residue: 0.2435 time to fit residues: 177.8440 Evaluate side-chains 407 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 386 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 750 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 236 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 286 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 415 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 306 optimal weight: 10.0000 chunk 198 optimal weight: 0.0170 chunk 314 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN A 167 GLN A 218 ASN A 894 ASN J 53 ASN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 122 HIS ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 486 ASN O 509 ASN O 521 GLN O 678 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105552 restraints weight = 50177.715| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.49 r_work: 0.3022 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 37403 Z= 0.130 Angle : 0.534 13.948 50723 Z= 0.279 Chirality : 0.044 0.275 5780 Planarity : 0.004 0.057 6261 Dihedral : 9.215 144.328 5276 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.33 % Allowed : 12.27 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.16 (0.12), residues: 4382 helix: 0.14 (0.13), residues: 1541 sheet: -0.68 (0.19), residues: 724 loop : -1.46 (0.12), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 24 TYR 0.016 0.001 TYR A 466 PHE 0.033 0.001 PHE A 938 TRP 0.017 0.001 TRP O 677 HIS 0.009 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (37386) covalent geometry : angle 0.52292 / 0.28 (50702) hydrogen bonds : bond 0.04056 / 2.70 ( 1467) hydrogen bonds : angle 4.66989 / 3.17 ( 4200) metal coordination : bond 0.01228 / 0.77 ( 16) metal coordination : angle 5.26788 / 3.49 ( 21) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 405 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8610 (tt0) cc_final: 0.8185 (tp40) REVERT: A 413 ASN cc_start: 0.8920 (t0) cc_final: 0.8451 (t0) REVERT: A 520 ASP cc_start: 0.8450 (m-30) cc_final: 0.7989 (t0) REVERT: A 677 MET cc_start: 0.8828 (ttp) cc_final: 0.8552 (ttt) REVERT: A 783 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8086 (m-10) REVERT: A 929 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8799 (mt) REVERT: A 1047 PHE cc_start: 0.9044 (m-80) cc_final: 0.8818 (m-80) REVERT: A 1057 GLU cc_start: 0.8174 (tt0) cc_final: 0.7963 (mt-10) REVERT: A 1086 MET cc_start: 0.8779 (mmm) cc_final: 0.8572 (mmp) REVERT: A 1152 ASP cc_start: 0.8778 (t70) cc_final: 0.8207 (t0) REVERT: B 205 TYR cc_start: 0.8372 (m-80) cc_final: 0.8065 (m-80) REVERT: B 216 GLN cc_start: 0.7818 (pm20) cc_final: 0.7379 (pm20) REVERT: B 226 LYS cc_start: 0.8209 (ptpt) cc_final: 0.7668 (tttp) REVERT: B 256 MET cc_start: 0.9299 (mmt) cc_final: 0.8901 (mmt) REVERT: B 286 TYR cc_start: 0.7449 (t80) cc_final: 0.7179 (t80) REVERT: B 313 HIS cc_start: 0.7414 (t-90) cc_final: 0.6892 (t70) REVERT: B 354 MET cc_start: 0.9064 (mmm) cc_final: 0.8597 (mmm) REVERT: B 372 ASP cc_start: 0.7681 (m-30) cc_final: 0.7432 (m-30) REVERT: B 478 ARG cc_start: 0.8132 (mtp180) cc_final: 0.7804 (mtp180) REVERT: B 649 MET cc_start: 0.8252 (mmp) cc_final: 0.8021 (mmm) REVERT: B 945 ASN cc_start: 0.8246 (p0) cc_final: 0.7995 (p0) REVERT: C 105 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8196 (m-30) REVERT: C 201 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7458 (mt-10) REVERT: C 276 ARG cc_start: 0.8433 (mtm-85) cc_final: 0.8212 (mtm-85) REVERT: F 109 MET cc_start: 0.8900 (mpp) cc_final: 0.8700 (mmt) REVERT: G 84 ILE cc_start: 0.5340 (OUTLIER) cc_final: 0.4689 (mp) REVERT: J 26 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8851 (mmtm) REVERT: L 69 MET cc_start: 0.6852 (mtm) cc_final: 0.6410 (ppp) REVERT: L 279 GLN cc_start: 0.8311 (tp-100) cc_final: 0.8020 (tp-100) REVERT: O 114 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7354 (ttm-80) REVERT: O 297 GLU cc_start: 0.5401 (tp30) cc_final: 0.4988 (tp30) REVERT: O 348 LYS cc_start: 0.7449 (mmtt) cc_final: 0.6719 (tttt) REVERT: O 814 PHE cc_start: 0.8105 (t80) cc_final: 0.7832 (t80) REVERT: S 84 ASN cc_start: 0.8290 (m-40) cc_final: 0.8067 (m110) REVERT: S 135 ASN cc_start: 0.8007 (t0) cc_final: 0.7650 (t0) outliers start: 54 outliers final: 30 residues processed: 441 average time/residue: 0.2312 time to fit residues: 167.3353 Evaluate side-chains 420 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 386 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain S residue 128 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 414 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 253 optimal weight: 0.9990 chunk 366 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 257 optimal weight: 0.0170 chunk 131 optimal weight: 3.9990 chunk 172 optimal weight: 0.0770 chunk 75 optimal weight: 2.9990 chunk 357 optimal weight: 7.9990 chunk 266 optimal weight: 3.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 HIS ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 429 HIS B 754 GLN L 7 ASN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 58 ASN S 149 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105032 restraints weight = 49914.177| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.47 r_work: 0.3040 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37403 Z= 0.131 Angle : 0.518 12.346 50723 Z= 0.271 Chirality : 0.044 0.274 5780 Planarity : 0.003 0.056 6261 Dihedral : 9.072 143.115 5276 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.58 % Allowed : 13.04 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -0.75 (0.12), residues: 4382 helix: 0.55 (0.13), residues: 1548 sheet: -0.50 (0.19), residues: 714 loop : -1.27 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1031 TYR 0.014 0.001 TYR B 340 PHE 0.031 0.001 PHE A 938 TRP 0.016 0.001 TRP O 677 HIS 0.011 0.001 HIS L 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (37386) covalent geometry : angle 0.50946 / 0.27 (50702) hydrogen bonds : bond 0.03861 / 2.57 ( 1467) hydrogen bonds : angle 4.52153 / 3.07 ( 4200) metal coordination : bond 0.01114 / 0.70 ( 16) metal coordination : angle 4.63713 / 3.10 ( 21) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 394 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8599 (tt0) cc_final: 0.8179 (tp40) REVERT: A 413 ASN cc_start: 0.8917 (t0) cc_final: 0.8442 (t0) REVERT: A 520 ASP cc_start: 0.8448 (m-30) cc_final: 0.8007 (t0) REVERT: A 677 MET cc_start: 0.8826 (ttp) cc_final: 0.8558 (ttt) REVERT: A 783 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8181 (m-10) REVERT: A 1031 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7620 (tm-30) REVERT: A 1152 ASP cc_start: 0.8755 (t70) cc_final: 0.8231 (t0) REVERT: A 1265 GLU cc_start: 0.8094 (pp20) cc_final: 0.7559 (pp20) REVERT: B 205 TYR cc_start: 0.8375 (m-80) cc_final: 0.8059 (m-80) REVERT: B 216 GLN cc_start: 0.7833 (pm20) cc_final: 0.7434 (pm20) REVERT: B 226 LYS cc_start: 0.8165 (ptpt) cc_final: 0.7671 (tttp) REVERT: B 256 MET cc_start: 0.9316 (mmt) cc_final: 0.8945 (mmt) REVERT: B 286 TYR cc_start: 0.7442 (t80) cc_final: 0.7201 (t80) REVERT: B 313 HIS cc_start: 0.7431 (t-90) cc_final: 0.6918 (t70) REVERT: B 354 MET cc_start: 0.9104 (mmm) cc_final: 0.8757 (mmm) REVERT: B 372 ASP cc_start: 0.7691 (m-30) cc_final: 0.7446 (m-30) REVERT: B 478 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7750 (mtp180) REVERT: B 945 ASN cc_start: 0.8089 (p0) cc_final: 0.7838 (p0) REVERT: C 105 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8166 (m-30) REVERT: C 201 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7518 (mt-10) REVERT: C 276 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8229 (mtm-85) REVERT: G 84 ILE cc_start: 0.5187 (OUTLIER) cc_final: 0.4563 (mp) REVERT: J 26 LYS cc_start: 0.9246 (mmmm) cc_final: 0.8858 (mmtm) REVERT: L 69 MET cc_start: 0.6816 (mtm) cc_final: 0.6342 (ppp) REVERT: L 279 GLN cc_start: 0.8338 (tp-100) cc_final: 0.8127 (tp-100) REVERT: O 97 ASP cc_start: 0.8298 (t0) cc_final: 0.7842 (m-30) REVERT: O 114 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7400 (ttm-80) REVERT: O 297 GLU cc_start: 0.5166 (tp30) cc_final: 0.4734 (tp30) REVERT: O 307 ASP cc_start: 0.7433 (t0) cc_final: 0.6899 (t0) REVERT: O 308 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7657 (pttm) REVERT: O 348 LYS cc_start: 0.7461 (mmtt) cc_final: 0.6748 (tttt) REVERT: O 757 MET cc_start: 0.8388 (mtt) cc_final: 0.8033 (mtp) REVERT: O 814 PHE cc_start: 0.8017 (t80) cc_final: 0.7688 (t80) REVERT: S 135 ASN cc_start: 0.8104 (t0) cc_final: 0.7694 (t0) outliers start: 64 outliers final: 41 residues processed: 438 average time/residue: 0.2347 time to fit residues: 169.3720 Evaluate side-chains 419 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 374 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 308 LYS Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 631 GLU Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 1 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 424 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 261 ASN A 894 ASN B 967 GLN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 486 ASN O 678 GLN S 145 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102127 restraints weight = 50112.333| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.53 r_work: 0.2991 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 37403 Z= 0.232 Angle : 0.589 12.683 50723 Z= 0.307 Chirality : 0.047 0.277 5780 Planarity : 0.004 0.057 6261 Dihedral : 9.173 143.531 5276 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.10 % Allowed : 13.33 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -0.69 (0.12), residues: 4382 helix: 0.57 (0.13), residues: 1553 sheet: -0.48 (0.19), residues: 717 loop : -1.20 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 51 TYR 0.021 0.002 TYR O 333 PHE 0.035 0.002 PHE A 938 TRP 0.030 0.002 TRP O 677 HIS 0.008 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.23 (37386) covalent geometry : angle 0.58092 / 0.31 (50702) hydrogen bonds : bond 0.04480 / 2.98 ( 1467) hydrogen bonds : angle 4.63371 / 3.16 ( 4200) metal coordination : bond 0.01598 / 0.93 ( 16) metal coordination : angle 4.81116 / 3.20 ( 21) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 384 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: A 239 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8120 (t) REVERT: A 344 GLN cc_start: 0.8620 (tt0) cc_final: 0.8225 (tp40) REVERT: A 413 ASN cc_start: 0.8918 (t0) cc_final: 0.8441 (t0) REVERT: A 520 ASP cc_start: 0.8526 (m-30) cc_final: 0.8091 (t0) REVERT: A 677 MET cc_start: 0.8863 (ttp) cc_final: 0.8591 (ttt) REVERT: A 783 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8342 (m-10) REVERT: A 1084 LYS cc_start: 0.8500 (tttt) cc_final: 0.8089 (ttmm) REVERT: A 1152 ASP cc_start: 0.8815 (t70) cc_final: 0.8307 (t0) REVERT: A 1265 GLU cc_start: 0.8167 (pp20) cc_final: 0.7661 (pp20) REVERT: B 205 TYR cc_start: 0.8367 (m-80) cc_final: 0.8137 (m-80) REVERT: B 216 GLN cc_start: 0.7784 (pm20) cc_final: 0.7450 (pm20) REVERT: B 226 LYS cc_start: 0.8209 (ptpt) cc_final: 0.7731 (tttp) REVERT: B 256 MET cc_start: 0.9311 (mmt) cc_final: 0.8847 (mmt) REVERT: B 286 TYR cc_start: 0.7546 (t80) cc_final: 0.7253 (t80) REVERT: B 409 HIS cc_start: 0.7311 (t-90) cc_final: 0.6945 (t70) REVERT: B 478 ARG cc_start: 0.8137 (mtp180) cc_final: 0.7899 (mtp180) REVERT: B 945 ASN cc_start: 0.8105 (p0) cc_final: 0.7882 (p0) REVERT: B 1016 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9041 (mt) REVERT: C 201 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7510 (mt-10) REVERT: C 276 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.8265 (mtm-85) REVERT: G 84 ILE cc_start: 0.5356 (OUTLIER) cc_final: 0.4711 (mp) REVERT: J 26 LYS cc_start: 0.9279 (mmmm) cc_final: 0.8922 (mmtm) REVERT: L 7 ASN cc_start: 0.8319 (m-40) cc_final: 0.7867 (m110) REVERT: L 69 MET cc_start: 0.6646 (mtm) cc_final: 0.6289 (ppp) REVERT: L 196 MET cc_start: 0.8039 (tmm) cc_final: 0.7628 (tmm) REVERT: O 97 ASP cc_start: 0.8347 (t0) cc_final: 0.7962 (m-30) REVERT: O 297 GLU cc_start: 0.5520 (tp30) cc_final: 0.5128 (tp30) REVERT: O 348 LYS cc_start: 0.7529 (mmtt) cc_final: 0.6767 (tttt) REVERT: O 814 PHE cc_start: 0.8042 (t80) cc_final: 0.7783 (t80) REVERT: S 135 ASN cc_start: 0.8159 (t0) cc_final: 0.7840 (t0) outliers start: 85 outliers final: 58 residues processed: 444 average time/residue: 0.2388 time to fit residues: 174.1138 Evaluate side-chains 437 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 375 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 631 GLU Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 191 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 317 optimal weight: 6.9990 chunk 274 optimal weight: 2.9990 chunk 286 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 409 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 894 ASN B 967 GLN G 37 HIS L 121 ASN ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104269 restraints weight = 49992.956| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.51 r_work: 0.3018 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37403 Z= 0.135 Angle : 0.524 12.063 50723 Z= 0.274 Chirality : 0.044 0.277 5780 Planarity : 0.003 0.056 6261 Dihedral : 9.035 141.627 5276 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.98 % Allowed : 14.25 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.12), residues: 4382 helix: 0.83 (0.13), residues: 1555 sheet: -0.42 (0.19), residues: 715 loop : -1.09 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 304 TYR 0.015 0.001 TYR B 340 PHE 0.030 0.001 PHE A 938 TRP 0.018 0.001 TRP O 677 HIS 0.008 0.001 HIS L 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (37386) covalent geometry : angle 0.51641 / 0.27 (50702) hydrogen bonds : bond 0.03920 / 2.60 ( 1467) hydrogen bonds : angle 4.48976 / 3.05 ( 4200) metal coordination : bond 0.01126 / 0.70 ( 16) metal coordination : angle 4.47767 / 2.97 ( 21) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 385 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8142 (t) REVERT: A 344 GLN cc_start: 0.8575 (tt0) cc_final: 0.8189 (tp40) REVERT: A 413 ASN cc_start: 0.8872 (t0) cc_final: 0.8418 (t0) REVERT: A 489 GLU cc_start: 0.7983 (pm20) cc_final: 0.7723 (pm20) REVERT: A 520 ASP cc_start: 0.8492 (m-30) cc_final: 0.8019 (t0) REVERT: A 631 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 677 MET cc_start: 0.8846 (ttp) cc_final: 0.8586 (ttt) REVERT: A 783 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8278 (m-10) REVERT: A 1031 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 1084 LYS cc_start: 0.8478 (tttt) cc_final: 0.8073 (ttmm) REVERT: A 1152 ASP cc_start: 0.8769 (t70) cc_final: 0.8250 (t0) REVERT: A 1265 GLU cc_start: 0.8182 (pp20) cc_final: 0.7756 (pp20) REVERT: B 205 TYR cc_start: 0.8380 (m-80) cc_final: 0.8161 (m-80) REVERT: B 216 GLN cc_start: 0.7701 (pm20) cc_final: 0.7382 (pm20) REVERT: B 226 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7716 (tttp) REVERT: B 256 MET cc_start: 0.9276 (mmt) cc_final: 0.8882 (mmt) REVERT: B 286 TYR cc_start: 0.7499 (t80) cc_final: 0.7215 (t80) REVERT: B 354 MET cc_start: 0.9088 (mmm) cc_final: 0.8680 (mmm) REVERT: B 372 ASP cc_start: 0.7713 (m-30) cc_final: 0.7470 (m-30) REVERT: B 409 HIS cc_start: 0.7252 (t-90) cc_final: 0.6921 (t70) REVERT: B 478 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7727 (mtp180) REVERT: B 945 ASN cc_start: 0.8059 (p0) cc_final: 0.7839 (p0) REVERT: C 105 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: C 276 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8248 (mtm-85) REVERT: G 51 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8343 (mtp-110) REVERT: G 84 ILE cc_start: 0.5381 (OUTLIER) cc_final: 0.4731 (mp) REVERT: J 26 LYS cc_start: 0.9254 (mmmm) cc_final: 0.8897 (mmtm) REVERT: L 7 ASN cc_start: 0.8351 (m-40) cc_final: 0.7818 (m110) REVERT: L 196 MET cc_start: 0.8032 (tmm) cc_final: 0.7633 (tmm) REVERT: O 97 ASP cc_start: 0.8315 (t0) cc_final: 0.7938 (m-30) REVERT: O 297 GLU cc_start: 0.5591 (tp30) cc_final: 0.5139 (tp30) REVERT: O 348 LYS cc_start: 0.7639 (mmtt) cc_final: 0.6883 (tttt) REVERT: O 757 MET cc_start: 0.8542 (mtt) cc_final: 0.8211 (mtp) REVERT: O 814 PHE cc_start: 0.7993 (t80) cc_final: 0.7697 (t80) REVERT: S 135 ASN cc_start: 0.8219 (t0) cc_final: 0.7866 (t0) outliers start: 80 outliers final: 63 residues processed: 444 average time/residue: 0.2297 time to fit residues: 167.5179 Evaluate side-chains 431 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 364 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 747 CYS Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1154 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 266 ILE Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 631 GLU Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 33 optimal weight: 3.9990 chunk 269 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 167 optimal weight: 0.0030 chunk 355 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 226 optimal weight: 0.6980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 894 ASN B 967 GLN F 111 GLN ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105558 restraints weight = 50041.233| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.48 r_work: 0.3042 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 37403 Z= 0.112 Angle : 0.508 11.748 50723 Z= 0.265 Chirality : 0.043 0.278 5780 Planarity : 0.003 0.056 6261 Dihedral : 8.914 140.455 5276 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.90 % Allowed : 14.94 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -0.22 (0.13), residues: 4382 helix: 1.06 (0.13), residues: 1553 sheet: -0.33 (0.19), residues: 715 loop : -0.98 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 304 TYR 0.014 0.001 TYR B 340 PHE 0.029 0.001 PHE A 938 TRP 0.014 0.001 TRP O 677 HIS 0.009 0.001 HIS L 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (37386) covalent geometry : angle 0.50069 / 0.26 (50702) hydrogen bonds : bond 0.03668 / 2.44 ( 1467) hydrogen bonds : angle 4.37534 / 2.97 ( 4200) metal coordination : bond 0.00978 / 0.62 ( 16) metal coordination : angle 4.19141 / 2.80 ( 21) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 383 time to evaluate : 1.437 Fit side-chains revert: symmetry clash REVERT: A 239 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8136 (t) REVERT: A 344 GLN cc_start: 0.8586 (tt0) cc_final: 0.8176 (tp40) REVERT: A 413 ASN cc_start: 0.8898 (t0) cc_final: 0.8445 (t0) REVERT: A 520 ASP cc_start: 0.8464 (m-30) cc_final: 0.7989 (t0) REVERT: A 631 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 677 MET cc_start: 0.8853 (ttp) cc_final: 0.8568 (ttt) REVERT: A 783 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8279 (m-10) REVERT: A 1031 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 1084 LYS cc_start: 0.8451 (tttt) cc_final: 0.8031 (ttmm) REVERT: A 1152 ASP cc_start: 0.8802 (t70) cc_final: 0.8284 (t0) REVERT: A 1265 GLU cc_start: 0.8172 (pp20) cc_final: 0.7738 (pp20) REVERT: B 205 TYR cc_start: 0.8372 (m-80) cc_final: 0.8131 (m-80) REVERT: B 216 GLN cc_start: 0.7537 (pm20) cc_final: 0.7221 (pm20) REVERT: B 226 LYS cc_start: 0.8155 (ptpt) cc_final: 0.7684 (tttp) REVERT: B 256 MET cc_start: 0.9253 (mmt) cc_final: 0.8859 (mmt) REVERT: B 286 TYR cc_start: 0.7493 (t80) cc_final: 0.7178 (t80) REVERT: B 289 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: B 354 MET cc_start: 0.9140 (mmm) cc_final: 0.8656 (mmm) REVERT: B 372 ASP cc_start: 0.7841 (m-30) cc_final: 0.7581 (m-30) REVERT: B 906 GLU cc_start: 0.7588 (mp0) cc_final: 0.7323 (mp0) REVERT: B 945 ASN cc_start: 0.8078 (p0) cc_final: 0.7850 (p0) REVERT: C 105 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8095 (m-30) REVERT: C 187 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8029 (p90) REVERT: C 231 MET cc_start: 0.7616 (tpt) cc_final: 0.7386 (tpt) REVERT: C 276 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.8228 (mtm-85) REVERT: G 51 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8208 (mtp-110) REVERT: G 84 ILE cc_start: 0.5222 (OUTLIER) cc_final: 0.4610 (mp) REVERT: J 26 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8864 (mmtm) REVERT: L 196 MET cc_start: 0.8103 (tmm) cc_final: 0.7692 (tmm) REVERT: O 97 ASP cc_start: 0.8268 (t0) cc_final: 0.7859 (m-30) REVERT: O 114 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7496 (ttm-80) REVERT: O 297 GLU cc_start: 0.5562 (tp30) cc_final: 0.5094 (tp30) REVERT: O 348 LYS cc_start: 0.7561 (mmtt) cc_final: 0.6824 (tttt) REVERT: O 757 MET cc_start: 0.8540 (mtt) cc_final: 0.8168 (mtp) REVERT: O 814 PHE cc_start: 0.7919 (t80) cc_final: 0.7626 (t80) REVERT: S 135 ASN cc_start: 0.8243 (t0) cc_final: 0.7878 (t0) REVERT: S 147 TYR cc_start: 0.7613 (m-80) cc_final: 0.7059 (m-80) outliers start: 77 outliers final: 61 residues processed: 441 average time/residue: 0.2326 time to fit residues: 168.9367 Evaluate side-chains 432 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 365 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 266 ILE Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 114 optimal weight: 3.9990 chunk 240 optimal weight: 0.7980 chunk 177 optimal weight: 0.1980 chunk 103 optimal weight: 0.6980 chunk 279 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 392 optimal weight: 0.5980 chunk 436 optimal weight: 0.9990 chunk 371 optimal weight: 7.9990 chunk 178 optimal weight: 0.7980 chunk 410 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 894 ASN B 967 GLN L 7 ASN ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 486 ASN O 678 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106152 restraints weight = 49868.622| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.47 r_work: 0.3047 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 37403 Z= 0.107 Angle : 0.503 11.763 50723 Z= 0.263 Chirality : 0.043 0.278 5780 Planarity : 0.003 0.056 6261 Dihedral : 8.870 140.000 5276 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.98 % Allowed : 15.04 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -0.12 (0.13), residues: 4382 helix: 1.17 (0.13), residues: 1552 sheet: -0.29 (0.20), residues: 713 loop : -0.91 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 304 TYR 0.014 0.001 TYR A 466 PHE 0.029 0.001 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.012 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (37386) covalent geometry : angle 0.49661 / 0.26 (50702) hydrogen bonds : bond 0.03595 / 2.39 ( 1467) hydrogen bonds : angle 4.34345 / 2.95 ( 4200) metal coordination : bond 0.00922 / 0.59 ( 16) metal coordination : angle 4.05534 / 2.71 ( 21) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 382 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 239 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8126 (t) REVERT: A 344 GLN cc_start: 0.8566 (tt0) cc_final: 0.8155 (tp40) REVERT: A 413 ASN cc_start: 0.8909 (t0) cc_final: 0.8464 (t0) REVERT: A 520 ASP cc_start: 0.8464 (m-30) cc_final: 0.7997 (t0) REVERT: A 536 MET cc_start: 0.8676 (mtt) cc_final: 0.8426 (mtt) REVERT: A 631 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 677 MET cc_start: 0.8855 (ttp) cc_final: 0.8574 (ttt) REVERT: A 783 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.8274 (m-10) REVERT: A 1031 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 1084 LYS cc_start: 0.8411 (tttt) cc_final: 0.7992 (ttmm) REVERT: A 1152 ASP cc_start: 0.8789 (t70) cc_final: 0.8282 (t0) REVERT: A 1265 GLU cc_start: 0.8147 (pp20) cc_final: 0.7748 (pp20) REVERT: B 205 TYR cc_start: 0.8372 (m-80) cc_final: 0.8051 (m-80) REVERT: B 216 GLN cc_start: 0.7523 (pm20) cc_final: 0.7232 (pm20) REVERT: B 226 LYS cc_start: 0.8160 (ptpt) cc_final: 0.7686 (tttp) REVERT: B 256 MET cc_start: 0.9229 (mmt) cc_final: 0.8909 (mmt) REVERT: B 286 TYR cc_start: 0.7483 (t80) cc_final: 0.7129 (t80) REVERT: B 289 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: B 354 MET cc_start: 0.9122 (mmm) cc_final: 0.8615 (mmm) REVERT: B 372 ASP cc_start: 0.7833 (m-30) cc_final: 0.7567 (m-30) REVERT: B 945 ASN cc_start: 0.8072 (p0) cc_final: 0.7850 (p0) REVERT: C 105 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8149 (m-30) REVERT: C 187 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8048 (p90) REVERT: C 231 MET cc_start: 0.7629 (tpt) cc_final: 0.7411 (tpt) REVERT: G 84 ILE cc_start: 0.5223 (OUTLIER) cc_final: 0.4614 (mp) REVERT: J 26 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8833 (mmtm) REVERT: L 196 MET cc_start: 0.8081 (tmm) cc_final: 0.7659 (tmm) REVERT: O 97 ASP cc_start: 0.8257 (t0) cc_final: 0.7838 (m-30) REVERT: O 114 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7501 (ttm-80) REVERT: O 297 GLU cc_start: 0.5578 (tp30) cc_final: 0.5109 (tp30) REVERT: O 757 MET cc_start: 0.8527 (mtt) cc_final: 0.8160 (mtp) REVERT: O 814 PHE cc_start: 0.7895 (t80) cc_final: 0.7569 (t80) REVERT: S 45 MET cc_start: 0.6832 (tpt) cc_final: 0.5713 (ptp) REVERT: S 135 ASN cc_start: 0.8242 (t0) cc_final: 0.7871 (t0) REVERT: S 147 TYR cc_start: 0.7595 (m-80) cc_final: 0.7061 (m-80) outliers start: 80 outliers final: 67 residues processed: 443 average time/residue: 0.2296 time to fit residues: 167.4556 Evaluate side-chains 442 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 369 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 266 ILE Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 351 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 359 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 316 optimal weight: 0.8980 chunk 306 optimal weight: 5.9990 chunk 239 optimal weight: 0.0030 chunk 25 optimal weight: 0.0070 overall best weight: 0.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 894 ASN A1217 ASN B 295 HIS B 967 GLN L 7 ASN L 46 GLN ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 729 HIS S 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106740 restraints weight = 49945.063| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.48 r_work: 0.3061 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 37403 Z= 0.100 Angle : 0.498 11.319 50723 Z= 0.259 Chirality : 0.043 0.279 5780 Planarity : 0.003 0.055 6261 Dihedral : 8.782 138.938 5276 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.93 % Allowed : 15.14 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.03 (0.13), residues: 4382 helix: 1.27 (0.13), residues: 1554 sheet: -0.19 (0.20), residues: 709 loop : -0.83 (0.13), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 51 TYR 0.014 0.001 TYR A 466 PHE 0.028 0.001 PHE A 938 TRP 0.013 0.001 TRP A 365 HIS 0.010 0.001 HIS L 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (37386) covalent geometry : angle 0.49163 / 0.26 (50702) hydrogen bonds : bond 0.03443 / 2.29 ( 1467) hydrogen bonds : angle 4.27515 / 2.90 ( 4200) metal coordination : bond 0.00835 / 0.54 ( 16) metal coordination : angle 3.86471 / 2.58 ( 21) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 396 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 136 MET cc_start: 0.5533 (tpt) cc_final: 0.5315 (tpt) REVERT: A 344 GLN cc_start: 0.8555 (tt0) cc_final: 0.8156 (tp40) REVERT: A 413 ASN cc_start: 0.8877 (t0) cc_final: 0.8456 (t0) REVERT: A 520 ASP cc_start: 0.8443 (m-30) cc_final: 0.8027 (t0) REVERT: A 631 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 677 MET cc_start: 0.8863 (ttp) cc_final: 0.8599 (ttt) REVERT: A 783 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8298 (m-10) REVERT: A 1031 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 1084 LYS cc_start: 0.8414 (tttt) cc_final: 0.7457 (mmtp) REVERT: A 1152 ASP cc_start: 0.8800 (t70) cc_final: 0.8356 (t0) REVERT: A 1265 GLU cc_start: 0.8165 (pp20) cc_final: 0.7829 (pp20) REVERT: B 205 TYR cc_start: 0.8357 (m-80) cc_final: 0.8053 (m-80) REVERT: B 216 GLN cc_start: 0.7505 (pm20) cc_final: 0.7223 (pm20) REVERT: B 226 LYS cc_start: 0.8124 (ptpt) cc_final: 0.7691 (tttp) REVERT: B 256 MET cc_start: 0.9197 (mmt) cc_final: 0.8887 (mmt) REVERT: B 286 TYR cc_start: 0.7467 (t80) cc_final: 0.7125 (t80) REVERT: B 289 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7732 (m-30) REVERT: B 295 HIS cc_start: 0.7526 (t-90) cc_final: 0.7153 (t-170) REVERT: B 354 MET cc_start: 0.9121 (mmm) cc_final: 0.8656 (mmm) REVERT: B 372 ASP cc_start: 0.7808 (m-30) cc_final: 0.7543 (m-30) REVERT: B 945 ASN cc_start: 0.8028 (p0) cc_final: 0.7813 (p0) REVERT: C 105 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: C 187 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8065 (p90) REVERT: G 51 ARG cc_start: 0.8510 (mtp85) cc_final: 0.8169 (mtp-110) REVERT: G 84 ILE cc_start: 0.5227 (OUTLIER) cc_final: 0.4635 (mp) REVERT: J 26 LYS cc_start: 0.9183 (mmmm) cc_final: 0.8819 (mmtm) REVERT: L 196 MET cc_start: 0.8130 (tmm) cc_final: 0.7740 (tmm) REVERT: O 97 ASP cc_start: 0.8234 (t0) cc_final: 0.7867 (m-30) REVERT: O 297 GLU cc_start: 0.5538 (tp30) cc_final: 0.5075 (tp30) REVERT: O 757 MET cc_start: 0.8535 (mtt) cc_final: 0.8171 (mtp) REVERT: O 814 PHE cc_start: 0.7934 (t80) cc_final: 0.7570 (t80) REVERT: S 45 MET cc_start: 0.6863 (tpt) cc_final: 0.5749 (ptp) REVERT: S 135 ASN cc_start: 0.8247 (t0) cc_final: 0.7816 (t0) REVERT: S 147 TYR cc_start: 0.7555 (m-80) cc_final: 0.7070 (m-80) outliers start: 78 outliers final: 61 residues processed: 452 average time/residue: 0.2249 time to fit residues: 166.2089 Evaluate side-chains 442 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 376 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 266 ILE Chi-restraints excluded: chain O residue 317 LEU Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 58 ASN Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 25 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 161 optimal weight: 0.6980 chunk 417 optimal weight: 0.9980 chunk 287 optimal weight: 0.9990 chunk 297 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 324 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 376 optimal weight: 0.3980 chunk 129 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 967 GLN ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106478 restraints weight = 49985.556| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.42 r_work: 0.3054 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37403 Z= 0.115 Angle : 0.504 11.535 50723 Z= 0.262 Chirality : 0.043 0.279 5780 Planarity : 0.003 0.055 6261 Dihedral : 8.780 138.977 5276 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.68 % Allowed : 15.73 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.05 (0.13), residues: 4382 helix: 1.29 (0.13), residues: 1554 sheet: -0.19 (0.20), residues: 710 loop : -0.81 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 304 TYR 0.014 0.001 TYR A 466 PHE 0.029 0.001 PHE A 938 TRP 0.014 0.001 TRP O 677 HIS 0.010 0.001 HIS L 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (37386) covalent geometry : angle 0.49825 / 0.26 (50702) hydrogen bonds : bond 0.03507 / 2.33 ( 1467) hydrogen bonds : angle 4.27843 / 2.90 ( 4200) metal coordination : bond 0.00892 / 0.57 ( 16) metal coordination : angle 3.89008 / 2.60 ( 21) Misc. bond : bond 0.00036 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 375 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8539 (tt0) cc_final: 0.8140 (tp40) REVERT: A 413 ASN cc_start: 0.8903 (t0) cc_final: 0.8459 (t0) REVERT: A 520 ASP cc_start: 0.8434 (m-30) cc_final: 0.8025 (t0) REVERT: A 631 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 677 MET cc_start: 0.8847 (ttp) cc_final: 0.8570 (ttt) REVERT: A 783 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8310 (m-10) REVERT: A 1031 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7582 (tm-30) REVERT: A 1084 LYS cc_start: 0.8396 (tttt) cc_final: 0.7406 (mmtp) REVERT: A 1152 ASP cc_start: 0.8817 (t70) cc_final: 0.8358 (t0) REVERT: A 1265 GLU cc_start: 0.8175 (pp20) cc_final: 0.7812 (pp20) REVERT: B 205 TYR cc_start: 0.8358 (m-80) cc_final: 0.8054 (m-80) REVERT: B 226 LYS cc_start: 0.8121 (ptpt) cc_final: 0.7673 (tttp) REVERT: B 256 MET cc_start: 0.9211 (mmt) cc_final: 0.8888 (mmt) REVERT: B 286 TYR cc_start: 0.7461 (t80) cc_final: 0.7118 (t80) REVERT: B 289 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: B 354 MET cc_start: 0.9148 (mmm) cc_final: 0.8662 (mmm) REVERT: B 372 ASP cc_start: 0.7806 (m-30) cc_final: 0.7531 (m-30) REVERT: B 945 ASN cc_start: 0.8045 (p0) cc_final: 0.7827 (p0) REVERT: C 105 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: C 187 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8060 (p90) REVERT: G 51 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8135 (mtp-110) REVERT: G 84 ILE cc_start: 0.5218 (OUTLIER) cc_final: 0.4640 (mp) REVERT: J 26 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8814 (mmtm) REVERT: L 196 MET cc_start: 0.8087 (tmm) cc_final: 0.7662 (tmm) REVERT: O 97 ASP cc_start: 0.8193 (t0) cc_final: 0.7806 (m-30) REVERT: O 297 GLU cc_start: 0.5519 (tp30) cc_final: 0.5054 (tp30) REVERT: O 757 MET cc_start: 0.8423 (mtt) cc_final: 0.8050 (mtp) REVERT: O 814 PHE cc_start: 0.7906 (t80) cc_final: 0.7540 (t80) REVERT: S 45 MET cc_start: 0.6840 (tpt) cc_final: 0.5718 (ptp) REVERT: S 135 ASN cc_start: 0.8181 (t0) cc_final: 0.7842 (t0) outliers start: 68 outliers final: 60 residues processed: 425 average time/residue: 0.2392 time to fit residues: 167.1305 Evaluate side-chains 435 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 370 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 852 ASP Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 737 CYS Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 956 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 266 ILE Chi-restraints excluded: chain O residue 317 LEU Chi-restraints excluded: chain O residue 362 VAL Chi-restraints excluded: chain O residue 475 VAL Chi-restraints excluded: chain O residue 565 LEU Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 750 VAL Chi-restraints excluded: chain O residue 751 VAL Chi-restraints excluded: chain S residue 128 ILE Chi-restraints excluded: chain S residue 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 437 optimal weight: 5.9990 chunk 6 optimal weight: 0.0570 chunk 207 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 402 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 391 optimal weight: 2.9990 chunk 341 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN B 967 GLN L 7 ASN ** L 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 550 ASN S 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104276 restraints weight = 49866.637| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.45 r_work: 0.3028 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37403 Z= 0.156 Angle : 0.534 11.451 50723 Z= 0.277 Chirality : 0.044 0.280 5780 Planarity : 0.004 0.056 6261 Dihedral : 8.856 139.783 5276 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.75 % Allowed : 15.70 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.01 (0.13), residues: 4382 helix: 1.23 (0.13), residues: 1554 sheet: -0.22 (0.20), residues: 712 loop : -0.81 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 304 TYR 0.016 0.001 TYR A 466 PHE 0.031 0.001 PHE A 938 TRP 0.020 0.001 TRP O 677 HIS 0.010 0.001 HIS L 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (37386) covalent geometry : angle 0.52755 / 0.28 (50702) hydrogen bonds : bond 0.03852 / 2.55 ( 1467) hydrogen bonds : angle 4.35902 / 2.96 ( 4200) metal coordination : bond 0.01070 / 0.66 ( 16) metal coordination : angle 4.10577 / 2.73 ( 21) Misc. bond : bond 0.00012 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10369.47 seconds wall clock time: 178 minutes 17.02 seconds (10697.02 seconds total)