Starting phenix.real_space_refine on Mon Aug 10 03:51:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8of0_16840/08_2026/8of0_16840.cif Found real_map, /net/cci-nas-00/data/ceres_data/8of0_16840/08_2026/8of0_16840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8of0_16840/08_2026/8of0_16840.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8of0_16840/08_2026/8of0_16840.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8of0_16840/08_2026/8of0_16840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8of0_16840/08_2026/8of0_16840.map" model { file = "/net/cci-nas-00/data/ceres_data/8of0_16840/08_2026/8of0_16840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8of0_16840/08_2026/8of0_16840.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 75 5.49 5 Mg 1 5.21 5 S 244 5.16 5 C 26116 2.51 5 N 7306 2.21 5 O 7950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.15s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41700 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11159 Classifications: {'peptide': 1409} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1340} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9047 Classifications: {'peptide': 1131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1347 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 932 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 527 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 280 Classifications: {'RNAv2': 13} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "T" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 750 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "Q" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 83} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1149 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "O" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "S" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6629 Classifications: {'peptide': 818} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 784} Chain breaks: 12 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 69.156 100.801 92.348 1.00 65.49 S ATOM 494 SG CYS A 74 72.645 99.270 91.885 1.00 65.55 S ATOM 541 SG CYS A 81 70.660 98.479 95.037 1.00 52.10 S ATOM 776 SG CYS A 111 80.114 137.214 119.716 1.00104.50 S ATOM 804 SG CYS A 114 83.080 137.765 117.727 1.00107.43 S ATOM 1117 SG CYS A 154 82.838 139.158 121.370 1.00121.61 S ATOM 1144 SG CYS A 184 80.905 140.753 118.388 1.00119.44 S ATOM 19775 SG CYS B1196 85.562 109.025 95.523 1.00 58.30 S ATOM 19797 SG CYS B1199 83.383 110.007 98.432 1.00 59.95 S ATOM 19912 SG CYS B1214 81.969 109.463 94.917 1.00 79.09 S ATOM 19933 SG CYS B1217 84.080 112.604 95.936 1.00 85.58 S ATOM 20900 SG CYS C 88 62.340 33.066 100.652 1.00 58.92 S ATOM 20913 SG CYS C 90 59.650 35.555 99.571 1.00 73.13 S ATOM 20948 SG CYS C 94 58.936 32.026 100.798 1.00 49.36 S ATOM 20970 SG CYS C 97 60.005 34.721 103.287 1.00 43.47 S ATOM 28739 SG CYS I 86 59.650 88.261 192.194 1.00 75.69 S ATOM 28763 SG CYS I 89 56.276 86.332 193.236 1.00 82.01 S ATOM 28967 SG CYS I 114 57.611 86.131 189.784 1.00 66.40 S ATOM 29002 SG CYS I 119 56.379 89.480 191.239 1.00 70.66 S ATOM 28187 SG CYS I 17 50.762 128.636 177.365 1.00103.29 S ATOM 28211 SG CYS I 20 49.838 128.859 173.649 1.00105.11 S ATOM 28362 SG CYS I 39 53.221 129.819 174.556 1.00108.55 S ATOM 28387 SG CYS I 42 50.329 132.002 175.770 1.00114.48 S ATOM 29112 SG CYS J 7 61.337 41.849 133.956 1.00 42.72 S ATOM 29136 SG CYS J 10 62.972 38.514 133.235 1.00 29.34 S ATOM 29400 SG CYS J 44 63.717 40.364 136.499 1.00 29.07 S ATOM 29406 SG CYS J 45 60.392 38.635 135.857 1.00 27.32 S ATOM 30543 SG CYS L 19 28.978 64.756 115.748 1.00 67.81 S ATOM 30562 SG CYS L 22 26.483 62.201 115.268 1.00 73.08 S ATOM 30673 SG CYS L 36 26.250 65.032 113.016 1.00 76.07 S ATOM 30699 SG CYS L 39 25.474 65.654 116.810 1.00 82.44 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N GLY S1173 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1173 " occ=0.00 residue: pdb=" N GLY S1227 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1227 " occ=0.00 residue: pdb=" N GLY S1235 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1235 " occ=0.00 residue: pdb=" N GLY S1238 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1238 " occ=0.00 residue: pdb=" N GLY S1260 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1260 " occ=0.00 Time building chain proxies: 7.17, per 1000 atoms: 0.17 Number of scatterers: 41700 At special positions: 0 Unit cell: (155.4, 161.7, 239.4, 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 8 29.99 S 244 16.00 P 75 15.00 Mg 1 11.99 O 7950 8.00 N 7306 7.00 C 26116 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: 3.49 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 71 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 154 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1199 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1196 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1214 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1217 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 17 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 45 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9466 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 52 sheets defined 43.0% alpha, 16.2% beta 30 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 5.56 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.573A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.632A pdb=" N ARG A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.974A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 4.123A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.695A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.912A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.697A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.509A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 869 removed outlier: 5.322A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.546A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 931 " --> pdb=" O GLU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 Processing helix chain 'A' and resid 1086 through 1097 removed outlier: 3.510A pdb=" N GLU A1097 " --> pdb=" O GLN A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1165 through 1168 Processing helix chain 'A' and resid 1189 through 1197 removed outlier: 3.735A pdb=" N VAL A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.691A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1295 removed outlier: 4.055A pdb=" N PHE A1284 " --> pdb=" O ASP A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 3.585A pdb=" N LYS A1317 " --> pdb=" O THR A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1371 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.860A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.706A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1476 through 1481 Processing helix chain 'B' and resid 98 through 114 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 371 through 385 removed outlier: 4.251A pdb=" N MET B 375 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Proline residue: B 380 - end of helix removed outlier: 3.568A pdb=" N ALA B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 408 through 423 Processing helix chain 'B' and resid 434 through 454 Processing helix chain 'B' and resid 472 through 503 removed outlier: 4.091A pdb=" N ARG B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 512 removed outlier: 3.589A pdb=" N ALA B 511 " --> pdb=" O ASN B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 528 removed outlier: 3.671A pdb=" N SER B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 579 through 583 removed outlier: 3.583A pdb=" N TRP B 583 " --> pdb=" O ASN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 634 through 641 removed outlier: 3.991A pdb=" N ALA B 639 " --> pdb=" O ALA B 636 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP B 640 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 713 through 721 removed outlier: 3.531A pdb=" N ILE B 717 " --> pdb=" O LYS B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 727 removed outlier: 3.794A pdb=" N ASN B 727 " --> pdb=" O ARG B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 removed outlier: 3.508A pdb=" N LEU B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 749 Processing helix chain 'B' and resid 755 through 759 Processing helix chain 'B' and resid 776 through 781 removed outlier: 3.650A pdb=" N LEU B 781 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 3.755A pdb=" N ILE B 787 " --> pdb=" O CYS B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 794 Processing helix chain 'B' and resid 795 through 806 Processing helix chain 'B' and resid 838 through 843 removed outlier: 3.725A pdb=" N GLU B 842 " --> pdb=" O ARG B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 880 Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1054 through 1071 removed outlier: 3.877A pdb=" N LEU B1058 " --> pdb=" O THR B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1094 Processing helix chain 'B' and resid 1131 through 1135 Processing helix chain 'B' and resid 1154 through 1158 Processing helix chain 'B' and resid 1164 through 1175 Processing helix chain 'B' and resid 1176 through 1185 Processing helix chain 'B' and resid 1230 through 1242 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 270 Processing helix chain 'D' and resid 77 through 91 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 118 through 133 removed outlier: 3.622A pdb=" N LYS D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 144 removed outlier: 4.406A pdb=" N ALA D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 155 removed outlier: 3.588A pdb=" N LYS D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.504A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 122 Processing helix chain 'E' and resid 133 through 137 removed outlier: 4.203A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.753A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.734A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.672A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 105 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: 3.712A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 Processing helix chain 'K' and resid 82 through 115 removed outlier: 3.558A pdb=" N GLY K 115 " --> pdb=" O ASP K 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 36 removed outlier: 3.619A pdb=" N LEU Q 27 " --> pdb=" O THR Q 23 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS Q 28 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE Q 34 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 576 through 588 Processing helix chain 'M' and resid 589 through 592 Processing helix chain 'M' and resid 603 through 609 removed outlier: 3.697A pdb=" N LEU M 607 " --> pdb=" O LEU M 603 " (cutoff:3.500A) Processing helix chain 'M' and resid 611 through 622 Processing helix chain 'M' and resid 623 through 628 removed outlier: 4.691A pdb=" N GLU M 627 " --> pdb=" O VAL M 624 " (cutoff:3.500A) Processing helix chain 'M' and resid 629 through 641 Processing helix chain 'M' and resid 651 through 677 Processing helix chain 'O' and resid 66 through 83 Processing helix chain 'O' and resid 96 through 110 removed outlier: 3.930A pdb=" N LEU O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU O 102 " --> pdb=" O GLU O 98 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET O 105 " --> pdb=" O LEU O 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 285 through 292 Processing helix chain 'S' and resid 295 through 301 Processing helix chain 'S' and resid 309 through 325 removed outlier: 3.852A pdb=" N ALA S 317 " --> pdb=" O LEU S 313 " (cutoff:3.500A) Processing helix chain 'S' and resid 353 through 368 removed outlier: 4.250A pdb=" N GLN S 357 " --> pdb=" O PRO S 353 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET S 366 " --> pdb=" O ALA S 362 " (cutoff:3.500A) Processing helix chain 'S' and resid 372 through 379 Processing helix chain 'S' and resid 380 through 384 Processing helix chain 'S' and resid 389 through 425 removed outlier: 3.584A pdb=" N TRP S 397 " --> pdb=" O LEU S 393 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN S 398 " --> pdb=" O TRP S 394 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP S 399 " --> pdb=" O ARG S 395 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN S 405 " --> pdb=" O GLU S 401 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU S 416 " --> pdb=" O ASN S 412 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR S 425 " --> pdb=" O GLN S 421 " (cutoff:3.500A) Processing helix chain 'S' and resid 444 through 453 Processing helix chain 'S' and resid 456 through 471 removed outlier: 3.650A pdb=" N VAL S 463 " --> pdb=" O GLU S 459 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 3.916A pdb=" N TYR S 470 " --> pdb=" O HIS S 466 " (cutoff:3.500A) Processing helix chain 'S' and resid 473 through 484 removed outlier: 4.415A pdb=" N LYS S 477 " --> pdb=" O ARG S 473 " (cutoff:3.500A) Processing helix chain 'S' and resid 523 through 530 Processing helix chain 'S' and resid 532 through 538 Processing helix chain 'S' and resid 542 through 553 removed outlier: 3.616A pdb=" N ASN S 549 " --> pdb=" O GLN S 545 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG S 551 " --> pdb=" O GLY S 547 " (cutoff:3.500A) Processing helix chain 'S' and resid 567 through 572 removed outlier: 3.808A pdb=" N LYS S 571 " --> pdb=" O LEU S 567 " (cutoff:3.500A) Processing helix chain 'S' and resid 580 through 598 removed outlier: 3.827A pdb=" N LEU S 594 " --> pdb=" O TYR S 590 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN S 595 " --> pdb=" O MET S 591 " (cutoff:3.500A) Processing helix chain 'S' and resid 599 through 613 removed outlier: 3.825A pdb=" N GLU S 612 " --> pdb=" O GLN S 608 " (cutoff:3.500A) Processing helix chain 'S' and resid 621 through 628 removed outlier: 4.167A pdb=" N LYS S 626 " --> pdb=" O LYS S 622 " (cutoff:3.500A) Processing helix chain 'S' and resid 632 through 636 removed outlier: 4.111A pdb=" N TYR S 635 " --> pdb=" O HIS S 632 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER S 636 " --> pdb=" O TYR S 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 632 through 636' Processing helix chain 'S' and resid 651 through 660 removed outlier: 3.610A pdb=" N LYS S 655 " --> pdb=" O ASP S 651 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU S 660 " --> pdb=" O ILE S 656 " (cutoff:3.500A) Processing helix chain 'S' and resid 684 through 693 removed outlier: 4.392A pdb=" N GLU S 688 " --> pdb=" O THR S 684 " (cutoff:3.500A) Processing helix chain 'S' and resid 699 through 720 removed outlier: 3.703A pdb=" N MET S 711 " --> pdb=" O ARG S 707 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA S 712 " --> pdb=" O GLN S 708 " (cutoff:3.500A) Processing helix chain 'S' and resid 720 through 753 removed outlier: 3.593A pdb=" N MET S 725 " --> pdb=" O LEU S 721 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA S 726 " --> pdb=" O TYR S 722 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL S 741 " --> pdb=" O ALA S 737 " (cutoff:3.500A) Processing helix chain 'S' and resid 826 through 831 removed outlier: 3.663A pdb=" N GLN S 831 " --> pdb=" O GLU S 827 " (cutoff:3.500A) Processing helix chain 'S' and resid 832 through 843 removed outlier: 3.734A pdb=" N LEU S 836 " --> pdb=" O ASP S 832 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS S 837 " --> pdb=" O ILE S 833 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS S 843 " --> pdb=" O PHE S 839 " (cutoff:3.500A) Processing helix chain 'S' and resid 856 through 869 removed outlier: 3.538A pdb=" N GLU S 862 " --> pdb=" O GLN S 858 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG S 866 " --> pdb=" O GLU S 862 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE S 867 " --> pdb=" O ASP S 863 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS S 869 " --> pdb=" O LYS S 865 " (cutoff:3.500A) Processing helix chain 'S' and resid 887 through 896 Processing helix chain 'S' and resid 896 through 902 removed outlier: 3.920A pdb=" N GLU S 902 " --> pdb=" O LYS S 898 " (cutoff:3.500A) Processing helix chain 'S' and resid 910 through 922 removed outlier: 3.931A pdb=" N VAL S 914 " --> pdb=" O LEU S 910 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER S 915 " --> pdb=" O ARG S 911 " (cutoff:3.500A) Processing helix chain 'S' and resid 922 through 931 Processing helix chain 'S' and resid 933 through 940 removed outlier: 4.343A pdb=" N ILE S 937 " --> pdb=" O SER S 933 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU S 938 " --> pdb=" O ASP S 934 " (cutoff:3.500A) Processing helix chain 'S' and resid 950 through 970 removed outlier: 3.690A pdb=" N ASN S 956 " --> pdb=" O GLU S 952 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA S 957 " --> pdb=" O GLU S 953 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU S 961 " --> pdb=" O ALA S 957 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE S 962 " --> pdb=" O LEU S 958 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE S 963 " --> pdb=" O TYR S 959 " (cutoff:3.500A) Processing helix chain 'S' and resid 972 through 979 Processing helix chain 'S' and resid 985 through 989 removed outlier: 3.726A pdb=" N TYR S 988 " --> pdb=" O LEU S 985 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL S 989 " --> pdb=" O ILE S 986 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 985 through 989' Processing helix chain 'S' and resid 993 through 1008 removed outlier: 3.899A pdb=" N HIS S 999 " --> pdb=" O ARG S 995 " (cutoff:3.500A) Processing helix chain 'S' and resid 1013 through 1020 removed outlier: 3.510A pdb=" N LEU S1017 " --> pdb=" O SER S1013 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL S1018 " --> pdb=" O ARG S1014 " (cutoff:3.500A) Processing helix chain 'S' and resid 1024 through 1032 removed outlier: 3.856A pdb=" N ASN S1030 " --> pdb=" O LYS S1026 " (cutoff:3.500A) Processing helix chain 'S' and resid 1059 through 1061 No H-bonds generated for 'chain 'S' and resid 1059 through 1061' Processing helix chain 'S' and resid 1062 through 1069 removed outlier: 3.549A pdb=" N MET S1069 " --> pdb=" O TRP S1065 " (cutoff:3.500A) Processing helix chain 'S' and resid 1070 through 1074 Processing helix chain 'S' and resid 1086 through 1095 removed outlier: 3.503A pdb=" N LEU S1093 " --> pdb=" O LEU S1089 " (cutoff:3.500A) Processing helix chain 'S' and resid 1103 through 1115 removed outlier: 3.636A pdb=" N ALA S1108 " --> pdb=" O LEU S1104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU S1109 " --> pdb=" O ASP S1105 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU S1110 " --> pdb=" O ALA S1106 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG S1113 " --> pdb=" O GLU S1109 " (cutoff:3.500A) Processing helix chain 'S' and resid 1119 through 1131 Processing helix chain 'S' and resid 1145 through 1154 Processing helix chain 'S' and resid 1157 through 1162 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.384A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.303A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.885A pdb=" N LEU B1161 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1137 through 1139 removed outlier: 7.641A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.565A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.218A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.599A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB2, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB3, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB4, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 4.083A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.846A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB7, first strand: chain 'A' and resid 1408 through 1409 Processing sheet with id=AB8, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AB9, first strand: chain 'B' and resid 142 through 145 removed outlier: 5.500A pdb=" N TYR B 161 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 210 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU B 163 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR B 208 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE B 165 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR B 206 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLN B 167 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ALA B 199 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS B 228 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 201 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE B 205 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLN B 222 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LYS B 207 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN B 220 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL B 209 " --> pdb=" O GLN B 218 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLN B 218 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LYS B 211 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN B 216 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.887A pdb=" N LYS M 688 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 174 through 176 Processing sheet with id=AC3, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AC4, first strand: chain 'B' and resid 468 through 471 Processing sheet with id=AC5, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AC6, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AC7, first strand: chain 'B' and resid 709 through 710 Processing sheet with id=AC8, first strand: chain 'B' and resid 628 through 629 removed outlier: 5.425A pdb=" N TRP B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 646 " --> pdb=" O TRP B 650 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 652 " --> pdb=" O ILE B 644 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 824 through 828 removed outlier: 6.736A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 824 through 828 removed outlier: 6.736A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL B 984 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 836 through 837 Processing sheet with id=AD3, first strand: chain 'B' and resid 1102 through 1103 removed outlier: 7.323A pdb=" N VAL B 871 " --> pdb=" O GLY B1023 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN B1025 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET B 873 " --> pdb=" O GLN B1025 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE B1119 " --> pdb=" O ILE B 859 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 897 through 898 Processing sheet with id=AD5, first strand: chain 'B' and resid 905 through 906 removed outlier: 6.743A pdb=" N GLN B 915 " --> pdb=" O ASP B 968 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 942 through 944 removed outlier: 6.884A pdb=" N THR B 971 " --> pdb=" O ILE B 943 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1190 through 1196 Processing sheet with id=AD8, first strand: chain 'B' and resid 1204 through 1206 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.235A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.586A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.432A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 72 through 73 removed outlier: 6.754A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 72 through 73 Processing sheet with id=AE5, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.469A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE7, first strand: chain 'G' and resid 83 through 91 removed outlier: 6.845A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 118 through 120 removed outlier: 4.165A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR G 128 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE G 137 " --> pdb=" O TYR G 128 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 26 through 29 Processing sheet with id=AF1, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF3, first strand: chain 'Q' and resid 7 through 9 Processing sheet with id=AF4, first strand: chain 'O' and resid 18 through 21 Processing sheet with id=AF5, first strand: chain 'S' and resid 643 through 644 Processing sheet with id=AF6, first strand: chain 'S' and resid 805 through 810 removed outlier: 4.015A pdb=" N ASP S 807 " --> pdb=" O LEU S 798 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS S 796 " --> pdb=" O LEU S 809 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL S 781 " --> pdb=" O VAL S 799 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU S 782 " --> pdb=" O THR S 849 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ALA S 851 " --> pdb=" O LEU S 782 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE S 784 " --> pdb=" O ALA S 851 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL S 848 " --> pdb=" O GLU S 883 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL S 885 " --> pdb=" O VAL S 848 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL S 850 " --> pdb=" O VAL S 885 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 1170 through 1173 removed outlier: 6.325A pdb=" N LYS S1229 " --> pdb=" O THR S1172 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY S1238 " --> pdb=" O THR S1230 " (cutoff:3.500A) 1771 hydrogen bonds defined for protein. 4899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 12.03 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10025 1.33 - 1.45: 8426 1.45 - 1.57: 23652 1.57 - 1.69: 146 1.69 - 1.81: 385 Bond restraints: 42634 Sorted by residual: bond pdb=" C3' DC T 33 " pdb=" O3' DC T 33 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" C ILE B1049 " pdb=" N PRO B1050 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.30e-02 5.92e+03 1.28e+01 bond pdb=" C3' DT T 27 " pdb=" O3' DT T 27 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 1.02e+01 bond pdb=" C3' DG T 35 " pdb=" C2' DG T 35 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.67e+00 bond pdb=" C3' DC N 41 " pdb=" C2' DC N 41 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.38e+00 ... (remaining 42629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 56576 2.42 - 4.83: 1146 4.83 - 7.25: 127 7.25 - 9.66: 26 9.66 - 12.08: 8 Bond angle restraints: 57883 Sorted by residual: angle pdb=" CA PRO A 478 " pdb=" C PRO A 478 " pdb=" O PRO A 478 " ideal model delta sigma weight residual 121.38 116.88 4.50 7.70e-01 1.69e+00 3.42e+01 angle pdb=" CA PRO A 478 " pdb=" C PRO A 478 " pdb=" N TRP A 479 " ideal model delta sigma weight residual 116.45 121.40 -4.95 8.50e-01 1.38e+00 3.39e+01 angle pdb=" O4' DC T 33 " pdb=" C4' DC T 33 " pdb=" C3' DC T 33 " ideal model delta sigma weight residual 106.00 102.59 3.41 6.00e-01 2.78e+00 3.23e+01 angle pdb=" N VAL B 430 " pdb=" CA VAL B 430 " pdb=" C VAL B 430 " ideal model delta sigma weight residual 112.43 107.26 5.17 9.20e-01 1.18e+00 3.16e+01 angle pdb=" O4' DG T 26 " pdb=" C4' DG T 26 " pdb=" C3' DG T 26 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.64e+01 ... (remaining 57878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.23: 24908 30.23 - 60.47: 917 60.47 - 90.70: 78 90.70 - 120.93: 0 120.93 - 151.16: 1 Dihedral angle restraints: 25904 sinusoidal: 11298 harmonic: 14606 Sorted by residual: dihedral pdb=" C4' G P 36 " pdb=" C3' G P 36 " pdb=" C2' G P 36 " pdb=" C1' G P 36 " ideal model delta sinusoidal sigma weight residual 36.35 -35.77 72.12 1 3.10e+00 1.04e-01 6.92e+02 dihedral pdb=" C4' G P 34 " pdb=" C3' G P 34 " pdb=" C2' G P 34 " pdb=" C1' G P 34 " ideal model delta sinusoidal sigma weight residual 36.34 -35.46 71.80 1 3.10e+00 1.04e-01 6.87e+02 dihedral pdb=" C4' A P 35 " pdb=" C3' A P 35 " pdb=" C2' A P 35 " pdb=" C1' A P 35 " ideal model delta sinusoidal sigma weight residual 36.34 -34.72 71.07 1 3.10e+00 1.04e-01 6.75e+02 ... (remaining 25901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5970 0.099 - 0.199: 457 0.199 - 0.298: 29 0.298 - 0.398: 0 0.398 - 0.497: 1 Chirality restraints: 6457 Sorted by residual: chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CB THR B 551 " pdb=" CA THR B 551 " pdb=" OG1 THR B 551 " pdb=" CG2 THR B 551 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' A P 35 " pdb=" C3' A P 35 " pdb=" O2' A P 35 " pdb=" C1' A P 35 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 6454 not shown) Planarity restraints: 7234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 120 " 0.077 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO G 121 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO G 121 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO G 121 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 465 " -0.041 2.00e-02 2.50e+03 3.16e-02 1.99e+01 pdb=" CG TYR B 465 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR B 465 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 465 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 465 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 465 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 465 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 465 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1334 " -0.021 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" CG TRP A1334 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP A1334 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP A1334 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A1334 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP A1334 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A1334 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1334 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1334 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A1334 " 0.000 2.00e-02 2.50e+03 ... (remaining 7231 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 544 2.63 - 3.19: 35564 3.19 - 3.76: 68815 3.76 - 4.33: 97300 4.33 - 4.90: 154228 Nonbonded interactions: 356451 Sorted by model distance: nonbonded pdb=" O3' U P 46 " pdb="MG MG A2001 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.064 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 2.090 2.170 nonbonded pdb=" O MET M 575 " pdb=" OH TYR O 76 " model vdw 2.172 3.040 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2001 " model vdw 2.186 2.170 ... (remaining 356446 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=0.99 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: 8.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 48.390 Find NCS groups from input model: 0.320 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:2.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 42666 Z= 0.287 Angle : 0.852 12.081 57928 Z= 0.495 Chirality : 0.055 0.497 6457 Planarity : 0.006 0.119 7234 Dihedral : 15.105 151.164 16438 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.02 % Allowed : 0.36 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.11), residues: 4930 helix: -0.88 (0.11), residues: 1822 sheet: -0.65 (0.20), residues: 652 loop : -0.96 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 160 TYR 0.076 0.002 TYR B 465 PHE 0.035 0.003 PHE A 112 TRP 0.071 0.003 TRP A1334 HIS 0.011 0.001 HIS I 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.29 (42634) covalent geometry : angle 0.84436 / 0.49 (57883) hydrogen bonds : bond 0.18634 / 12.89 ( 1815) hydrogen bonds : angle 7.52901 / 5.36 ( 5053) metal coordination : bond 0.00805 / 0.60 ( 32) metal coordination : angle 4.17127 / 2.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 430 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP S 462 " (corrupted residue). Skipping it. REVERT: G 150 THR cc_start: 0.6842 (m) cc_final: 0.6141 (p) REVERT: I 44 TYR cc_start: 0.8112 (t80) cc_final: 0.7558 (t80) REVERT: I 57 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8309 (mtmm) REVERT: J 26 GLN cc_start: 0.7277 (pp30) cc_final: 0.6935 (tm-30) REVERT: S 1023 MET cc_start: -0.2630 (ppp) cc_final: -0.3965 (ptt) REVERT: S 1152 MET cc_start: 0.1510 (ptp) cc_final: 0.0984 (ptm) outliers start: 1 outliers final: 1 residues processed: 431 average time/residue: 0.2752 time to fit residues: 188.7108 Evaluate side-chains 327 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 462 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 494 optimal weight: 40.0000 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 GLN ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN ** M 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 405 GLN ** S 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1016 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.127772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.075334 restraints weight = 93261.705| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.05 r_work: 0.2802 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 42666 Z= 0.164 Angle : 0.671 16.394 57928 Z= 0.347 Chirality : 0.050 1.117 6457 Planarity : 0.005 0.061 7234 Dihedral : 11.375 146.836 6271 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.32 % Allowed : 5.88 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.12), residues: 4930 helix: -0.21 (0.11), residues: 1903 sheet: -0.57 (0.20), residues: 651 loop : -0.75 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B1218 TYR 0.025 0.002 TYR K 81 PHE 0.026 0.002 PHE B 433 TRP 0.030 0.002 TRP S 399 HIS 0.013 0.001 HIS M 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (42634) covalent geometry : angle 0.66334 / 0.35 (57883) hydrogen bonds : bond 0.05253 / 3.55 ( 1815) hydrogen bonds : angle 5.86270 / 4.19 ( 5053) metal coordination : bond 0.00670 / 0.50 ( 32) metal coordination : angle 3.73725 / 2.66 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 348 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.8521 (mtm) cc_final: 0.8272 (mtm) REVERT: A 334 ARG cc_start: 0.8527 (ttp-170) cc_final: 0.8132 (ttp80) REVERT: A 1296 MET cc_start: 0.7644 (tpt) cc_final: 0.7366 (ttm) REVERT: A 1484 MET cc_start: 0.7288 (mtm) cc_final: 0.7071 (mtt) REVERT: B 754 MET cc_start: 0.9165 (tpp) cc_final: 0.8804 (tpp) REVERT: D 104 MET cc_start: 0.9273 (mmm) cc_final: 0.8842 (mmm) REVERT: E 90 TYR cc_start: 0.8793 (m-80) cc_final: 0.8258 (m-80) REVERT: E 94 MET cc_start: 0.8879 (mmm) cc_final: 0.8536 (tpt) REVERT: F 82 GLU cc_start: 0.8311 (mp0) cc_final: 0.8096 (mp0) REVERT: F 86 GLU cc_start: 0.7881 (pm20) cc_final: 0.7630 (pm20) REVERT: G 32 THR cc_start: 0.9552 (m) cc_final: 0.9351 (p) REVERT: G 33 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8537 (mt-10) REVERT: G 73 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8791 (mtpp) REVERT: H 55 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8604 (ttmm) REVERT: I 35 LEU cc_start: 0.8346 (tp) cc_final: 0.8132 (tp) REVERT: I 57 LYS cc_start: 0.8764 (mtmt) cc_final: 0.7992 (mtmm) REVERT: K 93 ASP cc_start: 0.8811 (m-30) cc_final: 0.8520 (m-30) REVERT: Q 68 ARG cc_start: 0.8089 (tpp80) cc_final: 0.7729 (tpp80) outliers start: 14 outliers final: 6 residues processed: 356 average time/residue: 0.2509 time to fit residues: 146.7379 Evaluate side-chains 319 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 313 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain K residue 80 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 341 optimal weight: 0.6980 chunk 344 optimal weight: 3.9990 chunk 394 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 397 optimal weight: 0.0980 chunk 339 optimal weight: 4.9990 chunk 340 optimal weight: 1.9990 chunk 385 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 chunk 329 optimal weight: 20.0000 chunk 361 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN B 731 GLN B1057 HIS ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS I 46 GLN I 60 HIS L 23 HIS M 580 GLN ** M 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 869 HIS S1016 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.127515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.072813 restraints weight = 93760.838| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.04 r_work: 0.2763 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42666 Z= 0.156 Angle : 0.596 10.386 57928 Z= 0.311 Chirality : 0.046 0.886 6457 Planarity : 0.004 0.058 7234 Dihedral : 11.298 146.335 6269 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.75 % Allowed : 7.74 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.12), residues: 4930 helix: 0.27 (0.12), residues: 1907 sheet: -0.46 (0.21), residues: 624 loop : -0.64 (0.13), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG I 103 TYR 0.024 0.001 TYR K 81 PHE 0.024 0.001 PHE G 2 TRP 0.028 0.002 TRP A1334 HIS 0.013 0.001 HIS M 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (42634) covalent geometry : angle 0.58981 / 0.31 (57883) hydrogen bonds : bond 0.04371 / 2.92 ( 1815) hydrogen bonds : angle 5.41672 / 3.87 ( 5053) metal coordination : bond 0.00635 / 0.47 ( 32) metal coordination : angle 3.23342 / 2.34 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 335 time to evaluate : 1.591 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 329 MET cc_start: 0.8490 (mtm) cc_final: 0.8203 (mtm) REVERT: A 334 ARG cc_start: 0.8515 (ttp-170) cc_final: 0.8201 (ttp80) REVERT: A 1296 MET cc_start: 0.7837 (tpt) cc_final: 0.7626 (ttm) REVERT: A 1484 MET cc_start: 0.7303 (mtm) cc_final: 0.6985 (mtt) REVERT: B 126 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8256 (tm-30) REVERT: B 433 PHE cc_start: 0.8392 (m-80) cc_final: 0.8192 (m-80) REVERT: C 164 TYR cc_start: 0.9056 (m-80) cc_final: 0.8839 (m-10) REVERT: D 81 MET cc_start: 0.9296 (ppp) cc_final: 0.9034 (ppp) REVERT: D 88 GLN cc_start: 0.8894 (pp30) cc_final: 0.8608 (pp30) REVERT: D 104 MET cc_start: 0.9388 (mmm) cc_final: 0.8919 (mmm) REVERT: E 90 TYR cc_start: 0.8882 (m-80) cc_final: 0.8227 (m-80) REVERT: G 33 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8625 (mt-10) REVERT: H 55 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8600 (ttmm) REVERT: I 21 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8505 (t0) REVERT: I 64 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7617 (mm-30) REVERT: J 31 GLU cc_start: 0.9010 (mp0) cc_final: 0.8593 (mp0) REVERT: K 16 GLU cc_start: 0.8152 (tt0) cc_final: 0.7947 (tt0) REVERT: K 24 ASP cc_start: 0.8486 (t0) cc_final: 0.8269 (t0) REVERT: Q 68 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7765 (tpp80) REVERT: M 660 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7750 (tm-30) outliers start: 33 outliers final: 16 residues processed: 355 average time/residue: 0.2622 time to fit residues: 153.6128 Evaluate side-chains 329 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 312 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain M residue 645 ARG Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain S residue 448 MET Chi-restraints excluded: chain S residue 574 VAL Chi-restraints excluded: chain S residue 1261 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 278 optimal weight: 10.0000 chunk 257 optimal weight: 1.9990 chunk 387 optimal weight: 9.9990 chunk 389 optimal weight: 50.0000 chunk 194 optimal weight: 0.1980 chunk 481 optimal weight: 50.0000 chunk 477 optimal weight: 40.0000 chunk 492 optimal weight: 5.9990 chunk 299 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 331 optimal weight: 0.0040 overall best weight: 1.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS A 377 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** M 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.126242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.070489 restraints weight = 93801.590| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.93 r_work: 0.2725 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 42666 Z= 0.241 Angle : 0.619 9.326 57928 Z= 0.321 Chirality : 0.047 0.807 6457 Planarity : 0.004 0.056 7234 Dihedral : 11.269 146.159 6269 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.86 % Allowed : 9.41 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.12), residues: 4930 helix: 0.44 (0.12), residues: 1914 sheet: -0.49 (0.20), residues: 642 loop : -0.56 (0.13), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 617 TYR 0.027 0.002 TYR K 81 PHE 0.024 0.002 PHE D 113 TRP 0.024 0.002 TRP A1334 HIS 0.012 0.001 HIS M 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (42634) covalent geometry : angle 0.61033 / 0.32 (57883) hydrogen bonds : bond 0.04374 / 2.92 ( 1815) hydrogen bonds : angle 5.30489 / 3.79 ( 5053) metal coordination : bond 0.00959 / 0.67 ( 32) metal coordination : angle 3.76349 / 2.69 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 326 time to evaluate : 1.564 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 330 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7261 (mm110) REVERT: A 334 ARG cc_start: 0.8572 (ttp-170) cc_final: 0.8029 (ttp80) REVERT: A 1296 MET cc_start: 0.7929 (tpt) cc_final: 0.7650 (ttm) REVERT: B 433 PHE cc_start: 0.8422 (m-80) cc_final: 0.8183 (m-80) REVERT: C 164 TYR cc_start: 0.9093 (m-80) cc_final: 0.8837 (m-10) REVERT: D 68 PHE cc_start: 0.8502 (m-10) cc_final: 0.7989 (m-10) REVERT: D 87 LYS cc_start: 0.9222 (mmmm) cc_final: 0.9008 (mmmm) REVERT: D 104 MET cc_start: 0.9377 (mmm) cc_final: 0.9005 (mmm) REVERT: D 163 ARG cc_start: 0.7505 (ttt180) cc_final: 0.6954 (ptm160) REVERT: D 164 PHE cc_start: 0.7761 (m-80) cc_final: 0.7402 (m-80) REVERT: E 35 GLN cc_start: 0.9426 (OUTLIER) cc_final: 0.9188 (tm-30) REVERT: E 90 TYR cc_start: 0.8962 (m-80) cc_final: 0.8269 (m-80) REVERT: F 86 GLU cc_start: 0.7992 (pm20) cc_final: 0.7682 (pm20) REVERT: G 33 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8640 (mt-10) REVERT: I 44 TYR cc_start: 0.8326 (t80) cc_final: 0.8121 (t80) REVERT: I 56 ASN cc_start: 0.9044 (t0) cc_final: 0.8768 (t0) REVERT: I 57 LYS cc_start: 0.8673 (mtmt) cc_final: 0.7813 (mtmt) REVERT: I 60 HIS cc_start: 0.7027 (t-170) cc_final: 0.6655 (t-170) REVERT: J 31 GLU cc_start: 0.9040 (mp0) cc_final: 0.8580 (mp0) REVERT: K 13 PHE cc_start: 0.8341 (p90) cc_final: 0.7908 (p90) REVERT: K 16 GLU cc_start: 0.8120 (tt0) cc_final: 0.7812 (tt0) REVERT: K 24 ASP cc_start: 0.8580 (t0) cc_final: 0.8338 (t0) REVERT: K 93 ASP cc_start: 0.8849 (m-30) cc_final: 0.8551 (m-30) REVERT: L 38 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8612 (mm-30) REVERT: M 602 VAL cc_start: 0.4520 (OUTLIER) cc_final: 0.4223 (p) REVERT: M 660 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7670 (tm-30) outliers start: 38 outliers final: 20 residues processed: 352 average time/residue: 0.2591 time to fit residues: 150.2819 Evaluate side-chains 330 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 308 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain M residue 602 VAL Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain S residue 448 MET Chi-restraints excluded: chain S residue 1261 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 306 optimal weight: 0.9980 chunk 329 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 488 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 396 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 279 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** M 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.126596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.071980 restraints weight = 93289.784| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.97 r_work: 0.2743 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 42666 Z= 0.163 Angle : 0.575 9.189 57928 Z= 0.299 Chirality : 0.045 0.753 6457 Planarity : 0.004 0.055 7234 Dihedral : 11.252 146.061 6269 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.04 % Allowed : 10.03 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.12), residues: 4930 helix: 0.62 (0.12), residues: 1915 sheet: -0.47 (0.20), residues: 642 loop : -0.50 (0.13), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1218 TYR 0.020 0.001 TYR K 81 PHE 0.021 0.001 PHE B 506 TRP 0.023 0.002 TRP A1334 HIS 0.011 0.001 HIS M 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (42634) covalent geometry : angle 0.56735 / 0.30 (57883) hydrogen bonds : bond 0.04037 / 2.68 ( 1815) hydrogen bonds : angle 5.15819 / 3.68 ( 5053) metal coordination : bond 0.00679 / 0.49 ( 32) metal coordination : angle 3.46557 / 2.54 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 331 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ARG cc_start: 0.8564 (ttp-170) cc_final: 0.8158 (ttp80) REVERT: A 1296 MET cc_start: 0.8023 (tpt) cc_final: 0.7791 (ttm) REVERT: B 126 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 433 PHE cc_start: 0.8433 (m-80) cc_final: 0.8150 (m-80) REVERT: B 1218 ARG cc_start: 0.8226 (mmp80) cc_final: 0.7998 (mmp80) REVERT: C 164 TYR cc_start: 0.9050 (m-80) cc_final: 0.8777 (m-10) REVERT: D 87 LYS cc_start: 0.9260 (mmmm) cc_final: 0.9036 (mmmm) REVERT: D 104 MET cc_start: 0.9364 (mmm) cc_final: 0.8990 (mmm) REVERT: D 163 ARG cc_start: 0.7528 (ttt180) cc_final: 0.6786 (ptm160) REVERT: D 164 PHE cc_start: 0.7843 (m-80) cc_final: 0.7374 (m-80) REVERT: E 35 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.9177 (tm-30) REVERT: E 90 TYR cc_start: 0.9031 (m-80) cc_final: 0.8311 (m-80) REVERT: F 86 GLU cc_start: 0.7930 (pm20) cc_final: 0.7668 (pm20) REVERT: G 33 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8629 (mt-10) REVERT: G 78 ARG cc_start: 0.8373 (tpp80) cc_final: 0.7889 (tpp-160) REVERT: G 146 LYS cc_start: 0.8606 (tptp) cc_final: 0.8291 (tptp) REVERT: H 37 MET cc_start: 0.8238 (mmt) cc_final: 0.7829 (mmt) REVERT: H 55 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8654 (ttmm) REVERT: I 56 ASN cc_start: 0.9009 (t0) cc_final: 0.8683 (t0) REVERT: I 57 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8239 (mtmt) REVERT: J 26 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8346 (tm-30) REVERT: J 31 GLU cc_start: 0.9027 (mp0) cc_final: 0.8579 (mp0) REVERT: K 13 PHE cc_start: 0.8341 (p90) cc_final: 0.8054 (p90) REVERT: K 16 GLU cc_start: 0.8126 (tt0) cc_final: 0.7837 (tt0) REVERT: K 24 ASP cc_start: 0.8571 (t0) cc_final: 0.8341 (t0) REVERT: K 93 ASP cc_start: 0.8858 (m-30) cc_final: 0.8539 (m-30) REVERT: L 22 CYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8583 (p) REVERT: L 38 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8628 (mm-30) REVERT: M 660 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7772 (tm-30) outliers start: 46 outliers final: 25 residues processed: 362 average time/residue: 0.2375 time to fit residues: 142.7830 Evaluate side-chains 342 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 315 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1190 GLN Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain S residue 448 MET Chi-restraints excluded: chain S residue 574 VAL Chi-restraints excluded: chain S residue 1261 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 166 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 150 optimal weight: 0.0670 chunk 348 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 385 optimal weight: 50.0000 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 471 optimal weight: 50.0000 chunk 43 optimal weight: 0.6980 chunk 334 optimal weight: 4.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 ASN B 731 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.127324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.073072 restraints weight = 93705.735| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.06 r_work: 0.2761 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 42666 Z= 0.122 Angle : 0.555 9.621 57928 Z= 0.289 Chirality : 0.044 0.696 6457 Planarity : 0.004 0.054 7234 Dihedral : 11.204 145.496 6269 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.07 % Allowed : 10.46 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.12), residues: 4930 helix: 0.76 (0.12), residues: 1919 sheet: -0.46 (0.20), residues: 656 loop : -0.42 (0.13), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 112 TYR 0.020 0.001 TYR M 616 PHE 0.025 0.001 PHE D 113 TRP 0.021 0.001 TRP A1334 HIS 0.011 0.001 HIS M 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (42634) covalent geometry : angle 0.54858 / 0.29 (57883) hydrogen bonds : bond 0.03820 / 2.52 ( 1815) hydrogen bonds : angle 5.04954 / 3.60 ( 5053) metal coordination : bond 0.00495 / 0.37 ( 32) metal coordination : angle 3.09018 / 2.24 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 341 time to evaluate : 1.557 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 334 ARG cc_start: 0.8548 (ttp-170) cc_final: 0.8297 (ttp80) REVERT: A 1296 MET cc_start: 0.8012 (tpt) cc_final: 0.7779 (ttm) REVERT: B 126 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8301 (tm-30) REVERT: B 316 MET cc_start: 0.8893 (ttp) cc_final: 0.8631 (ttt) REVERT: B 433 PHE cc_start: 0.8401 (m-80) cc_final: 0.8090 (m-80) REVERT: B 731 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8330 (tp40) REVERT: C 164 TYR cc_start: 0.9039 (m-80) cc_final: 0.8756 (m-10) REVERT: D 81 MET cc_start: 0.9484 (ppp) cc_final: 0.9081 (ppp) REVERT: D 87 LYS cc_start: 0.9307 (mmmm) cc_final: 0.9077 (mmmm) REVERT: D 104 MET cc_start: 0.9406 (mmm) cc_final: 0.9083 (mmm) REVERT: D 163 ARG cc_start: 0.7581 (ttt180) cc_final: 0.6784 (ptm160) REVERT: D 164 PHE cc_start: 0.7865 (m-80) cc_final: 0.7364 (m-80) REVERT: E 35 GLN cc_start: 0.9417 (OUTLIER) cc_final: 0.9170 (tm-30) REVERT: E 90 TYR cc_start: 0.8994 (m-80) cc_final: 0.8290 (m-80) REVERT: F 86 GLU cc_start: 0.7944 (pm20) cc_final: 0.7674 (pm20) REVERT: G 33 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8607 (mt-10) REVERT: G 78 ARG cc_start: 0.8346 (tpp80) cc_final: 0.7940 (tpp-160) REVERT: H 55 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8674 (ttmm) REVERT: I 56 ASN cc_start: 0.8951 (t0) cc_final: 0.8574 (t0) REVERT: I 57 LYS cc_start: 0.8598 (mtmt) cc_final: 0.7367 (mtmm) REVERT: I 60 HIS cc_start: 0.6915 (t-170) cc_final: 0.6571 (t-170) REVERT: J 26 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8357 (tm-30) REVERT: J 31 GLU cc_start: 0.9043 (mp0) cc_final: 0.8592 (mp0) REVERT: K 13 PHE cc_start: 0.8380 (p90) cc_final: 0.8013 (p90) REVERT: K 16 GLU cc_start: 0.8119 (tt0) cc_final: 0.7858 (tt0) REVERT: K 24 ASP cc_start: 0.8497 (t0) cc_final: 0.8227 (t0) REVERT: K 93 ASP cc_start: 0.8861 (m-30) cc_final: 0.8534 (m-30) REVERT: L 22 CYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8634 (p) REVERT: L 38 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8660 (mm-30) REVERT: M 660 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7753 (tm-30) REVERT: O 79 TYR cc_start: 0.5073 (OUTLIER) cc_final: 0.4684 (t80) outliers start: 47 outliers final: 32 residues processed: 375 average time/residue: 0.2284 time to fit residues: 143.7715 Evaluate side-chains 350 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 314 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1190 GLN Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain M residue 598 VAL Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain S residue 448 MET Chi-restraints excluded: chain S residue 574 VAL Chi-restraints excluded: chain S residue 1261 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 371 optimal weight: 1.9990 chunk 340 optimal weight: 0.9990 chunk 492 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 454 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 353 optimal weight: 2.9990 chunk 483 optimal weight: 50.0000 chunk 57 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 539 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN S 608 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.125983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.070260 restraints weight = 93600.586| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.94 r_work: 0.2720 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 42666 Z= 0.250 Angle : 0.611 9.530 57928 Z= 0.315 Chirality : 0.047 0.688 6457 Planarity : 0.004 0.054 7234 Dihedral : 11.236 145.484 6269 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.11 % Allowed : 11.34 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.12), residues: 4930 helix: 0.75 (0.12), residues: 1925 sheet: -0.44 (0.20), residues: 647 loop : -0.40 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 112 TYR 0.022 0.002 TYR K 81 PHE 0.033 0.002 PHE D 113 TRP 0.020 0.002 TRP A1334 HIS 0.011 0.001 HIS Q 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.25 (42634) covalent geometry : angle 0.60269 / 0.31 (57883) hydrogen bonds : bond 0.04128 / 2.74 ( 1815) hydrogen bonds : angle 5.07287 / 3.62 ( 5053) metal coordination : bond 0.01000 / 0.69 ( 32) metal coordination : angle 3.62849 / 2.60 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 318 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1296 MET cc_start: 0.8145 (tpt) cc_final: 0.7892 (ttm) REVERT: B 433 PHE cc_start: 0.8440 (m-80) cc_final: 0.8115 (m-80) REVERT: C 27 ASP cc_start: 0.8276 (m-30) cc_final: 0.8057 (m-30) REVERT: C 164 TYR cc_start: 0.9082 (m-80) cc_final: 0.8786 (m-80) REVERT: D 80 HIS cc_start: 0.9519 (t70) cc_final: 0.9250 (t70) REVERT: D 87 LYS cc_start: 0.9354 (mmmm) cc_final: 0.9100 (mmmm) REVERT: D 104 MET cc_start: 0.9410 (mmm) cc_final: 0.9080 (mmm) REVERT: D 163 ARG cc_start: 0.7676 (ttt180) cc_final: 0.6859 (ptm160) REVERT: D 164 PHE cc_start: 0.7888 (m-80) cc_final: 0.7323 (m-80) REVERT: E 35 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.9195 (tm-30) REVERT: E 90 TYR cc_start: 0.9070 (m-80) cc_final: 0.8477 (m-80) REVERT: E 94 MET cc_start: 0.8755 (mmm) cc_final: 0.8500 (tpt) REVERT: F 86 GLU cc_start: 0.7928 (pm20) cc_final: 0.7648 (pm20) REVERT: G 33 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8662 (mt-10) REVERT: G 78 ARG cc_start: 0.8367 (tpp80) cc_final: 0.7967 (tpp-160) REVERT: G 146 LYS cc_start: 0.8612 (tptp) cc_final: 0.8286 (tptp) REVERT: H 37 MET cc_start: 0.8239 (mmt) cc_final: 0.7990 (mmt) REVERT: I 57 LYS cc_start: 0.8482 (mtmt) cc_final: 0.8079 (mtmm) REVERT: J 26 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8315 (tm-30) REVERT: J 31 GLU cc_start: 0.9047 (mp0) cc_final: 0.8604 (mp0) REVERT: K 16 GLU cc_start: 0.8114 (tt0) cc_final: 0.7893 (tt0) REVERT: K 24 ASP cc_start: 0.8590 (t0) cc_final: 0.8308 (t0) REVERT: K 93 ASP cc_start: 0.8836 (m-30) cc_final: 0.8505 (m-30) REVERT: L 22 CYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8522 (p) REVERT: L 38 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8666 (mm-30) REVERT: M 660 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7886 (tm-30) REVERT: O 79 TYR cc_start: 0.5127 (OUTLIER) cc_final: 0.4766 (t80) REVERT: S 591 MET cc_start: 0.4045 (mmm) cc_final: 0.3613 (mmt) outliers start: 49 outliers final: 35 residues processed: 352 average time/residue: 0.2290 time to fit residues: 135.4057 Evaluate side-chains 349 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 311 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 1169 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain S residue 448 MET Chi-restraints excluded: chain S residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 412 optimal weight: 0.0970 chunk 216 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 207 optimal weight: 0.5980 chunk 486 optimal weight: 30.0000 chunk 427 optimal weight: 30.0000 chunk 280 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 453 optimal weight: 8.9990 chunk 473 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS I 100 HIS J 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.127265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.072123 restraints weight = 93436.745| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.98 r_work: 0.2766 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 42666 Z= 0.127 Angle : 0.572 13.739 57928 Z= 0.295 Chirality : 0.045 0.649 6457 Planarity : 0.004 0.053 7234 Dihedral : 11.224 145.208 6269 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.23 % Allowed : 11.66 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.12), residues: 4930 helix: 0.85 (0.12), residues: 1923 sheet: -0.45 (0.20), residues: 650 loop : -0.34 (0.13), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 109 TYR 0.022 0.001 TYR M 616 PHE 0.028 0.001 PHE M 593 TRP 0.024 0.002 TRP A1334 HIS 0.010 0.001 HIS M 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (42634) covalent geometry : angle 0.56514 / 0.29 (57883) hydrogen bonds : bond 0.03757 / 2.48 ( 1815) hydrogen bonds : angle 4.98399 / 3.55 ( 5053) metal coordination : bond 0.00535 / 0.40 ( 32) metal coordination : angle 3.16149 / 2.30 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 324 time to evaluate : 1.426 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 334 ARG cc_start: 0.8525 (ttp-170) cc_final: 0.8075 (ttp80) REVERT: A 1296 MET cc_start: 0.8118 (tpt) cc_final: 0.7893 (ttm) REVERT: B 126 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 316 MET cc_start: 0.8883 (ttp) cc_final: 0.8621 (ttt) REVERT: B 433 PHE cc_start: 0.8422 (m-80) cc_final: 0.8070 (m-80) REVERT: C 27 ASP cc_start: 0.8243 (m-30) cc_final: 0.8013 (m-30) REVERT: C 164 TYR cc_start: 0.9027 (m-80) cc_final: 0.8730 (m-80) REVERT: D 87 LYS cc_start: 0.9356 (mmmm) cc_final: 0.9088 (mmmm) REVERT: D 163 ARG cc_start: 0.7621 (ttt180) cc_final: 0.6828 (ptm160) REVERT: D 164 PHE cc_start: 0.7829 (m-80) cc_final: 0.7277 (m-80) REVERT: E 35 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.9184 (tm-30) REVERT: E 90 TYR cc_start: 0.9062 (m-80) cc_final: 0.8481 (m-80) REVERT: E 94 MET cc_start: 0.8731 (mmm) cc_final: 0.8474 (tpt) REVERT: F 86 GLU cc_start: 0.7920 (pm20) cc_final: 0.7643 (pm20) REVERT: G 33 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8638 (mt-10) REVERT: G 146 LYS cc_start: 0.8610 (tptp) cc_final: 0.8274 (tptp) REVERT: H 37 MET cc_start: 0.8183 (mmt) cc_final: 0.7926 (mmt) REVERT: H 55 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8617 (ttmm) REVERT: I 56 ASN cc_start: 0.8985 (t0) cc_final: 0.8534 (t0) REVERT: I 57 LYS cc_start: 0.8520 (mtmt) cc_final: 0.7130 (mtmm) REVERT: I 60 HIS cc_start: 0.6732 (t-170) cc_final: 0.6458 (t-170) REVERT: J 26 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8361 (tm-30) REVERT: J 31 GLU cc_start: 0.9016 (mp0) cc_final: 0.8574 (mp0) REVERT: K 13 PHE cc_start: 0.8361 (p90) cc_final: 0.7777 (p90) REVERT: K 16 GLU cc_start: 0.8117 (tt0) cc_final: 0.7810 (tt0) REVERT: K 24 ASP cc_start: 0.8486 (t0) cc_final: 0.8213 (t0) REVERT: K 93 ASP cc_start: 0.8814 (m-30) cc_final: 0.8483 (m-30) REVERT: L 22 CYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8629 (p) REVERT: L 38 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8655 (mm-30) REVERT: Q 68 ARG cc_start: 0.8298 (tpp80) cc_final: 0.8015 (tpp-160) REVERT: M 660 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7934 (tm-30) REVERT: O 79 TYR cc_start: 0.5078 (OUTLIER) cc_final: 0.4720 (t80) REVERT: O 105 MET cc_start: 0.8327 (mmm) cc_final: 0.7575 (mpp) REVERT: S 591 MET cc_start: 0.3880 (mmm) cc_final: 0.3527 (mmt) outliers start: 54 outliers final: 32 residues processed: 361 average time/residue: 0.2373 time to fit residues: 142.7771 Evaluate side-chains 354 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 319 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1190 GLN Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain B residue 1169 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain S residue 448 MET Chi-restraints excluded: chain S residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 297 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 330 optimal weight: 30.0000 chunk 48 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 353 optimal weight: 0.9990 chunk 492 optimal weight: 8.9990 chunk 457 optimal weight: 9.9990 chunk 452 optimal weight: 40.0000 chunk 438 optimal weight: 30.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN O 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.126051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.070437 restraints weight = 93830.424| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.94 r_work: 0.2724 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 42666 Z= 0.227 Angle : 0.613 13.544 57928 Z= 0.313 Chirality : 0.046 0.648 6457 Planarity : 0.004 0.054 7234 Dihedral : 11.227 145.141 6269 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.93 % Allowed : 12.05 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.12), residues: 4930 helix: 0.84 (0.12), residues: 1930 sheet: -0.44 (0.20), residues: 645 loop : -0.31 (0.13), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 358 TYR 0.039 0.002 TYR M 621 PHE 0.030 0.002 PHE M 593 TRP 0.026 0.002 TRP A1334 HIS 0.009 0.001 HIS M 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (42634) covalent geometry : angle 0.60413 / 0.31 (57883) hydrogen bonds : bond 0.04018 / 2.66 ( 1815) hydrogen bonds : angle 4.99197 / 3.57 ( 5053) metal coordination : bond 0.00995 / 0.69 ( 32) metal coordination : angle 3.68515 / 2.65 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 319 time to evaluate : 1.500 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: C 27 ASP cc_start: 0.8238 (m-30) cc_final: 0.8024 (m-30) REVERT: C 164 TYR cc_start: 0.9080 (m-80) cc_final: 0.8776 (m-80) REVERT: D 68 PHE cc_start: 0.8400 (m-10) cc_final: 0.8122 (m-10) REVERT: D 80 HIS cc_start: 0.9573 (t70) cc_final: 0.9256 (t70) REVERT: D 87 LYS cc_start: 0.9347 (mmmm) cc_final: 0.9124 (mmmm) REVERT: D 104 MET cc_start: 0.9465 (mmm) cc_final: 0.9103 (mmm) REVERT: D 164 PHE cc_start: 0.7866 (m-80) cc_final: 0.7192 (m-80) REVERT: E 35 GLN cc_start: 0.9440 (OUTLIER) cc_final: 0.9197 (tm-30) REVERT: E 90 TYR cc_start: 0.9125 (m-80) cc_final: 0.8573 (m-80) REVERT: E 94 MET cc_start: 0.8732 (mmm) cc_final: 0.8484 (tpt) REVERT: F 86 GLU cc_start: 0.7945 (pm20) cc_final: 0.7659 (pm20) REVERT: G 33 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8658 (mt-10) REVERT: G 146 LYS cc_start: 0.8604 (tptp) cc_final: 0.8252 (tptp) REVERT: H 55 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8626 (ttmm) REVERT: I 57 LYS cc_start: 0.8452 (mtmt) cc_final: 0.7030 (mtmm) REVERT: I 60 HIS cc_start: 0.6718 (t-170) cc_final: 0.6403 (t-170) REVERT: J 26 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8381 (tm-30) REVERT: J 31 GLU cc_start: 0.9042 (mp0) cc_final: 0.8607 (mp0) REVERT: J 65 LEU cc_start: 0.8253 (mt) cc_final: 0.8043 (tt) REVERT: K 24 ASP cc_start: 0.8522 (t0) cc_final: 0.8248 (t0) REVERT: K 93 ASP cc_start: 0.8833 (m-30) cc_final: 0.8508 (m-30) REVERT: L 22 CYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8499 (p) REVERT: L 38 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8651 (mm-30) REVERT: Q 68 ARG cc_start: 0.8205 (tpp80) cc_final: 0.7940 (tpp-160) REVERT: M 660 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7916 (tm-30) REVERT: O 79 TYR cc_start: 0.5221 (OUTLIER) cc_final: 0.4770 (t80) REVERT: S 523 MET cc_start: 0.7606 (mmm) cc_final: 0.7282 (tmm) outliers start: 41 outliers final: 30 residues processed: 348 average time/residue: 0.2214 time to fit residues: 129.6281 Evaluate side-chains 348 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 315 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1190 GLN Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain S residue 448 MET Chi-restraints excluded: chain S residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 412 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 405 optimal weight: 0.8980 chunk 343 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 403 optimal weight: 0.7980 chunk 357 optimal weight: 0.8980 chunk 464 optimal weight: 40.0000 chunk 431 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 304 ASN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS J 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.126861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.072278 restraints weight = 93543.135| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.02 r_work: 0.2750 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42666 Z= 0.145 Angle : 0.585 18.287 57928 Z= 0.300 Chirality : 0.045 0.619 6457 Planarity : 0.004 0.053 7234 Dihedral : 11.224 144.983 6269 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.88 % Allowed : 12.18 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.12), residues: 4930 helix: 0.89 (0.12), residues: 1934 sheet: -0.45 (0.20), residues: 646 loop : -0.29 (0.13), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 359 TYR 0.030 0.001 TYR M 621 PHE 0.038 0.001 PHE M 593 TRP 0.024 0.001 TRP A1334 HIS 0.010 0.001 HIS M 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (42634) covalent geometry : angle 0.57897 / 0.30 (57883) hydrogen bonds : bond 0.03759 / 2.48 ( 1815) hydrogen bonds : angle 4.93891 / 3.52 ( 5053) metal coordination : bond 0.00612 / 0.45 ( 32) metal coordination : angle 3.13130 / 2.27 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 323 time to evaluate : 1.474 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 1284 PHE cc_start: 0.7934 (m-10) cc_final: 0.7629 (m-80) REVERT: B 307 ARG cc_start: 0.7653 (mtm110) cc_final: 0.7389 (mmm160) REVERT: B 316 MET cc_start: 0.8848 (ttp) cc_final: 0.8589 (ttt) REVERT: B 433 PHE cc_start: 0.8591 (m-80) cc_final: 0.8214 (m-80) REVERT: C 27 ASP cc_start: 0.8201 (m-30) cc_final: 0.7984 (m-30) REVERT: C 164 TYR cc_start: 0.9055 (m-80) cc_final: 0.8752 (m-80) REVERT: D 68 PHE cc_start: 0.8179 (m-10) cc_final: 0.7939 (m-10) REVERT: D 80 HIS cc_start: 0.9580 (t70) cc_final: 0.9265 (t70) REVERT: D 81 MET cc_start: 0.9404 (ppp) cc_final: 0.9201 (ppp) REVERT: D 87 LYS cc_start: 0.9340 (mmmm) cc_final: 0.9113 (mmmm) REVERT: D 104 MET cc_start: 0.9462 (mmm) cc_final: 0.9102 (mmm) REVERT: D 163 ARG cc_start: 0.7608 (ttt-90) cc_final: 0.6991 (ptm160) REVERT: D 164 PHE cc_start: 0.7993 (m-80) cc_final: 0.6912 (m-80) REVERT: E 35 GLN cc_start: 0.9443 (OUTLIER) cc_final: 0.9192 (tm-30) REVERT: E 90 TYR cc_start: 0.9139 (m-80) cc_final: 0.8684 (m-80) REVERT: E 94 MET cc_start: 0.8644 (mmm) cc_final: 0.8375 (tpt) REVERT: F 86 GLU cc_start: 0.7934 (pm20) cc_final: 0.7668 (pm20) REVERT: G 33 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8623 (mt-10) REVERT: G 146 LYS cc_start: 0.8633 (tptp) cc_final: 0.8281 (tptp) REVERT: H 55 LYS cc_start: 0.8845 (ttmm) cc_final: 0.8619 (ttmm) REVERT: I 56 ASN cc_start: 0.8965 (t0) cc_final: 0.8520 (t0) REVERT: I 57 LYS cc_start: 0.8454 (mtmt) cc_final: 0.7076 (mtmm) REVERT: I 60 HIS cc_start: 0.6593 (t-170) cc_final: 0.6331 (t-170) REVERT: J 26 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8377 (tm-30) REVERT: J 31 GLU cc_start: 0.9017 (mp0) cc_final: 0.8590 (mp0) REVERT: J 65 LEU cc_start: 0.8291 (mt) cc_final: 0.8030 (tt) REVERT: K 13 PHE cc_start: 0.8321 (p90) cc_final: 0.8009 (p90) REVERT: K 16 GLU cc_start: 0.8286 (tt0) cc_final: 0.8057 (tt0) REVERT: K 24 ASP cc_start: 0.8473 (t0) cc_final: 0.8198 (t0) REVERT: K 93 ASP cc_start: 0.8829 (m-30) cc_final: 0.8486 (m-30) REVERT: L 22 CYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8624 (p) REVERT: L 38 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8605 (mm-30) REVERT: Q 68 ARG cc_start: 0.8165 (tpp80) cc_final: 0.7914 (tpp-160) REVERT: M 593 PHE cc_start: 0.7371 (t80) cc_final: 0.7167 (t80) REVERT: M 660 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7957 (tm-30) REVERT: O 79 TYR cc_start: 0.5072 (OUTLIER) cc_final: 0.4642 (t80) REVERT: S 523 MET cc_start: 0.7558 (mmm) cc_final: 0.7205 (tmm) outliers start: 39 outliers final: 28 residues processed: 349 average time/residue: 0.2307 time to fit residues: 135.5108 Evaluate side-chains 348 residues out of total 4440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 317 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1190 GLN Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 465 TYR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 886 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 177 GLN Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain S residue 448 MET Chi-restraints excluded: chain S residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 437 optimal weight: 50.0000 chunk 7 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 chunk 492 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 271 optimal weight: 0.0970 chunk 395 optimal weight: 10.0000 chunk 304 optimal weight: 0.8980 chunk 208 optimal weight: 0.7980 chunk 267 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 ASN B 731 GLN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 HIS ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.127058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.072511 restraints weight = 94315.527| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.06 r_work: 0.2760 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42666 Z= 0.138 Angle : 0.574 13.354 57928 Z= 0.294 Chirality : 0.045 0.595 6457 Planarity : 0.004 0.054 7234 Dihedral : 11.187 144.562 6269 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.79 % Allowed : 12.36 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.12), residues: 4930 helix: 0.98 (0.12), residues: 1939 sheet: -0.40 (0.20), residues: 646 loop : -0.25 (0.13), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 78 TYR 0.027 0.001 TYR M 621 PHE 0.027 0.001 PHE M 593 TRP 0.024 0.001 TRP A1334 HIS 0.010 0.001 HIS M 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (42634) covalent geometry : angle 0.56757 / 0.29 (57883) hydrogen bonds : bond 0.03665 / 2.41 ( 1815) hydrogen bonds : angle 4.86907 / 3.47 ( 5053) metal coordination : bond 0.00582 / 0.42 ( 32) metal coordination : angle 3.04025 / 2.21 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12666.53 seconds wall clock time: 217 minutes 5.60 seconds (13025.60 seconds total)