Starting phenix.real_space_refine on Mon Sep 14 22:01:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vbc_31878/09_2026/7vbc_31878.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbc_31878/09_2026/7vbc_31878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vbc_31878/09_2026/7vbc_31878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbc_31878/09_2026/7vbc_31878.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vbc_31878/09_2026/7vbc_31878.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vbc_31878/09_2026/7vbc_31878.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vbc_31878/09_2026/7vbc_31878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbc_31878/09_2026/7vbc_31878.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.112 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 188 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 5 6.06 5 P 39 5.49 5 Mg 1 5.21 5 S 226 5.16 5 C 21078 2.51 5 N 5832 2.21 5 O 6233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.21s 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: 33414 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1477, 11775 Classifications: {'peptide': 1477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 71, 'TRANS': 1405} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8912 Classifications: {'peptide': 1123} Link IDs: {'PTRANS': 63, 'TRANS': 1059} Chain breaks: 1 Chain: "C" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2697 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain: "E" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1641 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 10, 'TRANS': 188} Chain breaks: 1 Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "H" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1176 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 863 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 379 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1105 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 24, 'TRANS': 126} Chain: "G" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1229 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "M" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 867 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "R" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 128 Classifications: {'RNAv2': 6} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna3p': 5} Chain: "T" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 415 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "U" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 282 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} 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: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 455 SG CYS A 64 60.733 54.068 57.791 1.00 70.96 S ATOM 529 SG CYS A 74 63.053 55.707 59.323 1.00 63.65 S ATOM 767 SG CYS A 104 61.764 106.330 46.911 1.00 76.34 S ATOM 1517 SG CYS A 205 64.778 108.738 46.331 1.00 87.17 S ATOM 20240 SG CYS B1070 74.206 64.067 47.501 1.00 51.70 S ATOM 20262 SG CYS B1073 74.291 67.017 45.977 1.00 54.67 S ATOM 20396 SG CYS B1098 71.031 63.729 46.863 1.00 72.84 S ATOM 20417 SG CYS B1101 72.960 64.544 44.248 1.00 83.89 S ATOM 26866 SG CYS J 7 77.793 46.388 127.804 1.00 34.15 S ATOM 26890 SG CYS J 10 81.523 44.624 129.269 1.00 21.98 S ATOM 27154 SG CYS J 44 80.852 47.764 129.666 1.00 21.89 S ATOM 27160 SG CYS J 45 78.846 45.572 131.825 1.00 24.31 S ATOM 28230 SG CYS L 19 36.383 46.381 111.478 1.00 40.38 S ATOM 28366 SG CYS L 36 34.024 44.317 109.993 1.00 44.67 S ATOM 28392 SG CYS L 39 32.941 46.773 111.820 1.00 47.99 S Residues with excluded nonbonded symmetry interactions: 161 residue: pdb=" N GLY N 127 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 127 " occ=0.00 residue: pdb=" N GLY N 144 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 144 " occ=0.00 residue: pdb=" N GLY N 153 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 153 " occ=0.00 residue: pdb=" N GLY N 154 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 154 " occ=0.00 residue: pdb=" N SER G 46 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER G 46 " occ=0.00 residue: pdb=" N CYS G 47 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS G 47 " occ=0.00 residue: pdb=" N LEU G 48 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU G 48 " occ=0.00 residue: pdb=" N VAL G 49 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL G 49 " occ=0.00 residue: pdb=" N ALA G 50 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 50 " occ=0.00 residue: pdb=" N GLY G 51 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY G 51 " occ=0.00 residue: pdb=" N PRO G 52 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO G 52 " occ=0.00 residue: pdb=" N HIS G 53 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS G 53 " occ=0.00 ... (remaining 149 not shown) Time building chain proxies: 7.01, per 1000 atoms: 0.21 Number of scatterers: 33414 At special positions: 0 Unit cell: (155.992, 161.262, 176.018, 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 5 29.99 S 226 16.00 P 39 15.00 Mg 1 11.99 O 6233 8.00 N 5832 7.00 C 21078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 64 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 205 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 104 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1073 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1101 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1070 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 44 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 7 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 39 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 36 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 19 " Number of angles added : 12 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7670 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 38 sheets defined 33.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 132 through 144 removed outlier: 4.667A pdb=" N TYR A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 172 removed outlier: 4.260A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.957A pdb=" N ALA A 179 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A 180 " --> pdb=" O GLN A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 184 through 199 removed outlier: 3.540A pdb=" N LYS A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.700A pdb=" N LYS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 296 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 322 through 348 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.503A pdb=" N ILE A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.908A pdb=" N ASP A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.642A pdb=" N LYS A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.830A pdb=" N TYR A 585 " --> pdb=" O ASN A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.784A pdb=" N GLU A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 634 through 642 removed outlier: 3.567A pdb=" N GLY A 638 " --> pdb=" O HIS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 684 through 696 removed outlier: 3.810A pdb=" N ASN A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 removed outlier: 3.654A pdb=" N MET A 732 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N CYS A 733 " --> pdb=" O ASP A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 770 Processing helix chain 'A' and resid 770 through 792 removed outlier: 3.674A pdb=" N SER A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 820 removed outlier: 3.608A pdb=" N THR A 820 " --> pdb=" O ILE A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 831 removed outlier: 3.772A pdb=" N ALA A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 851 Processing helix chain 'A' and resid 857 through 866 removed outlier: 3.847A pdb=" N ILE A 861 " --> pdb=" O ASP A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 881 removed outlier: 3.588A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 910 Processing helix chain 'A' and resid 944 through 948 Processing helix chain 'A' and resid 960 through 996 removed outlier: 3.655A pdb=" N LEU A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1030 removed outlier: 3.614A pdb=" N LYS A1028 " --> pdb=" O ASP A1025 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN A1030 " --> pdb=" O PRO A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1043 Processing helix chain 'A' and resid 1043 through 1051 Processing helix chain 'A' and resid 1052 through 1059 removed outlier: 3.705A pdb=" N VAL A1056 " --> pdb=" O HIS A1052 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1057 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1079 Processing helix chain 'A' and resid 1087 through 1092 Processing helix chain 'A' and resid 1095 through 1103 removed outlier: 4.500A pdb=" N ALA A1102 " --> pdb=" O GLU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1126 removed outlier: 4.043A pdb=" N GLN A1118 " --> pdb=" O SER A1114 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 3.765A pdb=" N ALA A1140 " --> pdb=" O LYS A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.531A pdb=" N VAL A1149 " --> pdb=" O PRO A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1179 removed outlier: 3.800A pdb=" N THR A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A1176 " --> pdb=" O GLN A1172 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A1179 " --> pdb=" O ALA A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1202 removed outlier: 3.948A pdb=" N THR A1194 " --> pdb=" O ASP A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1226 removed outlier: 3.758A pdb=" N LEU A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1244 through 1252 Processing helix chain 'A' and resid 1271 through 1286 removed outlier: 3.926A pdb=" N LYS A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A1280 " --> pdb=" O LYS A1276 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A1286 " --> pdb=" O LYS A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1293 No H-bonds generated for 'chain 'A' and resid 1291 through 1293' Processing helix chain 'A' and resid 1323 through 1331 removed outlier: 4.030A pdb=" N TYR A1326 " --> pdb=" O PRO A1323 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A1327 " --> pdb=" O HIS A1324 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLN A1328 " --> pdb=" O ALA A1325 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A1329 " --> pdb=" O TYR A1326 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A1330 " --> pdb=" O TYR A1327 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A1331 " --> pdb=" O GLN A1328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1323 through 1331' Processing helix chain 'A' and resid 1334 through 1345 Processing helix chain 'A' and resid 1345 through 1359 removed outlier: 4.115A pdb=" N MET A1351 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1509 removed outlier: 3.639A pdb=" N ARG A1501 " --> pdb=" O ALA A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1547 Processing helix chain 'A' and resid 1585 through 1592 removed outlier: 4.968A pdb=" N LYS A1590 " --> pdb=" O GLU A1587 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A1592 " --> pdb=" O PHE A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1612 Processing helix chain 'A' and resid 1613 through 1631 removed outlier: 4.247A pdb=" N ARG A1619 " --> pdb=" O GLU A1615 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1620 " --> pdb=" O ALA A1616 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A1631 " --> pdb=" O ASP A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1649 removed outlier: 3.758A pdb=" N LEU A1641 " --> pdb=" O ASP A1637 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A1643 " --> pdb=" O ARG A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1687 Processing helix chain 'A' and resid 1695 through 1702 removed outlier: 3.656A pdb=" N VAL A1702 " --> pdb=" O ALA A1698 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 51 removed outlier: 3.582A pdb=" N SER B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 46 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 61 removed outlier: 4.003A pdb=" N GLY B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.664A pdb=" N GLU B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 159' Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.677A pdb=" N LYS B 199 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR B 200 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY B 202 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.524A pdb=" N ILE B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.830A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 319 through 332 removed outlier: 3.554A pdb=" N ILE B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 358 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 376 through 404 removed outlier: 3.636A pdb=" N GLU B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.560A pdb=" N MET B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 removed outlier: 3.667A pdb=" N THR B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 removed outlier: 4.092A pdb=" N PHE B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 removed outlier: 3.652A pdb=" N TYR B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 removed outlier: 3.662A pdb=" N ALA B 479 " --> pdb=" O ALA B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 538 removed outlier: 3.652A pdb=" N CYS B 535 " --> pdb=" O PRO B 531 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.610A pdb=" N ILE B 640 " --> pdb=" O MET B 637 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE B 641 " --> pdb=" O GLU B 638 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET B 642 " --> pdb=" O GLN B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 642' Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.559A pdb=" N ASN B 680 " --> pdb=" O SER B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 removed outlier: 3.504A pdb=" N ASN B 685 " --> pdb=" O GLN B 681 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 690 " --> pdb=" O MET B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 730 Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 800 through 804 removed outlier: 3.838A pdb=" N LEU B 804 " --> pdb=" O PRO B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 924 removed outlier: 3.662A pdb=" N ARG B 923 " --> pdb=" O GLY B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 942 removed outlier: 4.199A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 968 Processing helix chain 'B' and resid 1038 through 1048 removed outlier: 3.761A pdb=" N ARG B1042 " --> pdb=" O GLY B1038 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP B1043 " --> pdb=" O GLU B1039 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B1044 " --> pdb=" O MET B1040 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS B1048 " --> pdb=" O ALA B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1062 Processing helix chain 'B' and resid 1113 through 1125 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 248 through 256 removed outlier: 3.953A pdb=" N GLU C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 317 through 341 Processing helix chain 'E' and resid 5 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.717A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.937A pdb=" N LYS E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 4.289A pdb=" N ILE E 126 " --> pdb=" O PRO E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 removed outlier: 3.845A pdb=" N THR E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.755A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 48 through 60 Processing helix chain 'K' and resid 93 through 128 removed outlier: 3.659A pdb=" N ASN K 101 " --> pdb=" O GLN K 97 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG K 128 " --> pdb=" O GLN K 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 36 Processing helix chain 'N' and resid 52 through 57 Processing helix chain 'N' and resid 99 through 102 Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.785A pdb=" N LEU G 64 " --> pdb=" O PRO G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 74 removed outlier: 3.800A pdb=" N ARG G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 160 removed outlier: 3.738A pdb=" N GLU G 159 " --> pdb=" O PRO G 156 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN G 160 " --> pdb=" O LYS G 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 156 through 160' Processing helix chain 'M' and resid 35 through 39 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.517A pdb=" N ASN M 82 " --> pdb=" O LEU M 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1690 through 1691 removed outlier: 4.803A pdb=" N GLY A 14 " --> pdb=" O ASP B1133 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B1133 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 88 removed outlier: 10.825A pdb=" N LEU A 83 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N VAL A 303 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N LEU A 85 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE A 301 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.671A pdb=" N THR A 224 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 436 through 437 removed outlier: 3.837A pdb=" N VAL A 437 " --> pdb=" O ILE B1035 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE B1035 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 447 removed outlier: 6.040A pdb=" N CYS A 446 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE A 456 " --> pdb=" O ARG A 567 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 471 removed outlier: 4.137A pdb=" N MET A 496 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS A 541 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA A 494 " --> pdb=" O HIS A 541 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 708 Processing sheet with id=AA9, first strand: chain 'A' and resid 917 through 918 Processing sheet with id=AB1, first strand: chain 'A' and resid 1000 through 1001 removed outlier: 6.862A pdb=" N VAL A1007 " --> pdb=" O VAL A1015 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1562 through 1565 removed outlier: 3.685A pdb=" N VAL A1577 " --> pdb=" O ASN A1565 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A1266 " --> pdb=" O LEU A1578 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1288 through 1289 removed outlier: 3.716A pdb=" N VAL A1288 " --> pdb=" O TYR A1554 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A1554 " --> pdb=" O VAL A1288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1298 through 1300 Processing sheet with id=AB5, first strand: chain 'A' and resid 1713 through 1714 Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 68 removed outlier: 3.530A pdb=" N PHE B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP B 117 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA B 80 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR B 115 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 82 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS B 113 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 116 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE B 133 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 118 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LYS B 131 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TRP B 120 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE B 129 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 122 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS B 127 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.507A pdb=" N LEU B 182 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET B 181 " --> pdb=" O CYS B 471 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 190 through 193 removed outlier: 5.363A pdb=" N TYR B 208 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN B 223 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE B 239 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 519 through 520 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 632 through 635 current: chain 'B' and resid 658 through 660 Processing sheet with id=AC1, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AC2, first strand: chain 'B' and resid 594 through 598 Processing sheet with id=AC3, first strand: chain 'B' and resid 695 through 696 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 695 through 696 current: chain 'B' and resid 913 through 915 removed outlier: 7.462A pdb=" N MET B 757 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 896 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 759 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYS B 882 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 712 through 714 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 771 through 780 current: chain 'B' and resid 847 through 855 removed outlier: 7.965A pdb=" N CYS B 847 " --> pdb=" O PRO B 874 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL B 849 " --> pdb=" O ARG B 872 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG B 872 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 851 " --> pdb=" O THR B 870 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N CYS B 866 " --> pdb=" O CYS B 855 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 866 through 874 current: chain 'L' and resid 25 through 26 Processing sheet with id=AC5, first strand: chain 'B' and resid 828 through 830 removed outlier: 3.516A pdb=" N TYR B 828 " --> pdb=" O PHE B 837 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 835 " --> pdb=" O ASN B 830 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1018 through 1019 removed outlier: 3.565A pdb=" N GLN B1024 " --> pdb=" O ASP B1019 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1065 through 1069 removed outlier: 3.552A pdb=" N ASP B1108 " --> pdb=" O VAL B1069 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1079 through 1080 Processing sheet with id=AC9, first strand: chain 'C' and resid 13 through 14 removed outlier: 4.699A pdb=" N LEU C 236 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N ASP C 304 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N ARG C 234 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 173 through 176 removed outlier: 4.561A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU C 207 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN C 96 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASP C 209 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL C 94 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C 211 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 92 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 167 through 168 removed outlier: 3.519A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 263 through 265 Processing sheet with id=AD4, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.169A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.523A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.560A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 90 through 91 removed outlier: 5.453A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 27 through 31 Processing sheet with id=AD9, first strand: chain 'N' and resid 18 through 20 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 18 through 20 current: chain 'N' and resid 76 through 85 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 76 through 85 current: chain 'N' and resid 105 through 107 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 105 through 107 current: chain 'M' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 68 through 72 current: chain 'M' and resid 98 through 111 Processing sheet with id=AE1, first strand: chain 'G' and resid 48 through 59 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 48 through 59 current: chain 'G' and resid 112 through 123 No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'I' and resid 96 through 100 1018 hydrogen bonds defined for protein. 2814 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: 8.08 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5476 1.29 - 1.43: 8859 1.43 - 1.57: 19432 1.57 - 1.70: 76 1.70 - 1.84: 349 Bond restraints: 34192 Sorted by residual: bond pdb=" C ARG M 66 " pdb=" N LEU M 67 " ideal model delta sigma weight residual 1.331 1.221 0.110 1.22e-02 6.72e+03 8.11e+01 bond pdb=" C PRO B 590 " pdb=" O PRO B 590 " ideal model delta sigma weight residual 1.246 1.176 0.070 8.50e-03 1.38e+04 6.80e+01 bond pdb=" C ALA M 61 " pdb=" N ALA M 62 " ideal model delta sigma weight residual 1.331 1.227 0.104 1.34e-02 5.57e+03 6.02e+01 bond pdb=" C ASN N 155 " pdb=" N PRO N 156 " ideal model delta sigma weight residual 1.329 1.419 -0.089 1.18e-02 7.18e+03 5.74e+01 bond pdb=" C GLU N 100 " pdb=" N ALA N 101 " ideal model delta sigma weight residual 1.334 1.240 0.093 1.24e-02 6.50e+03 5.67e+01 ... (remaining 34187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 45073 4.05 - 8.10: 1180 8.10 - 12.15: 120 12.15 - 16.20: 8 16.20 - 20.25: 3 Bond angle restraints: 46384 Sorted by residual: angle pdb=" N VAL C 164 " pdb=" CA VAL C 164 " pdb=" C VAL C 164 " ideal model delta sigma weight residual 112.12 98.64 13.48 8.40e-01 1.42e+00 2.57e+02 angle pdb=" C CYS J 10 " pdb=" CA CYS J 10 " pdb=" CB CYS J 10 " ideal model delta sigma weight residual 110.90 90.65 20.25 1.58e+00 4.01e-01 1.64e+02 angle pdb=" C GLU A 875 " pdb=" N ILE A 876 " pdb=" CA ILE A 876 " ideal model delta sigma weight residual 121.34 102.85 18.49 1.62e+00 3.81e-01 1.30e+02 angle pdb=" N GLU A1507 " pdb=" CA GLU A1507 " pdb=" C GLU A1507 " ideal model delta sigma weight residual 111.07 99.36 11.71 1.07e+00 8.73e-01 1.20e+02 angle pdb=" N THR K 25 " pdb=" CA THR K 25 " pdb=" C THR K 25 " ideal model delta sigma weight residual 113.18 100.91 12.27 1.21e+00 6.83e-01 1.03e+02 ... (remaining 46379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 18163 18.04 - 36.07: 1844 36.07 - 54.11: 530 54.11 - 72.15: 119 72.15 - 90.18: 36 Dihedral angle restraints: 20692 sinusoidal: 8800 harmonic: 11892 Sorted by residual: dihedral pdb=" N GLN A 553 " pdb=" C GLN A 553 " pdb=" CA GLN A 553 " pdb=" CB GLN A 553 " ideal model delta harmonic sigma weight residual 122.80 150.77 -27.97 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" C GLN A 553 " pdb=" N GLN A 553 " pdb=" CA GLN A 553 " pdb=" CB GLN A 553 " ideal model delta harmonic sigma weight residual -122.60 -150.32 27.72 0 2.50e+00 1.60e-01 1.23e+02 dihedral pdb=" C CYS J 10 " pdb=" N CYS J 10 " pdb=" CA CYS J 10 " pdb=" CB CYS J 10 " ideal model delta harmonic sigma weight residual -122.60 -101.38 -21.22 0 2.50e+00 1.60e-01 7.20e+01 ... (remaining 20689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 4932 0.249 - 0.498: 189 0.498 - 0.746: 11 0.746 - 0.995: 0 0.995 - 1.244: 1 Chirality restraints: 5133 Sorted by residual: chirality pdb=" CA GLN A 553 " pdb=" N GLN A 553 " pdb=" C GLN A 553 " pdb=" CB GLN A 553 " both_signs ideal model delta sigma weight residual False 2.51 1.27 1.24 2.00e-01 2.50e+01 3.87e+01 chirality pdb=" CA PRO C 259 " pdb=" N PRO C 259 " pdb=" C PRO C 259 " pdb=" CB PRO C 259 " both_signs ideal model delta sigma weight residual False 2.72 1.98 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CB THR K 25 " pdb=" CA THR K 25 " pdb=" OG1 THR K 25 " pdb=" CG2 THR K 25 " both_signs ideal model delta sigma weight residual False 2.55 1.89 0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 5130 not shown) Planarity restraints: 5869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B1056 " 0.036 2.00e-02 2.50e+03 7.47e-02 5.58e+01 pdb=" C ASP B1056 " -0.129 2.00e-02 2.50e+03 pdb=" O ASP B1056 " 0.048 2.00e-02 2.50e+03 pdb=" N ARG B1057 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B1058 " -0.033 2.00e-02 2.50e+03 6.57e-02 4.32e+01 pdb=" C LEU B1058 " 0.114 2.00e-02 2.50e+03 pdb=" O LEU B1058 " -0.041 2.00e-02 2.50e+03 pdb=" N PHE B1059 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 721 " 0.031 2.00e-02 2.50e+03 6.41e-02 4.11e+01 pdb=" C PRO A 721 " -0.111 2.00e-02 2.50e+03 pdb=" O PRO A 721 " 0.041 2.00e-02 2.50e+03 pdb=" N ARG A 722 " 0.038 2.00e-02 2.50e+03 ... (remaining 5866 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 28 2.15 - 2.84: 11447 2.84 - 3.53: 43831 3.53 - 4.21: 81060 4.21 - 4.90: 140731 Nonbonded interactions: 277097 Sorted by model distance: nonbonded pdb=" C7 DT T 0 " pdb=" O6 DG U 1 " model vdw 1.468 3.460 nonbonded pdb=" OH TYR M 69 " pdb=" O ASP I 16 " model vdw 1.721 3.040 nonbonded pdb=" NH1 ARG A 429 " pdb=" OP1 DG T 1 " model vdw 1.729 3.120 nonbonded pdb=" OD2 ASP B 543 " pdb=" N CYS M 81 " model vdw 1.815 3.120 nonbonded pdb=" O ASN B 536 " pdb=" N GLU N 119 " model vdw 1.836 3.120 ... (remaining 277092 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 36.690 Find NCS groups from input model: 0.290 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 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 : 0.011 0.723 34208 Z= 0.717 Angle : 1.539 64.213 46396 Z= 1.054 Chirality : 0.101 1.244 5133 Planarity : 0.008 0.116 5869 Dihedral : 16.401 90.183 13022 Min Nonbonded Distance : 1.468 Molprobity Statistics. All-atom Clashscore : 33.54 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.11 % Favored : 90.44 % Rotamer: Outliers : 6.11 % Allowed : 7.53 % Favored : 86.37 % Cbeta Deviations : 2.19 % Peptide Plane: Cis-proline : 0.46 % 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: -3.43 (0.12), residues: 4050 helix: -1.83 (0.13), residues: 1209 sheet: -1.87 (0.19), residues: 646 loop : -2.73 (0.12), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 183 TYR 0.046 0.002 TYR B 826 PHE 0.050 0.002 PHE B 75 TRP 0.029 0.002 TRP A 9 HIS 0.021 0.002 HIS C 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00963 / 0.69 (34192) covalent geometry : angle 1.48819 / 1.05 (46384) hydrogen bonds : bond 0.19595 / 13.47 ( 1018) hydrogen bonds : angle 7.58552 / 5.33 ( 2814) metal coordination : bond 0.24931 / 15.02 ( 16) metal coordination : angle 24.54042 / 12.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 852 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.6255 (mt) cc_final: 0.5857 (mt) REVERT: A 412 ASP cc_start: 0.3599 (OUTLIER) cc_final: 0.3390 (m-30) REVERT: A 618 TYR cc_start: 0.8352 (t80) cc_final: 0.8079 (t80) REVERT: A 635 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7111 (mpp) REVERT: A 664 LYS cc_start: 0.4223 (OUTLIER) cc_final: 0.3608 (ptpp) REVERT: A 1044 TYR cc_start: 0.7476 (t80) cc_final: 0.7007 (t80) REVERT: A 1239 MET cc_start: 0.4380 (ptt) cc_final: 0.2919 (tpp) REVERT: A 1268 VAL cc_start: 0.5184 (OUTLIER) cc_final: 0.4927 (t) REVERT: A 1606 HIS cc_start: 0.5936 (OUTLIER) cc_final: 0.5608 (t-90) REVERT: B 31 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: B 338 SER cc_start: 0.6977 (OUTLIER) cc_final: 0.6659 (m) REVERT: B 364 ASP cc_start: 0.7604 (m-30) cc_final: 0.7213 (m-30) REVERT: B 524 PHE cc_start: 0.5075 (m-80) cc_final: 0.4551 (t80) REVERT: B 584 LEU cc_start: 0.8081 (mt) cc_final: 0.7476 (mt) REVERT: B 659 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6978 (tt0) REVERT: B 691 MET cc_start: 0.7647 (mtp) cc_final: 0.7173 (mtp) REVERT: K 60 MET cc_start: 0.6864 (mmm) cc_final: 0.6428 (mmm) REVERT: N 60 HIS cc_start: -0.0449 (OUTLIER) cc_final: -0.1121 (p-80) REVERT: G 98 VAL cc_start: 0.1008 (OUTLIER) cc_final: 0.0027 (m) outliers start: 219 outliers final: 56 residues processed: 995 average time/residue: 0.2390 time to fit residues: 375.5937 Evaluate side-chains 591 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 525 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1606 HIS Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 1025 PRO Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1105 ASP Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS A 80 HIS A 347 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN A 486 ASN A 564 HIS ** A 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN A 595 ASN A 600 GLN A 617 GLN A 632 GLN A 652 HIS A 704 ASN A 728 ASN A 753 HIS ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 GLN A 850 HIS A 859 ASN A 877 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 GLN A1043 ASN A1051 GLN A1068 HIS A1076 GLN A1109 ASN A1118 GLN A1177 GLN A1313 GLN A1329 GLN A1579 ASN A1683 GLN A1690 HIS B 18 HIS B 31 GLN B 97 ASN B 147 ASN B 150 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 313 ASN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS B 473 HIS B 639 GLN B 734 ASN B 846 ASN B 887 HIS ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1004 HIS B1097 ASN C 32 ASN C 48 ASN C 127 GLN C 151 HIS C 165 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN J 61 ASN K 45 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 GLN M 72 ASN I 14 GLN ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.221486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.181712 restraints weight = 42594.508| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.45 r_work: 0.3961 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.932 34208 Z= 0.411 Angle : 0.847 27.781 46396 Z= 0.434 Chirality : 0.051 0.286 5133 Planarity : 0.006 0.101 5869 Dihedral : 12.115 83.225 5030 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.19 % Favored : 92.69 % Rotamer: Outliers : 4.10 % Allowed : 14.22 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.58 (0.12), residues: 4050 helix: -0.97 (0.14), residues: 1219 sheet: -1.58 (0.19), residues: 655 loop : -2.23 (0.12), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 66 TYR 0.038 0.002 TYR A 754 PHE 0.033 0.002 PHE B 265 TRP 0.029 0.002 TRP B 494 HIS 0.009 0.002 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (34192) covalent geometry : angle 0.82456 / 0.43 (46384) hydrogen bonds : bond 0.05397 / 3.57 ( 1018) hydrogen bonds : angle 5.55115 / 3.84 ( 2814) metal coordination : bond 0.48354 / 24.18 ( 16) metal coordination : angle 12.11072 / 7.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 562 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.4384 (mmt) cc_final: 0.4126 (mmt) REVERT: A 256 LEU cc_start: 0.6163 (mt) cc_final: 0.5412 (mt) REVERT: A 319 MET cc_start: 0.3883 (tpt) cc_final: 0.3432 (tpt) REVERT: A 412 ASP cc_start: 0.3401 (OUTLIER) cc_final: 0.2935 (m-30) REVERT: A 512 MET cc_start: 0.7827 (tmm) cc_final: 0.7580 (tpt) REVERT: A 635 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7444 (mpp) REVERT: A 676 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8558 (mp) REVERT: A 935 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6558 (mp) REVERT: A 1239 MET cc_start: 0.4635 (ptt) cc_final: 0.2770 (tpp) REVERT: A 1268 VAL cc_start: 0.6496 (OUTLIER) cc_final: 0.6177 (t) REVERT: A 1498 MET cc_start: 0.2845 (mpp) cc_final: 0.2627 (tpp) REVERT: A 1534 MET cc_start: 0.3466 (mtp) cc_final: 0.3007 (mtt) REVERT: A 1679 GLN cc_start: 0.6398 (mp10) cc_final: 0.6012 (mp10) REVERT: A 1714 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6255 (mt-10) REVERT: B 94 LYS cc_start: 0.7905 (tptp) cc_final: 0.7129 (tttm) REVERT: B 158 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: B 267 GLU cc_start: 0.6445 (tp30) cc_final: 0.5847 (mt-10) REVERT: B 430 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.6931 (t80) REVERT: B 585 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.5552 (mtm-85) REVERT: B 632 GLU cc_start: 0.6896 (tt0) cc_final: 0.6518 (tt0) REVERT: B 659 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: B 828 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6777 (p90) REVERT: B 1005 MET cc_start: 0.7893 (mtt) cc_final: 0.7671 (mtp) REVERT: C 298 ARG cc_start: 0.7705 (tpp-160) cc_final: 0.7488 (tpm170) REVERT: E 73 PHE cc_start: 0.4736 (t80) cc_final: 0.4365 (t80) REVERT: H 18 GLU cc_start: 0.7062 (pm20) cc_final: 0.6443 (pm20) REVERT: H 66 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6869 (mm-30) REVERT: K 60 MET cc_start: 0.7869 (mmm) cc_final: 0.7586 (mmm) REVERT: G 98 VAL cc_start: 0.0547 (OUTLIER) cc_final: 0.0039 (t) REVERT: I 107 GLU cc_start: 0.6259 (mm-30) cc_final: 0.5850 (mm-30) outliers start: 147 outliers final: 77 residues processed: 655 average time/residue: 0.2168 time to fit residues: 233.0166 Evaluate side-chains 552 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 464 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 582 CYS Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1529 VAL Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 391 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS A 578 HIS ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 ASN ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 HIS C 181 GLN C 290 ASN K 31 GLN K 81 ASN K 85 GLN N 60 HIS I 92 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.219950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.176514 restraints weight = 42476.694| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.11 r_work: 0.3942 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 34208 Z= 0.165 Angle : 0.711 24.149 46396 Z= 0.366 Chirality : 0.047 0.228 5133 Planarity : 0.005 0.057 5869 Dihedral : 11.476 84.516 4975 Min Nonbonded Distance : 1.378 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 3.90 % Allowed : 16.28 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 4050 helix: -0.28 (0.15), residues: 1203 sheet: -1.36 (0.19), residues: 662 loop : -2.02 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 802 TYR 0.029 0.002 TYR A 754 PHE 0.024 0.002 PHE B1119 TRP 0.018 0.002 TRP A 9 HIS 0.014 0.001 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (34192) covalent geometry : angle 0.69388 / 0.36 (46384) hydrogen bonds : bond 0.04948 / 3.32 ( 1018) hydrogen bonds : angle 5.18796 / 3.59 ( 2814) metal coordination : bond 0.04473 / 2.23 ( 16) metal coordination : angle 9.67909 / 6.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 495 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.4520 (mmt) cc_final: 0.4149 (mmt) REVERT: A 197 LYS cc_start: 0.6640 (tmtt) cc_final: 0.5652 (mmtp) REVERT: A 256 LEU cc_start: 0.6083 (mt) cc_final: 0.5300 (mt) REVERT: A 348 GLU cc_start: 0.3366 (OUTLIER) cc_final: 0.1779 (mm-30) REVERT: A 412 ASP cc_start: 0.3592 (OUTLIER) cc_final: 0.2963 (m-30) REVERT: A 635 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7681 (mpp) REVERT: A 676 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8477 (mp) REVERT: A 935 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6794 (mp) REVERT: A 1239 MET cc_start: 0.4626 (ptt) cc_final: 0.2791 (tpp) REVERT: A 1264 MET cc_start: 0.4712 (tpp) cc_final: 0.4229 (mpp) REVERT: A 1498 MET cc_start: 0.3181 (mpp) cc_final: 0.2832 (tpp) REVERT: A 1512 ILE cc_start: 0.4603 (OUTLIER) cc_final: 0.4325 (mt) REVERT: A 1534 MET cc_start: 0.3739 (mtp) cc_final: 0.3246 (mtt) REVERT: A 1587 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5807 (tp30) REVERT: A 1606 HIS cc_start: 0.6009 (OUTLIER) cc_final: 0.5615 (t-90) REVERT: A 1679 GLN cc_start: 0.6495 (mp10) cc_final: 0.6048 (mp10) REVERT: B 94 LYS cc_start: 0.7904 (tptp) cc_final: 0.7125 (tttm) REVERT: B 205 TYR cc_start: 0.5831 (m-10) cc_final: 0.5440 (m-10) REVERT: B 235 MET cc_start: 0.6315 (mtm) cc_final: 0.5900 (ttm) REVERT: B 267 GLU cc_start: 0.6673 (tp30) cc_final: 0.6113 (mt-10) REVERT: B 632 GLU cc_start: 0.7220 (tt0) cc_final: 0.6808 (tt0) REVERT: B 659 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: B 691 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7744 (mtp) REVERT: B 809 ASP cc_start: 0.7490 (m-30) cc_final: 0.7237 (t0) REVERT: B 828 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6577 (p90) REVERT: B 1005 MET cc_start: 0.8017 (mtt) cc_final: 0.7768 (mtp) REVERT: B 1056 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.6597 (m-30) REVERT: C 32 ASN cc_start: 0.1853 (OUTLIER) cc_final: 0.0920 (p0) REVERT: E 73 PHE cc_start: 0.5389 (t80) cc_final: 0.5020 (t80) REVERT: H 18 GLU cc_start: 0.7032 (pm20) cc_final: 0.6282 (pm20) REVERT: H 66 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6746 (mm-30) REVERT: J 48 MET cc_start: 0.9076 (tpt) cc_final: 0.8784 (mmm) REVERT: K 60 MET cc_start: 0.8113 (mmm) cc_final: 0.7900 (mmm) REVERT: K 104 MET cc_start: 0.7976 (mtp) cc_final: 0.7656 (mtm) REVERT: M 99 MET cc_start: 0.3501 (tpt) cc_final: 0.3299 (tpt) REVERT: M 109 MET cc_start: 0.4061 (tpp) cc_final: 0.3716 (mpp) REVERT: I 107 GLU cc_start: 0.6053 (mm-30) cc_final: 0.5752 (mm-30) REVERT: I 120 PHE cc_start: 0.7731 (t80) cc_final: 0.7469 (t80) outliers start: 140 outliers final: 74 residues processed: 596 average time/residue: 0.2204 time to fit residues: 216.0795 Evaluate side-chains 533 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 446 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1529 VAL Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1587 GLU Chi-restraints excluded: chain A residue 1606 HIS Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain B residue 1059 PHE Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 381 optimal weight: 0.0010 chunk 10 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 chunk 356 optimal weight: 20.0000 chunk 104 optimal weight: 0.0010 chunk 285 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 GLN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN A 597 HIS ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 297 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 81 ASN I 92 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.218073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.173553 restraints weight = 42146.923| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.18 r_work: 0.3875 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 34208 Z= 0.155 Angle : 0.684 21.841 46396 Z= 0.348 Chirality : 0.046 0.223 5133 Planarity : 0.005 0.058 5869 Dihedral : 11.175 84.909 4962 Min Nonbonded Distance : 1.416 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.19 % Favored : 92.74 % Rotamer: Outliers : 4.24 % Allowed : 16.89 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.13), residues: 4050 helix: -0.10 (0.15), residues: 1223 sheet: -1.18 (0.19), residues: 668 loop : -1.98 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1122 TYR 0.032 0.002 TYR A 754 PHE 0.023 0.001 PHE E 73 TRP 0.014 0.001 TRP C 40 HIS 0.007 0.001 HIS C 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (34192) covalent geometry : angle 0.66984 / 0.35 (46384) hydrogen bonds : bond 0.04607 / 3.07 ( 1018) hydrogen bonds : angle 5.01166 / 3.47 ( 2814) metal coordination : bond 0.02970 / 1.50 ( 16) metal coordination : angle 8.72134 / 5.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 491 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.4321 (mmt) cc_final: 0.4032 (mmt) REVERT: A 197 LYS cc_start: 0.6503 (tmtt) cc_final: 0.5538 (mmtp) REVERT: A 256 LEU cc_start: 0.6069 (mt) cc_final: 0.5231 (mt) REVERT: A 412 ASP cc_start: 0.3530 (OUTLIER) cc_final: 0.2877 (m-30) REVERT: A 512 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6369 (tmm) REVERT: A 676 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8431 (mp) REVERT: A 935 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7141 (mp) REVERT: A 1056 VAL cc_start: 0.8595 (t) cc_final: 0.8314 (p) REVERT: A 1239 MET cc_start: 0.4824 (ptt) cc_final: 0.4000 (tmm) REVERT: A 1264 MET cc_start: 0.4919 (tpp) cc_final: 0.3833 (mpp) REVERT: A 1512 ILE cc_start: 0.4143 (OUTLIER) cc_final: 0.3808 (mt) REVERT: A 1534 MET cc_start: 0.4060 (mtp) cc_final: 0.3760 (mtt) REVERT: A 1587 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.5783 (tp30) REVERT: A 1679 GLN cc_start: 0.6525 (mp10) cc_final: 0.6052 (mp10) REVERT: A 1683 GLN cc_start: 0.7608 (mp10) cc_final: 0.7386 (mp10) REVERT: B 40 ARG cc_start: 0.7969 (tmm-80) cc_final: 0.7736 (tmm-80) REVERT: B 94 LYS cc_start: 0.7895 (tptp) cc_final: 0.7303 (tttm) REVERT: B 235 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5714 (ttm) REVERT: B 267 GLU cc_start: 0.6662 (tp30) cc_final: 0.5977 (mt-10) REVERT: B 631 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: B 632 GLU cc_start: 0.7165 (tt0) cc_final: 0.6772 (tt0) REVERT: B 659 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: B 686 MET cc_start: 0.8401 (mtt) cc_final: 0.8108 (mtt) REVERT: B 809 ASP cc_start: 0.7466 (m-30) cc_final: 0.7218 (t0) REVERT: B 1005 MET cc_start: 0.7952 (mtt) cc_final: 0.7665 (mtp) REVERT: C 32 ASN cc_start: 0.1824 (OUTLIER) cc_final: 0.0862 (p0) REVERT: C 55 HIS cc_start: 0.7770 (t-170) cc_final: 0.7265 (t-170) REVERT: C 293 LEU cc_start: 0.9008 (mt) cc_final: 0.8783 (mp) REVERT: C 303 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7526 (mmp-170) REVERT: E 73 PHE cc_start: 0.5731 (t80) cc_final: 0.5372 (t80) REVERT: E 135 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6175 (mp) REVERT: H 18 GLU cc_start: 0.7222 (pm20) cc_final: 0.6404 (pm20) REVERT: K 104 MET cc_start: 0.8027 (mtp) cc_final: 0.7777 (mtm) REVERT: M 99 MET cc_start: 0.3730 (tpt) cc_final: 0.3495 (tpt) REVERT: I 107 GLU cc_start: 0.5789 (mm-30) cc_final: 0.5502 (mm-30) REVERT: I 120 PHE cc_start: 0.7696 (t80) cc_final: 0.7432 (t80) outliers start: 152 outliers final: 101 residues processed: 602 average time/residue: 0.2112 time to fit residues: 208.6658 Evaluate side-chains 565 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 453 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1256 SER Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1529 VAL Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1587 GLU Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 580 HIS Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain B residue 1059 PHE Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 155 ASN Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 278 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 19 optimal weight: 0.1980 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1076 GLN ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS B 715 GLN C 42 GLN C 194 HIS C 290 ASN K 31 GLN K 81 ASN L 26 ASN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN I 92 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.204889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162090 restraints weight = 42079.352| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.17 r_work: 0.3747 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 34208 Z= 0.269 Angle : 0.795 26.898 46396 Z= 0.405 Chirality : 0.050 0.222 5133 Planarity : 0.006 0.062 5869 Dihedral : 11.155 85.824 4950 Min Nonbonded Distance : 1.441 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.22 % Favored : 91.68 % Rotamer: Outliers : 4.74 % Allowed : 17.62 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.12), residues: 4050 helix: -0.40 (0.14), residues: 1245 sheet: -1.19 (0.19), residues: 652 loop : -2.09 (0.12), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 621 TYR 0.024 0.002 TYR B 727 PHE 0.036 0.002 PHE E 73 TRP 0.023 0.002 TRP B 120 HIS 0.070 0.002 HIS I 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.27 (34192) covalent geometry : angle 0.77759 / 0.40 (46384) hydrogen bonds : bond 0.05555 / 3.70 ( 1018) hydrogen bonds : angle 5.22388 / 3.63 ( 2814) metal coordination : bond 0.02854 / 1.47 ( 16) metal coordination : angle 10.33540 / 6.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 494 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.4521 (pt0) cc_final: 0.3983 (mp0) REVERT: A 109 MET cc_start: 0.4698 (mmt) cc_final: 0.4178 (mmt) REVERT: A 163 GLN cc_start: 0.5126 (OUTLIER) cc_final: 0.4877 (mp10) REVERT: A 256 LEU cc_start: 0.6148 (mt) cc_final: 0.5173 (mt) REVERT: A 302 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6134 (mm) REVERT: A 423 LYS cc_start: 0.5691 (OUTLIER) cc_final: 0.5454 (mmtt) REVERT: A 512 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6548 (tmm) REVERT: A 635 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.7647 (mpp) REVERT: A 676 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8385 (mp) REVERT: A 935 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7594 (mp) REVERT: A 1056 VAL cc_start: 0.8671 (t) cc_final: 0.8324 (p) REVERT: A 1076 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8474 (mp10) REVERT: A 1198 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8719 (tp) REVERT: A 1239 MET cc_start: 0.4617 (ptt) cc_final: 0.4100 (ppp) REVERT: A 1534 MET cc_start: 0.4455 (mtp) cc_final: 0.3962 (mtt) REVERT: A 1587 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5878 (tp30) REVERT: A 1679 GLN cc_start: 0.6561 (mp10) cc_final: 0.6062 (mp10) REVERT: A 1683 GLN cc_start: 0.7718 (mp10) cc_final: 0.7447 (mp10) REVERT: B 40 ARG cc_start: 0.8072 (tmm-80) cc_final: 0.7840 (tmm-80) REVERT: B 94 LYS cc_start: 0.7991 (tptp) cc_final: 0.7384 (tttm) REVERT: B 195 ARG cc_start: 0.7597 (ttp-170) cc_final: 0.7279 (ttm170) REVERT: B 197 LYS cc_start: 0.7722 (tppt) cc_final: 0.7075 (ptpt) REVERT: B 235 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.5679 (ttm) REVERT: B 267 GLU cc_start: 0.6847 (tp30) cc_final: 0.6126 (mt-10) REVERT: B 535 CYS cc_start: 0.8050 (t) cc_final: 0.6904 (m) REVERT: B 631 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: B 632 GLU cc_start: 0.7377 (tt0) cc_final: 0.6851 (tt0) REVERT: B 659 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: B 691 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8000 (mtp) REVERT: B 809 ASP cc_start: 0.7715 (m-30) cc_final: 0.7243 (t0) REVERT: C 55 HIS cc_start: 0.7689 (t-170) cc_final: 0.7368 (t-170) REVERT: C 124 TYR cc_start: 0.8956 (m-80) cc_final: 0.8738 (m-80) REVERT: E 73 PHE cc_start: 0.6240 (OUTLIER) cc_final: 0.5683 (t80) REVERT: H 66 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6545 (mm-30) REVERT: K 98 ARG cc_start: 0.8517 (ttp-170) cc_final: 0.7953 (ttp-110) REVERT: K 104 MET cc_start: 0.8165 (mtp) cc_final: 0.7860 (mtm) REVERT: M 99 MET cc_start: 0.3692 (tpt) cc_final: 0.3389 (tpt) REVERT: I 97 TYR cc_start: 0.8015 (p90) cc_final: 0.7759 (p90) REVERT: I 107 GLU cc_start: 0.5764 (mm-30) cc_final: 0.5513 (mm-30) REVERT: I 120 PHE cc_start: 0.7779 (t80) cc_final: 0.7557 (t80) outliers start: 170 outliers final: 106 residues processed: 617 average time/residue: 0.2256 time to fit residues: 227.1597 Evaluate side-chains 568 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 447 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1256 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1529 VAL Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1587 GLU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 29 optimal weight: 10.0000 chunk 203 optimal weight: 0.5980 chunk 326 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 364 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 321 optimal weight: 2.9990 chunk 359 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN A 790 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS B 330 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN B1097 ASN C 143 GLN C 290 ASN E 169 GLN K 31 GLN K 97 GLN M 30 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.207053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.163017 restraints weight = 42243.269| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.46 r_work: 0.3782 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 34208 Z= 0.215 Angle : 0.731 26.068 46396 Z= 0.370 Chirality : 0.048 0.210 5133 Planarity : 0.005 0.062 5869 Dihedral : 11.052 88.237 4947 Min Nonbonded Distance : 1.487 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.58 % Favored : 92.35 % Rotamer: Outliers : 4.35 % Allowed : 18.73 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.13), residues: 4050 helix: -0.25 (0.15), residues: 1235 sheet: -1.20 (0.20), residues: 650 loop : -2.06 (0.12), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 166 TYR 0.019 0.002 TYR A1044 PHE 0.032 0.002 PHE A 71 TRP 0.015 0.002 TRP B 120 HIS 0.011 0.001 HIS I 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (34192) covalent geometry : angle 0.71360 / 0.37 (46384) hydrogen bonds : bond 0.05139 / 3.38 ( 1018) hydrogen bonds : angle 5.17705 / 3.60 ( 2814) metal coordination : bond 0.02260 / 1.17 ( 16) metal coordination : angle 9.84041 / 6.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 476 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.4547 (pt0) cc_final: 0.4297 (mm-30) REVERT: A 109 MET cc_start: 0.4686 (mmt) cc_final: 0.4154 (mmt) REVERT: A 163 GLN cc_start: 0.5110 (OUTLIER) cc_final: 0.4828 (mp10) REVERT: A 256 LEU cc_start: 0.6221 (mt) cc_final: 0.5236 (mt) REVERT: A 302 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.6017 (mm) REVERT: A 334 ASP cc_start: 0.6113 (m-30) cc_final: 0.5874 (t0) REVERT: A 424 LYS cc_start: 0.7091 (tptt) cc_final: 0.6853 (tttt) REVERT: A 512 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.6397 (tmm) REVERT: A 557 HIS cc_start: 0.8428 (OUTLIER) cc_final: 0.8185 (p-80) REVERT: A 676 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8324 (mp) REVERT: A 790 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: A 800 GLU cc_start: 0.8034 (pt0) cc_final: 0.7769 (tt0) REVERT: A 935 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7923 (mp) REVERT: A 969 MET cc_start: 0.8030 (mtt) cc_final: 0.7690 (mtt) REVERT: A 1129 GLU cc_start: 0.5463 (mp0) cc_final: 0.5158 (mp0) REVERT: A 1239 MET cc_start: 0.4797 (ptt) cc_final: 0.4219 (ppp) REVERT: A 1534 MET cc_start: 0.5031 (mtp) cc_final: 0.4207 (mtt) REVERT: A 1587 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5780 (tp30) REVERT: A 1679 GLN cc_start: 0.6445 (mp10) cc_final: 0.5903 (mp10) REVERT: B 8 ARG cc_start: 0.7709 (mmm160) cc_final: 0.7416 (ptt-90) REVERT: B 40 ARG cc_start: 0.7840 (tmm-80) cc_final: 0.7631 (tmm-80) REVERT: B 94 LYS cc_start: 0.7959 (tptp) cc_final: 0.7416 (tttm) REVERT: B 195 ARG cc_start: 0.7468 (ttp-170) cc_final: 0.7149 (ttm170) REVERT: B 197 LYS cc_start: 0.7781 (tppt) cc_final: 0.7165 (ptpt) REVERT: B 235 MET cc_start: 0.5915 (OUTLIER) cc_final: 0.5534 (ttm) REVERT: B 267 GLU cc_start: 0.6648 (tp30) cc_final: 0.5967 (mt-10) REVERT: B 585 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6855 (ttm-80) REVERT: B 631 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: B 632 GLU cc_start: 0.7047 (tt0) cc_final: 0.6398 (tt0) REVERT: B 691 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7819 (mtp) REVERT: B 809 ASP cc_start: 0.7618 (m-30) cc_final: 0.7212 (t0) REVERT: C 55 HIS cc_start: 0.7541 (t-170) cc_final: 0.7278 (t-170) REVERT: C 65 MET cc_start: 0.8436 (ttm) cc_final: 0.8155 (ttm) REVERT: C 83 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8031 (mm-30) REVERT: C 124 TYR cc_start: 0.8958 (m-80) cc_final: 0.8719 (m-80) REVERT: C 210 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8160 (pp) REVERT: C 337 LEU cc_start: 0.8304 (mt) cc_final: 0.8092 (mt) REVERT: E 9 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7028 (mtm180) REVERT: E 73 PHE cc_start: 0.5935 (t80) cc_final: 0.5549 (t80) REVERT: F 100 ARG cc_start: 0.6352 (ttm170) cc_final: 0.6103 (ttm170) REVERT: H 51 ASP cc_start: 0.7489 (m-30) cc_final: 0.6928 (t0) REVERT: H 66 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6652 (mm-30) REVERT: H 78 THR cc_start: 0.8293 (p) cc_final: 0.8068 (t) REVERT: H 128 ASP cc_start: 0.7081 (t70) cc_final: 0.6666 (t70) REVERT: K 104 MET cc_start: 0.8054 (mtp) cc_final: 0.7681 (mtm) REVERT: N 130 LEU cc_start: 0.0703 (OUTLIER) cc_final: 0.0485 (mp) REVERT: M 99 MET cc_start: 0.3549 (tpt) cc_final: 0.3251 (tpt) REVERT: I 107 GLU cc_start: 0.5928 (mm-30) cc_final: 0.5653 (mm-30) outliers start: 156 outliers final: 108 residues processed: 586 average time/residue: 0.2078 time to fit residues: 199.9739 Evaluate side-chains 578 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 456 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1256 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1529 VAL Chi-restraints excluded: chain A residue 1587 GLU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 144 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 173 optimal weight: 0.3980 chunk 127 optimal weight: 0.8980 chunk 382 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 400 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN A 790 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1076 GLN ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN C 166 HIS J 26 GLN K 31 GLN I 92 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.210955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.167004 restraints weight = 41778.097| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.08 r_work: 0.3846 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34208 Z= 0.143 Angle : 0.680 23.135 46396 Z= 0.343 Chirality : 0.045 0.218 5133 Planarity : 0.005 0.064 5869 Dihedral : 10.859 89.569 4943 Min Nonbonded Distance : 1.517 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.48 % Favored : 92.44 % Rotamer: Outliers : 3.85 % Allowed : 19.49 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.13), residues: 4050 helix: 0.03 (0.15), residues: 1235 sheet: -1.08 (0.20), residues: 640 loop : -1.96 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1132 TYR 0.035 0.001 TYR A 754 PHE 0.029 0.001 PHE A 71 TRP 0.019 0.001 TRP A1174 HIS 0.007 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (34192) covalent geometry : angle 0.66452 / 0.34 (46384) hydrogen bonds : bond 0.04673 / 3.08 ( 1018) hydrogen bonds : angle 5.00434 / 3.48 ( 2814) metal coordination : bond 0.01822 / 0.94 ( 16) metal coordination : angle 8.87840 / 5.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 470 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.4722 (mmt) cc_final: 0.4207 (mmt) REVERT: A 256 LEU cc_start: 0.6231 (mt) cc_final: 0.5211 (mt) REVERT: A 302 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6358 (mm) REVERT: A 423 LYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5510 (mmtt) REVERT: A 512 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.6470 (tmm) REVERT: A 635 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7565 (mpp) REVERT: A 676 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 790 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: A 800 GLU cc_start: 0.8116 (pt0) cc_final: 0.7832 (tt0) REVERT: A 1122 ARG cc_start: 0.8379 (tmt170) cc_final: 0.8022 (tmt170) REVERT: A 1129 GLU cc_start: 0.5385 (mp0) cc_final: 0.5134 (mp0) REVERT: A 1239 MET cc_start: 0.4891 (ptt) cc_final: 0.4231 (ppp) REVERT: A 1534 MET cc_start: 0.5045 (mtp) cc_final: 0.4178 (mtt) REVERT: A 1587 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5875 (tp30) REVERT: A 1679 GLN cc_start: 0.6519 (mp10) cc_final: 0.5965 (mp10) REVERT: B 8 ARG cc_start: 0.7856 (mmm160) cc_final: 0.7383 (ptt-90) REVERT: B 94 LYS cc_start: 0.7955 (tptp) cc_final: 0.7602 (tptm) REVERT: B 176 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7503 (mt-10) REVERT: B 183 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.6397 (mt) REVERT: B 197 LYS cc_start: 0.7786 (tppt) cc_final: 0.7163 (ptpt) REVERT: B 212 MET cc_start: 0.7817 (ttt) cc_final: 0.7615 (ttt) REVERT: B 235 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.5721 (ttm) REVERT: B 267 GLU cc_start: 0.6690 (tp30) cc_final: 0.6019 (mt-10) REVERT: B 585 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6226 (mtm-85) REVERT: B 631 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: B 632 GLU cc_start: 0.7214 (tt0) cc_final: 0.6564 (tt0) REVERT: B 691 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8162 (mtm) REVERT: B 809 ASP cc_start: 0.7733 (m-30) cc_final: 0.7196 (t0) REVERT: B 871 MET cc_start: 0.8756 (mtm) cc_final: 0.8462 (mtm) REVERT: C 65 MET cc_start: 0.8571 (ttm) cc_final: 0.8313 (ttm) REVERT: C 83 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8158 (mm-30) REVERT: C 184 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5462 (tt) REVERT: C 298 ARG cc_start: 0.7551 (tpm170) cc_final: 0.7338 (tpm170) REVERT: C 303 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7568 (mmp-170) REVERT: C 337 LEU cc_start: 0.8160 (mt) cc_final: 0.7954 (mt) REVERT: E 9 ARG cc_start: 0.7502 (ttt180) cc_final: 0.7051 (mtm180) REVERT: E 73 PHE cc_start: 0.6299 (OUTLIER) cc_final: 0.5908 (t80) REVERT: H 21 LYS cc_start: 0.8681 (tppt) cc_final: 0.8260 (tttm) REVERT: H 51 ASP cc_start: 0.7608 (m-30) cc_final: 0.6925 (t0) REVERT: H 66 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6513 (mm-30) REVERT: H 78 THR cc_start: 0.8290 (p) cc_final: 0.8040 (t) REVERT: K 104 MET cc_start: 0.8215 (mtp) cc_final: 0.7834 (mtm) REVERT: K 124 GLN cc_start: 0.7918 (mt0) cc_final: 0.7685 (tt0) REVERT: M 99 MET cc_start: 0.3683 (tpt) cc_final: 0.3398 (tpt) REVERT: I 107 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.5611 (mm-30) outliers start: 138 outliers final: 95 residues processed: 568 average time/residue: 0.2252 time to fit residues: 208.8248 Evaluate side-chains 554 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 444 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1587 GLU Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 454 CYS Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 92 HIS Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 107 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 111 optimal weight: 0.4980 chunk 322 optimal weight: 0.6980 chunk 294 optimal weight: 0.8980 chunk 257 optimal weight: 0.7980 chunk 396 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 285 optimal weight: 0.0070 chunk 261 optimal weight: 0.6980 chunk 372 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1717 GLN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS E 169 GLN K 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.212172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.171029 restraints weight = 41482.564| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.51 r_work: 0.3797 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34208 Z= 0.127 Angle : 0.666 19.993 46396 Z= 0.335 Chirality : 0.045 0.286 5133 Planarity : 0.005 0.067 5869 Dihedral : 10.696 89.731 4939 Min Nonbonded Distance : 1.537 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.04 % Favored : 92.86 % Rotamer: Outliers : 3.43 % Allowed : 19.93 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.13), residues: 4050 helix: 0.22 (0.15), residues: 1232 sheet: -1.02 (0.20), residues: 652 loop : -1.82 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A1132 TYR 0.040 0.001 TYR B 828 PHE 0.026 0.001 PHE A 71 TRP 0.014 0.001 TRP B 120 HIS 0.035 0.001 HIS I 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (34192) covalent geometry : angle 0.65439 / 0.33 (46384) hydrogen bonds : bond 0.04326 / 2.84 ( 1018) hydrogen bonds : angle 4.89133 / 3.41 ( 2814) metal coordination : bond 0.01620 / 0.84 ( 16) metal coordination : angle 7.75527 / 5.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 472 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.4702 (mmt) cc_final: 0.4213 (mmt) REVERT: A 256 LEU cc_start: 0.6232 (mt) cc_final: 0.5209 (mt) REVERT: A 302 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6559 (mm) REVERT: A 423 LYS cc_start: 0.5660 (OUTLIER) cc_final: 0.5400 (mmtt) REVERT: A 635 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7462 (mpp) REVERT: A 676 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 790 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: A 800 GLU cc_start: 0.8170 (pt0) cc_final: 0.7901 (tt0) REVERT: A 1122 ARG cc_start: 0.8434 (tmt170) cc_final: 0.8055 (tmt170) REVERT: A 1239 MET cc_start: 0.4965 (ptt) cc_final: 0.4266 (ppp) REVERT: A 1534 MET cc_start: 0.4959 (mtp) cc_final: 0.4048 (mtt) REVERT: A 1587 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.6005 (tp30) REVERT: A 1679 GLN cc_start: 0.6639 (mp10) cc_final: 0.6102 (mp10) REVERT: B 94 LYS cc_start: 0.7931 (tptp) cc_final: 0.7585 (tptm) REVERT: B 176 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7632 (mt-10) REVERT: B 197 LYS cc_start: 0.7811 (tppt) cc_final: 0.7176 (ptpt) REVERT: B 212 MET cc_start: 0.7794 (ttt) cc_final: 0.7581 (ttt) REVERT: B 235 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.5770 (ttm) REVERT: B 267 GLU cc_start: 0.6658 (tp30) cc_final: 0.6004 (mt-10) REVERT: B 631 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: B 632 GLU cc_start: 0.7188 (tt0) cc_final: 0.6633 (tt0) REVERT: B 691 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7990 (mtm) REVERT: B 809 ASP cc_start: 0.7814 (m-30) cc_final: 0.7304 (t0) REVERT: B 871 MET cc_start: 0.8765 (mtm) cc_final: 0.8517 (mtm) REVERT: C 65 MET cc_start: 0.8488 (ttm) cc_final: 0.8235 (ttm) REVERT: C 83 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8129 (mm-30) REVERT: C 184 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5500 (tt) REVERT: C 298 ARG cc_start: 0.7517 (tpm170) cc_final: 0.7305 (tpm170) REVERT: C 303 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7577 (mmp-170) REVERT: C 337 LEU cc_start: 0.8147 (mt) cc_final: 0.7870 (mt) REVERT: E 9 ARG cc_start: 0.7411 (ttt180) cc_final: 0.6989 (mtm180) REVERT: E 73 PHE cc_start: 0.6375 (OUTLIER) cc_final: 0.6017 (t80) REVERT: F 75 MET cc_start: 0.7723 (ttm) cc_final: 0.7517 (ttm) REVERT: H 21 LYS cc_start: 0.8677 (tppt) cc_final: 0.8288 (tttm) REVERT: H 66 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6566 (mm-30) REVERT: H 78 THR cc_start: 0.8284 (p) cc_final: 0.8031 (t) REVERT: J 26 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7438 (mm110) REVERT: K 31 GLN cc_start: 0.7523 (tt0) cc_final: 0.7310 (mt0) REVERT: K 104 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7928 (mtm) REVERT: M 99 MET cc_start: 0.3632 (tpt) cc_final: 0.3336 (tpt) REVERT: I 107 GLU cc_start: 0.5730 (OUTLIER) cc_final: 0.5514 (mm-30) outliers start: 123 outliers final: 90 residues processed: 551 average time/residue: 0.2165 time to fit residues: 195.9491 Evaluate side-chains 551 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 448 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1587 GLU Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 107 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 53 optimal weight: 0.9980 chunk 253 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 362 optimal weight: 3.9990 chunk 277 optimal weight: 0.7980 chunk 316 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 326 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN A 790 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS E 116 GLN I 92 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.211382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.169872 restraints weight = 41375.833| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.52 r_work: 0.3783 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34208 Z= 0.141 Angle : 0.671 19.839 46396 Z= 0.336 Chirality : 0.045 0.251 5133 Planarity : 0.005 0.067 5869 Dihedral : 10.612 89.573 4939 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.31 % Favored : 92.62 % Rotamer: Outliers : 3.40 % Allowed : 20.43 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 4050 helix: 0.29 (0.15), residues: 1238 sheet: -0.98 (0.20), residues: 652 loop : -1.78 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 191 TYR 0.030 0.001 TYR B 828 PHE 0.025 0.001 PHE A 71 TRP 0.013 0.001 TRP C 40 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (34192) covalent geometry : angle 0.65873 / 0.34 (46384) hydrogen bonds : bond 0.04357 / 2.85 ( 1018) hydrogen bonds : angle 4.85066 / 3.38 ( 2814) metal coordination : bond 0.01619 / 0.84 ( 16) metal coordination : angle 7.83446 / 5.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 464 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.4731 (mmt) cc_final: 0.4219 (mmt) REVERT: A 256 LEU cc_start: 0.6296 (mt) cc_final: 0.5231 (mt) REVERT: A 302 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6557 (mm) REVERT: A 405 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6789 (tp30) REVERT: A 423 LYS cc_start: 0.5604 (OUTLIER) cc_final: 0.5324 (mmtt) REVERT: A 635 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7471 (mpp) REVERT: A 790 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: A 800 GLU cc_start: 0.8201 (pt0) cc_final: 0.7913 (tt0) REVERT: A 1122 ARG cc_start: 0.8436 (tmt170) cc_final: 0.8051 (tmt170) REVERT: A 1239 MET cc_start: 0.5097 (ptt) cc_final: 0.4366 (ppp) REVERT: A 1534 MET cc_start: 0.4960 (mtp) cc_final: 0.4020 (mtt) REVERT: A 1679 GLN cc_start: 0.6585 (mp10) cc_final: 0.6057 (mp10) REVERT: B 94 LYS cc_start: 0.8036 (tptp) cc_final: 0.7622 (tptm) REVERT: B 176 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 197 LYS cc_start: 0.7813 (tppt) cc_final: 0.7160 (ptpt) REVERT: B 212 MET cc_start: 0.7826 (ttt) cc_final: 0.7618 (ttt) REVERT: B 235 MET cc_start: 0.6255 (OUTLIER) cc_final: 0.5748 (ttm) REVERT: B 267 GLU cc_start: 0.6774 (tp30) cc_final: 0.6048 (mt-10) REVERT: B 474 ARG cc_start: 0.8159 (tpt90) cc_final: 0.7914 (tpt90) REVERT: B 631 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: B 632 GLU cc_start: 0.7241 (tt0) cc_final: 0.6735 (tt0) REVERT: B 691 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8110 (mtm) REVERT: B 809 ASP cc_start: 0.7812 (m-30) cc_final: 0.7313 (t0) REVERT: B 871 MET cc_start: 0.8844 (mtm) cc_final: 0.8578 (mtm) REVERT: C 65 MET cc_start: 0.8529 (ttm) cc_final: 0.8307 (ttm) REVERT: C 83 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8143 (mm-30) REVERT: C 184 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5629 (tt) REVERT: C 243 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7664 (mp0) REVERT: C 298 ARG cc_start: 0.7610 (tpm170) cc_final: 0.7392 (tpm170) REVERT: C 303 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7580 (mmp-170) REVERT: C 337 LEU cc_start: 0.8145 (mt) cc_final: 0.7873 (mt) REVERT: E 9 ARG cc_start: 0.7371 (ttt180) cc_final: 0.6942 (mtm180) REVERT: E 73 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.6045 (t80) REVERT: F 75 MET cc_start: 0.7878 (ttm) cc_final: 0.7671 (ttm) REVERT: H 21 LYS cc_start: 0.8705 (tppt) cc_final: 0.8290 (tttm) REVERT: H 51 ASP cc_start: 0.7488 (m-30) cc_final: 0.6917 (t0) REVERT: H 66 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6705 (mm-30) REVERT: H 78 THR cc_start: 0.8264 (p) cc_final: 0.8025 (t) REVERT: J 26 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7395 (mm110) REVERT: K 31 GLN cc_start: 0.7517 (tt0) cc_final: 0.7291 (mt0) REVERT: K 90 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8439 (mt) REVERT: K 104 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7972 (mtm) outliers start: 122 outliers final: 98 residues processed: 545 average time/residue: 0.2218 time to fit residues: 198.8577 Evaluate side-chains 563 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 453 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 92 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 335 optimal weight: 6.9990 chunk 224 optimal weight: 0.3980 chunk 154 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 233 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 252 optimal weight: 0.8980 chunk 329 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS E 116 GLN M 98 GLN ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.211269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.166012 restraints weight = 41686.771| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.21 r_work: 0.3784 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34208 Z= 0.143 Angle : 0.674 19.809 46396 Z= 0.337 Chirality : 0.046 0.292 5133 Planarity : 0.005 0.068 5869 Dihedral : 10.567 89.299 4937 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.23 % Favored : 92.69 % Rotamer: Outliers : 3.23 % Allowed : 20.63 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.13), residues: 4050 helix: 0.32 (0.15), residues: 1239 sheet: -0.89 (0.21), residues: 630 loop : -1.74 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 191 TYR 0.033 0.001 TYR A1044 PHE 0.024 0.001 PHE A 71 TRP 0.015 0.001 TRP A1174 HIS 0.008 0.001 HIS I 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (34192) covalent geometry : angle 0.66212 / 0.34 (46384) hydrogen bonds : bond 0.04344 / 2.84 ( 1018) hydrogen bonds : angle 4.85743 / 3.38 ( 2814) metal coordination : bond 0.01589 / 0.82 ( 16) metal coordination : angle 7.74990 / 5.32 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 461 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.6791 (mp) cc_final: 0.6489 (tp) REVERT: A 109 MET cc_start: 0.4755 (mmt) cc_final: 0.4213 (mmt) REVERT: A 256 LEU cc_start: 0.6310 (mt) cc_final: 0.5248 (mt) REVERT: A 302 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6601 (mm) REVERT: A 405 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6802 (tp30) REVERT: A 423 LYS cc_start: 0.5638 (OUTLIER) cc_final: 0.5338 (mmtt) REVERT: A 635 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7490 (mpp) REVERT: A 800 GLU cc_start: 0.8189 (pt0) cc_final: 0.7908 (tt0) REVERT: A 1122 ARG cc_start: 0.8446 (tmt170) cc_final: 0.8067 (tmt170) REVERT: A 1239 MET cc_start: 0.5122 (ptt) cc_final: 0.4380 (ppp) REVERT: A 1534 MET cc_start: 0.5107 (mtp) cc_final: 0.4120 (mtt) REVERT: A 1679 GLN cc_start: 0.6612 (mp10) cc_final: 0.6057 (mp10) REVERT: A 1714 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6657 (mt-10) REVERT: B 94 LYS cc_start: 0.7967 (tptp) cc_final: 0.7636 (tptm) REVERT: B 176 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7657 (mt-10) REVERT: B 197 LYS cc_start: 0.7829 (tppt) cc_final: 0.7179 (ptpt) REVERT: B 212 MET cc_start: 0.7832 (ttt) cc_final: 0.7623 (ttt) REVERT: B 235 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.5770 (ttm) REVERT: B 267 GLU cc_start: 0.6755 (tp30) cc_final: 0.6055 (mt-10) REVERT: B 275 ASP cc_start: 0.7367 (p0) cc_final: 0.7100 (p0) REVERT: B 474 ARG cc_start: 0.8137 (tpt90) cc_final: 0.7885 (tpt90) REVERT: B 631 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: B 632 GLU cc_start: 0.7239 (tt0) cc_final: 0.6735 (tt0) REVERT: B 691 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8104 (mtm) REVERT: B 792 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6892 (mt) REVERT: B 809 ASP cc_start: 0.7801 (m-30) cc_final: 0.7311 (t0) REVERT: B 871 MET cc_start: 0.8835 (mtm) cc_final: 0.8565 (mtm) REVERT: C 65 MET cc_start: 0.8521 (ttm) cc_final: 0.8305 (ttm) REVERT: C 83 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8127 (mm-30) REVERT: C 184 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5639 (tt) REVERT: C 243 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: C 298 ARG cc_start: 0.7601 (tpm170) cc_final: 0.7385 (tpm170) REVERT: C 303 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7598 (mmp-170) REVERT: C 337 LEU cc_start: 0.8202 (mt) cc_final: 0.7935 (mt) REVERT: E 9 ARG cc_start: 0.7367 (ttt180) cc_final: 0.7004 (mtm180) REVERT: E 73 PHE cc_start: 0.6434 (OUTLIER) cc_final: 0.6082 (t80) REVERT: F 75 MET cc_start: 0.7913 (ttm) cc_final: 0.7697 (ttm) REVERT: H 21 LYS cc_start: 0.8745 (tppt) cc_final: 0.8311 (tttm) REVERT: H 51 ASP cc_start: 0.7526 (m-30) cc_final: 0.6991 (t0) REVERT: H 78 THR cc_start: 0.8227 (p) cc_final: 0.7989 (t) REVERT: J 26 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7418 (mm110) REVERT: K 31 GLN cc_start: 0.7336 (tt0) cc_final: 0.7049 (mt0) REVERT: K 37 ARG cc_start: 0.7529 (mtp180) cc_final: 0.7155 (mtm180) REVERT: K 104 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7984 (mtm) outliers start: 116 outliers final: 96 residues processed: 538 average time/residue: 0.2114 time to fit residues: 186.3211 Evaluate side-chains 565 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 457 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 999 TYR Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 189 optimal weight: 0.9980 chunk 369 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 340 optimal weight: 7.9990 chunk 303 optimal weight: 0.8980 chunk 246 optimal weight: 0.9990 chunk 266 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 197 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN A 790 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 HIS ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS E 116 GLN ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.212999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.168352 restraints weight = 41583.339| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.15 r_work: 0.3808 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34208 Z= 0.128 Angle : 0.652 18.064 46396 Z= 0.328 Chirality : 0.045 0.298 5133 Planarity : 0.005 0.068 5869 Dihedral : 10.451 89.581 4935 Min Nonbonded Distance : 1.550 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.96 % Favored : 92.96 % Rotamer: Outliers : 3.23 % Allowed : 20.69 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: -1.30 (0.13), residues: 4050 helix: 0.45 (0.15), residues: 1231 sheet: -0.92 (0.20), residues: 658 loop : -1.66 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 191 TYR 0.028 0.001 TYR A 754 PHE 0.023 0.001 PHE A 71 TRP 0.016 0.001 TRP A1174 HIS 0.006 0.001 HIS I 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (34192) covalent geometry : angle 0.64106 / 0.33 (46384) hydrogen bonds : bond 0.04158 / 2.72 ( 1018) hydrogen bonds : angle 4.77316 / 3.32 ( 2814) metal coordination : bond 0.01468 / 0.77 ( 16) metal coordination : angle 7.30017 / 5.00 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11856.10 seconds wall clock time: 202 minutes 36.06 seconds (12156.06 seconds total)