Starting phenix.real_space_refine on Sun Aug 9 23:47:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fbw_50297/08_2026/9fbw_50297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fbw_50297/08_2026/9fbw_50297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fbw_50297/08_2026/9fbw_50297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fbw_50297/08_2026/9fbw_50297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fbw_50297/08_2026/9fbw_50297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fbw_50297/08_2026/9fbw_50297.map" } resolution = 4.4 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= 0.000 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 240 5.49 5 Mg 8 5.21 5 S 119 5.16 5 Be 2 3.05 5 C 24288 2.51 5 N 6962 2.21 5 O 8056 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s 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: 39683 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 612 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "B" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 762 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 605 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 487 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 64} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 715 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 95} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "G" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 498 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2281 Classifications: {'DNA': 112} Link IDs: {'rna3p': 111} Chain: "J" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2311 Classifications: {'DNA': 112} Link IDs: {'rna3p': 111} Chain: "M" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5248 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 19, 'TRANS': 653} Chain breaks: 2 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 8, 'TYR:plan': 3, 'GLU:plan': 9, 'TRP:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 5, 'ASP:plan': 6, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 186 Chain: "R" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3335 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 25, 'TRANS': 385} Chain breaks: 1 Chain: "S" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1536 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "T" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3313 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 18, 'TRANS': 420} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "U" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 435} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3245 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 17, 'TRANS': 408} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "W" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3303 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "X" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3371 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "Y" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3342 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "Z" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1061 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 3, 'TRP:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" 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: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18150 SG CYS S 244 52.080 121.277 91.495 1.00390.63 S ATOM 18170 SG CYS S 247 49.482 120.994 91.916 1.00379.67 S ATOM 18311 SG CYS S 268 48.507 120.129 88.916 1.00450.58 S ATOM 18230 SG CYS S 256 55.749 113.629 82.346 1.00462.19 S ATOM 18251 SG CYS S 259 58.047 116.653 82.624 1.00542.32 S ATOM 18390 SG CYS S 277 57.007 115.327 79.130 1.00506.03 S Time building chain proxies: 8.17, per 1000 atoms: 0.21 Number of scatterers: 39683 At special positions: 0 Unit cell: (145.35, 191.25, 203.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 119 16.00 P 240 15.00 Mg 8 11.99 F 6 9.00 O 8056 8.00 N 6962 7.00 C 24288 6.00 Be 2 4.00 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S 501 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 247 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 268 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 244 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" NE2 HIS S 272 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 256 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 259 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 277 " Number of angles added : 3 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8482 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 41 sheets defined 46.4% alpha, 10.0% beta 106 base pairs and 149 stacking pairs defined. Time for finding SS restraints: 5.15 Creating SS restraints... Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 90 through 114 Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'B' and resid 44 through 55 Processing helix chain 'B' and resid 64 through 76 Processing helix chain 'B' and resid 87 through 114 Processing helix chain 'B' and resid 120 through 130 removed outlier: 3.528A pdb=" N LEU B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 41 Processing helix chain 'C' and resid 50 through 76 removed outlier: 4.293A pdb=" N VAL C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG C 55 " --> pdb=" O TYR C 51 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 76 " --> pdb=" O TYR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 removed outlier: 3.797A pdb=" N TYR C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 57 through 75 removed outlier: 4.431A pdb=" N HIS D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 removed outlier: 3.547A pdb=" N VAL D 86 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL D 87 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 37 Processing helix chain 'E' and resid 50 through 73 Processing helix chain 'E' and resid 80 through 91 Processing helix chain 'E' and resid 92 through 98 Processing helix chain 'G' and resid 40 through 52 Processing helix chain 'G' and resid 58 through 80 removed outlier: 3.524A pdb=" N ALA G 80 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 Processing helix chain 'G' and resid 94 through 105 Processing helix chain 'M' and resid 697 through 712 removed outlier: 3.781A pdb=" N LYS M 701 " --> pdb=" O ARG M 697 " (cutoff:3.500A) Processing helix chain 'M' and resid 726 through 742 removed outlier: 3.726A pdb=" N ALA M 739 " --> pdb=" O LEU M 735 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS M 740 " --> pdb=" O ALA M 736 " (cutoff:3.500A) Processing helix chain 'M' and resid 753 through 756 Processing helix chain 'M' and resid 757 through 767 removed outlier: 4.831A pdb=" N GLU M 763 " --> pdb=" O ASN M 759 " (cutoff:3.500A) Processing helix chain 'M' and resid 783 through 787 removed outlier: 3.535A pdb=" N LYS M 786 " --> pdb=" O ARG M 783 " (cutoff:3.500A) Processing helix chain 'M' and resid 802 through 809 removed outlier: 3.684A pdb=" N VAL M 806 " --> pdb=" O SER M 802 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL M 807 " --> pdb=" O TYR M 803 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN M 808 " --> pdb=" O GLN M 804 " (cutoff:3.500A) Processing helix chain 'M' and resid 834 through 842 removed outlier: 3.696A pdb=" N GLN M 838 " --> pdb=" O SER M 834 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN M 842 " --> pdb=" O GLN M 838 " (cutoff:3.500A) Processing helix chain 'M' and resid 859 through 871 removed outlier: 4.008A pdb=" N LEU M 866 " --> pdb=" O GLU M 862 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU M 867 " --> pdb=" O LEU M 863 " (cutoff:3.500A) Processing helix chain 'M' and resid 914 through 926 Processing helix chain 'M' and resid 954 through 972 Processing helix chain 'M' and resid 980 through 990 removed outlier: 3.754A pdb=" N ASN M 984 " --> pdb=" O MET M 980 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLN M 988 " --> pdb=" O ASN M 984 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU M 989 " --> pdb=" O CYS M 985 " (cutoff:3.500A) Processing helix chain 'M' and resid 1015 through 1028 removed outlier: 4.210A pdb=" N ASP M1020 " --> pdb=" O SER M1016 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL M1021 " --> pdb=" O ASP M1017 " (cutoff:3.500A) Processing helix chain 'M' and resid 1046 through 1054 removed outlier: 4.493A pdb=" N ASP M1051 " --> pdb=" O THR M1048 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS M1052 " --> pdb=" O LEU M1049 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP M1053 " --> pdb=" O ASN M1050 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU M1054 " --> pdb=" O ASP M1051 " (cutoff:3.500A) Processing helix chain 'M' and resid 1055 through 1065 Processing helix chain 'M' and resid 1071 through 1088 removed outlier: 3.782A pdb=" N VAL M1075 " --> pdb=" O PHE M1071 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU M1088 " --> pdb=" O GLN M1084 " (cutoff:3.500A) Processing helix chain 'M' and resid 1104 through 1133 Processing helix chain 'M' and resid 1140 through 1146 Processing helix chain 'M' and resid 1165 through 1173 removed outlier: 4.058A pdb=" N LEU M1171 " --> pdb=" O GLN M1167 " (cutoff:3.500A) Processing helix chain 'M' and resid 1173 through 1178 Processing helix chain 'M' and resid 1193 through 1198 Processing helix chain 'M' and resid 1209 through 1219 Processing helix chain 'M' and resid 1224 through 1230 Processing helix chain 'M' and resid 1248 through 1261 removed outlier: 4.229A pdb=" N ALA M1252 " --> pdb=" O LEU M1248 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE M1253 " --> pdb=" O GLN M1249 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU M1254 " --> pdb=" O LYS M1250 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN M1257 " --> pdb=" O ILE M1253 " (cutoff:3.500A) Processing helix chain 'M' and resid 1271 through 1276 Processing helix chain 'M' and resid 1277 through 1286 removed outlier: 3.537A pdb=" N PHE M1281 " --> pdb=" O VAL M1277 " (cutoff:3.500A) Processing helix chain 'M' and resid 1301 through 1310 Processing helix chain 'M' and resid 1347 through 1356 removed outlier: 3.696A pdb=" N CYS M1355 " --> pdb=" O CYS M1351 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS M1356 " --> pdb=" O GLN M1352 " (cutoff:3.500A) Processing helix chain 'M' and resid 1382 through 1387 Processing helix chain 'R' and resid 71 through 81 Processing helix chain 'R' and resid 108 through 121 Processing helix chain 'R' and resid 132 through 137 removed outlier: 3.747A pdb=" N PHE R 136 " --> pdb=" O PRO R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 141 removed outlier: 3.911A pdb=" N LYS R 141 " --> pdb=" O PRO R 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 138 through 141' Processing helix chain 'R' and resid 210 through 213 removed outlier: 3.932A pdb=" N VAL R 213 " --> pdb=" O TYR R 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 210 through 213' Processing helix chain 'R' and resid 219 through 233 removed outlier: 3.666A pdb=" N PHE R 233 " --> pdb=" O GLU R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 253 removed outlier: 3.621A pdb=" N VAL R 245 " --> pdb=" O GLU R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 265 Processing helix chain 'R' and resid 311 through 319 removed outlier: 4.179A pdb=" N GLU R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE R 317 " --> pdb=" O ILE R 313 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE R 318 " --> pdb=" O PRO R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 324 Processing helix chain 'R' and resid 329 through 341 Processing helix chain 'R' and resid 345 through 351 Processing helix chain 'R' and resid 359 through 362 Processing helix chain 'R' and resid 364 through 377 Processing helix chain 'R' and resid 391 through 406 Processing helix chain 'R' and resid 408 through 412 Processing helix chain 'R' and resid 423 through 431 removed outlier: 4.234A pdb=" N CYS R 427 " --> pdb=" O GLY R 423 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR R 428 " --> pdb=" O PRO R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 433 through 438 removed outlier: 3.547A pdb=" N ILE R 438 " --> pdb=" O GLN R 435 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 89 Processing helix chain 'S' and resid 91 through 107 removed outlier: 4.203A pdb=" N ILE S 95 " --> pdb=" O THR S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 114 No H-bonds generated for 'chain 'S' and resid 112 through 114' Processing helix chain 'S' and resid 115 through 125 Processing helix chain 'S' and resid 174 through 179 removed outlier: 3.686A pdb=" N TYR S 179 " --> pdb=" O ILE S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 201 removed outlier: 3.829A pdb=" N LYS S 199 " --> pdb=" O ILE S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 207 through 214 Processing helix chain 'S' and resid 218 through 227 removed outlier: 4.128A pdb=" N LYS S 222 " --> pdb=" O ASN S 218 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN S 223 " --> pdb=" O LEU S 219 " (cutoff:3.500A) Processing helix chain 'S' and resid 265 through 276 removed outlier: 3.539A pdb=" N PHE S 269 " --> pdb=" O SER S 265 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS S 270 " --> pdb=" O VAL S 266 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU S 271 " --> pdb=" O SER S 267 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU S 274 " --> pdb=" O LYS S 270 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.688A pdb=" N ALA T 67 " --> pdb=" O ASP T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 96 removed outlier: 3.596A pdb=" N LEU T 96 " --> pdb=" O ILE T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 110 No H-bonds generated for 'chain 'T' and resid 108 through 110' Processing helix chain 'T' and resid 116 through 129 removed outlier: 3.640A pdb=" N ILE T 129 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 182 through 193 removed outlier: 3.884A pdb=" N TYR T 186 " --> pdb=" O ASP T 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 248 through 258 removed outlier: 4.032A pdb=" N LEU T 252 " --> pdb=" O THR T 248 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG T 258 " --> pdb=" O VAL T 254 " (cutoff:3.500A) Processing helix chain 'T' and resid 264 through 273 removed outlier: 3.670A pdb=" N MET T 268 " --> pdb=" O ASP T 264 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 298 Processing helix chain 'T' and resid 317 through 328 removed outlier: 4.250A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 356 through 359 Processing helix chain 'T' and resid 360 through 365 Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 429 removed outlier: 4.045A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 453 Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 80 through 93 removed outlier: 4.168A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 107 removed outlier: 3.856A pdb=" N GLU U 105 " --> pdb=" O ALA U 102 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE U 106 " --> pdb=" O GLY U 103 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE U 107 " --> pdb=" O SER U 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 102 through 107' Processing helix chain 'U' and resid 112 through 124 Processing helix chain 'U' and resid 175 through 180 removed outlier: 3.848A pdb=" N THR U 180 " --> pdb=" O ILE U 176 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 250 Processing helix chain 'U' and resid 253 through 260 Processing helix chain 'U' and resid 266 through 283 removed outlier: 3.795A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 302 through 315 removed outlier: 3.550A pdb=" N GLU U 314 " --> pdb=" O ASN U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 339 through 343 Processing helix chain 'U' and resid 344 through 351 Processing helix chain 'U' and resid 360 through 375 removed outlier: 3.841A pdb=" N ILE U 364 " --> pdb=" O ASN U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 3.855A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 removed outlier: 3.802A pdb=" N VAL U 423 " --> pdb=" O GLU U 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 442 Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.765A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 removed outlier: 3.593A pdb=" N GLY V 97 " --> pdb=" O SER V 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 116 through 129 removed outlier: 3.698A pdb=" N ILE V 129 " --> pdb=" O PHE V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 182 through 192 Processing helix chain 'V' and resid 217 through 219 No H-bonds generated for 'chain 'V' and resid 217 through 219' Processing helix chain 'V' and resid 248 through 258 removed outlier: 3.678A pdb=" N ASN V 256 " --> pdb=" O LEU V 252 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 274 removed outlier: 3.963A pdb=" N LYS V 274 " --> pdb=" O GLY V 270 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 Processing helix chain 'V' and resid 313 through 316 Processing helix chain 'V' and resid 317 through 328 Processing helix chain 'V' and resid 356 through 359 Processing helix chain 'V' and resid 360 through 366 Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 417 Processing helix chain 'V' and resid 418 through 429 Processing helix chain 'V' and resid 435 through 446 removed outlier: 3.585A pdb=" N VAL V 439 " --> pdb=" O VAL V 435 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 457 Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.782A pdb=" N GLY W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 92 Processing helix chain 'W' and resid 112 through 125 removed outlier: 4.145A pdb=" N SER W 124 " --> pdb=" O ALA W 120 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE W 125 " --> pdb=" O PHE W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 174 through 180 removed outlier: 3.646A pdb=" N GLY W 178 " --> pdb=" O LYS W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 241 through 250 removed outlier: 3.708A pdb=" N ASN W 248 " --> pdb=" O ILE W 244 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER W 249 " --> pdb=" O ASP W 245 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 257 Processing helix chain 'W' and resid 266 through 284 removed outlier: 3.566A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 Processing helix chain 'W' and resid 340 through 343 Processing helix chain 'W' and resid 344 through 350 Processing helix chain 'W' and resid 360 through 375 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 396 through 412 removed outlier: 4.371A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 removed outlier: 3.611A pdb=" N VAL W 423 " --> pdb=" O GLU W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 432 through 443 removed outlier: 3.673A pdb=" N SER W 436 " --> pdb=" O ASP W 432 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 68 Processing helix chain 'X' and resid 84 through 97 removed outlier: 3.512A pdb=" N GLY X 97 " --> pdb=" O SER X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 106 through 111 Processing helix chain 'X' and resid 116 through 128 Processing helix chain 'X' and resid 184 through 193 removed outlier: 4.044A pdb=" N SER X 188 " --> pdb=" O THR X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 215 through 222 removed outlier: 4.565A pdb=" N THR X 220 " --> pdb=" O ALA X 217 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE X 222 " --> pdb=" O ALA X 219 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 274 Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.535A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN X 298 " --> pdb=" O LYS X 294 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 316 Processing helix chain 'X' and resid 317 through 328 Processing helix chain 'X' and resid 355 through 359 Processing helix chain 'X' and resid 360 through 365 Processing helix chain 'X' and resid 376 through 392 Processing helix chain 'X' and resid 396 through 410 removed outlier: 4.930A pdb=" N LEU X 402 " --> pdb=" O SER X 398 " (cutoff:3.500A) Processing helix chain 'X' and resid 411 through 429 removed outlier: 3.916A pdb=" N ALA X 415 " --> pdb=" O SER X 411 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA X 420 " --> pdb=" O LEU X 416 " (cutoff:3.500A) Proline residue: X 421 - end of helix Processing helix chain 'X' and resid 435 through 446 removed outlier: 3.528A pdb=" N VAL X 439 " --> pdb=" O VAL X 435 " (cutoff:3.500A) Processing helix chain 'X' and resid 448 through 457 Processing helix chain 'Y' and resid 47 through 64 removed outlier: 4.093A pdb=" N GLY Y 64 " --> pdb=" O MET Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 80 through 92 Processing helix chain 'Y' and resid 102 through 106 removed outlier: 3.805A pdb=" N ILE Y 106 " --> pdb=" O GLY Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 125 Processing helix chain 'Y' and resid 172 through 177 removed outlier: 3.813A pdb=" N ASP Y 177 " --> pdb=" O ASN Y 173 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 212 removed outlier: 3.885A pdb=" N ARG Y 210 " --> pdb=" O PHE Y 206 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP Y 211 " --> pdb=" O ALA Y 207 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR Y 212 " --> pdb=" O ARG Y 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 206 through 212' Processing helix chain 'Y' and resid 240 through 248 removed outlier: 3.559A pdb=" N ILE Y 244 " --> pdb=" O SER Y 240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 260 removed outlier: 3.915A pdb=" N THR Y 259 " --> pdb=" O LEU Y 255 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY Y 260 " --> pdb=" O ALA Y 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 255 through 260' Processing helix chain 'Y' and resid 266 through 283 removed outlier: 3.615A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 301 Processing helix chain 'Y' and resid 302 through 313 removed outlier: 3.527A pdb=" N PHE Y 306 " --> pdb=" O ASP Y 302 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG Y 311 " --> pdb=" O SER Y 307 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 413 removed outlier: 4.146A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 Processing helix chain 'Y' and resid 432 through 443 Processing helix chain 'Y' and resid 444 through 447 Processing helix chain 'Z' and resid 215 through 232 Processing helix chain 'Z' and resid 237 through 242 Processing helix chain 'Z' and resid 267 through 272 removed outlier: 3.565A pdb=" N ALA Z 272 " --> pdb=" O GLU Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 302 through 311 removed outlier: 3.527A pdb=" N ARG Z 306 " --> pdb=" O GLU Z 302 " (cutoff:3.500A) Processing helix chain 'Z' and resid 603 through 610 Processing helix chain 'Z' and resid 611 through 613 No H-bonds generated for 'chain 'Z' and resid 611 through 613' Processing helix chain 'Z' and resid 616 through 622 Processing helix chain 'Z' and resid 625 through 629 Processing sheet with id=AA1, first strand: chain 'M' and resid 748 through 750 removed outlier: 6.547A pdb=" N HIS M 748 " --> pdb=" O CYS M 799 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'M' and resid 944 through 950 removed outlier: 3.746A pdb=" N TYR M 945 " --> pdb=" O VAL M1364 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG M1368 " --> pdb=" O HIS M 947 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL M 949 " --> pdb=" O ARG M1368 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL M1336 " --> pdb=" O TYR M1367 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE M1369 " --> pdb=" O VAL M1336 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU M1266 " --> pdb=" O ILE M1337 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA M1265 " --> pdb=" O PHE M1317 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU M1319 " --> pdb=" O ALA M1265 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE M1267 " --> pdb=" O LEU M1319 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER M1320 " --> pdb=" O LEU M1292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 1008 through 1010 Processing sheet with id=AA4, first strand: chain 'R' and resid 6 through 9 Processing sheet with id=AA5, first strand: chain 'R' and resid 15 through 17 removed outlier: 3.663A pdb=" N PHE R 26 " --> pdb=" O PHE R 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 149 through 150 removed outlier: 3.701A pdb=" N ILE R 150 " --> pdb=" O VAL R 385 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE R 353 " --> pdb=" O SER R 386 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU R 189 " --> pdb=" O VAL R 354 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR R 356 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE R 191 " --> pdb=" O THR R 356 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN R 188 " --> pdb=" O VAL R 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 149 through 150 removed outlier: 3.701A pdb=" N ILE R 150 " --> pdb=" O VAL R 385 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE R 353 " --> pdb=" O SER R 386 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU R 189 " --> pdb=" O VAL R 354 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR R 356 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE R 191 " --> pdb=" O THR R 356 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN R 188 " --> pdb=" O VAL R 203 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR R 198 " --> pdb=" O LEU R 216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 286 through 288 removed outlier: 3.760A pdb=" N GLU R 273 " --> pdb=" O ARG R 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 254 through 255 Processing sheet with id=AB1, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB2, first strand: chain 'T' and resid 105 through 106 removed outlier: 4.009A pdb=" N ASP T 311 " --> pdb=" O LEU T 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE T 310 " --> pdb=" O VAL T 337 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA T 339 " --> pdb=" O ILE T 310 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE T 75 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER T 340 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU T 77 " --> pdb=" O SER T 340 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 210 through 214 removed outlier: 4.107A pdb=" N VAL T 212 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL T 199 " --> pdb=" O VAL T 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 210 through 214 removed outlier: 4.107A pdb=" N VAL T 212 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL T 199 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE T 304 " --> pdb=" O GLY T 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 147 through 149 Processing sheet with id=AB6, first strand: chain 'T' and resid 345 through 346 Processing sheet with id=AB7, first strand: chain 'T' and resid 394 through 395 removed outlier: 8.249A pdb=" N GLN T 394 " --> pdb=" O ILE T 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.618A pdb=" N MET U 44 " --> pdb=" O SER U 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 99 through 100 removed outlier: 6.024A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL U 71 " --> pdb=" O MET U 323 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 233 through 240 removed outlier: 3.584A pdb=" N VAL U 239 " --> pdb=" O ILE U 127 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE U 127 " --> pdb=" O VAL U 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 139 through 143 removed outlier: 6.697A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU U 158 " --> pdb=" O TYR U 169 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 102 through 103 removed outlier: 3.707A pdb=" N ILE V 75 " --> pdb=" O VAL V 336 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 176 through 180 removed outlier: 3.778A pdb=" N GLY V 142 " --> pdb=" O ILE V 200 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE V 200 " --> pdb=" O GLY V 142 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ASP V 198 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL V 199 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG V 214 " --> pdb=" O VAL V 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 176 through 180 removed outlier: 4.208A pdb=" N LYS V 137 " --> pdb=" O LYS V 241 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS V 241 " --> pdb=" O LYS V 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 345 through 346 removed outlier: 3.872A pdb=" N THR V 345 " --> pdb=" O SER V 355 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AC8, first strand: chain 'W' and resid 99 through 101 removed outlier: 3.636A pdb=" N MET W 322 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA W 74 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 160 through 161 Processing sheet with id=AD1, first strand: chain 'W' and resid 199 through 203 removed outlier: 3.520A pdb=" N THR W 200 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER W 191 " --> pdb=" O THR W 200 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU W 202 " --> pdb=" O VAL W 189 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL W 189 " --> pdb=" O LEU W 202 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 144 through 147 Processing sheet with id=AD3, first strand: chain 'W' and resid 330 through 331 Processing sheet with id=AD4, first strand: chain 'X' and resid 75 through 78 Processing sheet with id=AD5, first strand: chain 'X' and resid 102 through 105 removed outlier: 6.106A pdb=" N CYS X 103 " --> pdb=" O PHE X 309 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASP X 311 " --> pdb=" O CYS X 103 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU X 105 " --> pdb=" O ASP X 311 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 238 through 248 removed outlier: 3.850A pdb=" N LYS X 241 " --> pdb=" O LYS X 137 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS X 137 " --> pdb=" O LYS X 241 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE X 243 " --> pdb=" O GLU X 135 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU X 135 " --> pdb=" O ILE X 243 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 151 through 152 Processing sheet with id=AD8, first strand: chain 'X' and resid 166 through 172 Processing sheet with id=AD9, first strand: chain 'Y' and resid 99 through 100 removed outlier: 4.268A pdb=" N THR Y 99 " --> pdb=" O VAL Y 292 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE Y 294 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU Y 293 " --> pdb=" O MET Y 322 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA Y 324 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE Y 295 " --> pdb=" O ALA Y 324 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL Y 71 " --> pdb=" O MET Y 323 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'Y' and resid 230 through 237 removed outlier: 3.548A pdb=" N GLU Y 287 " --> pdb=" O LYS Y 128 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Y' and resid 157 through 161 Processing sheet with id=AE3, first strand: chain 'Y' and resid 190 through 192 Processing sheet with id=AE4, first strand: chain 'Y' and resid 330 through 331 Processing sheet with id=AE5, first strand: chain 'Y' and resid 378 through 379 removed outlier: 7.645A pdb=" N GLU Y 378 " --> pdb=" O VAL Y 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 1454 hydrogen bonds defined for protein. 4161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 273 hydrogen bonds 518 hydrogen bond angles 0 basepair planarities 106 basepair parallelities 149 stacking parallelities Total time for adding SS restraints: 10.45 Time building geometry restraints manager: 4.46 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: 10514 1.33 - 1.46: 7915 1.46 - 1.58: 21647 1.58 - 1.70: 470 1.70 - 1.82: 196 Bond restraints: 40742 Sorted by residual: bond pdb=" C1' DC I -75 " pdb=" N1 DC I -75 " ideal model delta sigma weight residual 1.468 1.528 -0.060 1.40e-02 5.10e+03 1.83e+01 bond pdb=" C3' DA J -13 " pdb=" C2' DA J -13 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.43e+01 bond pdb=" C3' DC J -2 " pdb=" C2' DC J -2 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DC J -26 " pdb=" C2' DC J -26 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC I -38 " pdb=" C2' DC I -38 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 40737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 55092 2.33 - 4.66: 877 4.66 - 7.00: 113 7.00 - 9.33: 11 9.33 - 11.66: 4 Bond angle restraints: 56097 Sorted by residual: angle pdb=" O4' DC J 60 " pdb=" C4' DC J 60 " pdb=" C3' DC J 60 " ideal model delta sigma weight residual 106.00 102.41 3.59 6.00e-01 2.78e+00 3.59e+01 angle pdb=" C ASN S 115 " pdb=" N VAL S 116 " pdb=" CA VAL S 116 " ideal model delta sigma weight residual 120.24 123.73 -3.49 6.30e-01 2.52e+00 3.07e+01 angle pdb=" O4' DA I -15 " pdb=" C4' DA I -15 " pdb=" C3' DA I -15 " ideal model delta sigma weight residual 106.00 102.86 3.14 6.00e-01 2.78e+00 2.75e+01 angle pdb=" O4' DA I 24 " pdb=" C4' DA I 24 " pdb=" C3' DA I 24 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" O4' DA J -14 " pdb=" C4' DA J -14 " pdb=" C3' DA J -14 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 ... (remaining 56092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 22697 34.54 - 69.08: 1431 69.08 - 103.62: 85 103.62 - 138.15: 1 138.15 - 172.69: 2 Dihedral angle restraints: 24216 sinusoidal: 11123 harmonic: 13093 Sorted by residual: dihedral pdb=" CA ARG B 63 " pdb=" C ARG B 63 " pdb=" N LYS B 64 " pdb=" CA LYS B 64 " ideal model delta harmonic sigma weight residual -180.00 -146.75 -33.25 0 5.00e+00 4.00e-02 4.42e+01 dihedral pdb=" CA ARG D 40 " pdb=" C ARG D 40 " pdb=" N GLY D 41 " pdb=" CA GLY D 41 " ideal model delta harmonic sigma weight residual 180.00 146.98 33.02 0 5.00e+00 4.00e-02 4.36e+01 dihedral pdb=" CA THR C 30 " pdb=" C THR C 30 " pdb=" N LYS C 31 " pdb=" CA LYS C 31 " ideal model delta harmonic sigma weight residual 180.00 148.38 31.62 0 5.00e+00 4.00e-02 4.00e+01 ... (remaining 24213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4572 0.042 - 0.084: 1548 0.084 - 0.126: 420 0.126 - 0.168: 49 0.168 - 0.209: 5 Chirality restraints: 6594 Sorted by residual: chirality pdb=" CA THR C 30 " pdb=" N THR C 30 " pdb=" C THR C 30 " pdb=" CB THR C 30 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CG LEU M1240 " pdb=" CB LEU M1240 " pdb=" CD1 LEU M1240 " pdb=" CD2 LEU M1240 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" CA PHE M 979 " pdb=" N PHE M 979 " pdb=" C PHE M 979 " pdb=" CB PHE M 979 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 6591 not shown) Planarity restraints: 6344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 65 " -0.049 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO B 66 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 66 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 66 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Z 584 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO Z 585 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO Z 585 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO Z 585 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA Z 602 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO Z 603 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO Z 603 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO Z 603 " -0.034 5.00e-02 4.00e+02 ... (remaining 6341 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 592 2.56 - 3.15: 33475 3.15 - 3.73: 69781 3.73 - 4.32: 88794 4.32 - 4.90: 137752 Nonbonded interactions: 330394 Sorted by model distance: nonbonded pdb=" O3A ADP W 501 " pdb="MG MG W 502 " model vdw 1.978 2.170 nonbonded pdb=" O1A ADP M1601 " pdb="MG MG M1603 " model vdw 2.002 2.170 nonbonded pdb=" O5' ADP U 502 " pdb="MG MG U 503 " model vdw 2.006 2.170 nonbonded pdb=" O3A ADP U 502 " pdb="MG MG U 503 " model vdw 2.025 2.170 nonbonded pdb=" O2 DC I -4 " pdb=" N2 DG J 4 " model vdw 2.031 2.496 ... (remaining 330389 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 Found NCS groups: ncs_group { reference = (chain 'T' and (resid 22 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 149 or (resid 150 and \ (name N or name CA or name C or name O or name CB )) or resid 166 through 170 o \ r (resid 171 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 72 through 186 or (resid 187 and (name N or name CA or name C or name O or name \ CB )) or resid 188 through 212 or resid 214 through 220 or (resid 221 through 22 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 224 through \ 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) or re \ sid 261 through 268 or (resid 269 and (name N or name CA or name C or name O or \ name CB )) or resid 270 or (resid 271 and (name N or name CA or name C or name O \ or name CB )) or resid 272 or (resid 273 and (name N or name CA or name C or na \ me O or name CB )) or resid 274 through 275 or (resid 276 and (name N or name CA \ or name C or name O or name CB )) or resid 277 through 462)) selection = (chain 'V' and (resid 22 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 141 or (resid 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 through 149 or (resid 150 \ and (name N or name CA or name C or name O or name CB )) or resid 166 through 19 \ 1 or (resid 192 through 193 and (name N or name CA or name C or name O or name C \ B )) or resid 194 through 212 or resid 214 through 226 or (resid 227 through 228 \ and (name N or name CA or name C or name O or name CB )) or resid 229 through 2 \ 57 or (resid 258 and (name N or name CA or name C or name O or name CB )) or res \ id 259 through 268 or (resid 269 and (name N or name CA or name C or name O or n \ ame CB )) or resid 270 or (resid 271 and (name N or name CA or name C or name O \ or name CB )) or resid 272 or (resid 273 and (name N or name CA or name C or nam \ e O or name CB )) or resid 274 through 275 or (resid 276 and (name N or name CA \ or name C or name O or name CB )) or resid 277 through 462)) selection = (chain 'X' and (resid 22 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 141 or (resid 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 through 150 or resid 166 t \ hrough 170 or (resid 171 and (name N or name CA or name C or name O or name CB ) \ ) or resid 172 through 186 or (resid 187 and (name N or name CA or name C or nam \ e O or name CB )) or resid 188 through 190 or (resid 191 through 193 and (name N \ or name CA or name C or name O or name CB )) or resid 194 through 220 or (resid \ 221 through 223 and (name N or name CA or name C or name O or name CB )) or res \ id 224 through 226 or (resid 227 through 228 and (name N or name CA or name C or \ name O or name CB )) or resid 229 through 257 or (resid 258 and (name N or name \ CA or name C or name O or name CB )) or resid 259 or (resid 260 and (name N or \ name CA or name C or name O or name CB )) or resid 261 through 462)) } ncs_group { reference = (chain 'U' and (resid 15 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 136 or (resid 137 and (name N or n \ ame CA or name C or name O or name CB )) or resid 138 or (resid 139 and (name N \ or name CA or name C or name O or name CB )) or resid 140 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 or (re \ sid 146 and (name N or name CA or name C or name O or name CB )) or (resid 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 155 and (name N or name CA or name C or name O or name CB \ )) or resid 156 or (resid 157 and (name N or name CA or name C or name O or nam \ e CB )) or resid 158 through 169 or (resid 170 and (name N or name CA or name C \ or name O or name CB )) or resid 171 through 180 or (resid 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 through 203 or (resid 204 a \ nd (name N or name CA or name C or name O or name CB )) or resid 205 through 207 \ or resid 221 through 222 or (resid 223 and (name N or name CA or name C or name \ O or name CB )) or resid 224 through 225 or (resid 226 and (name N or name CA o \ r name C or name O or name CB )) or resid 227 through 228 or (resid 229 and (nam \ e N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 and \ (name N or name CA or name C or name O or name CB )) or resid 232 through 281 or \ (resid 282 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 3 through 418 or (resid 419 and (name N or name CA or name C or name O or name C \ B )) or resid 420 through 421 or (resid 422 and (name N or name CA or name C or \ name O or name CB )) or resid 423 through 459 or resid 502 through 503)) selection = (chain 'W' and (resid 15 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 143 or (resid 144 and (name N or n \ ame CA or name C or name O or name CB )) or resid 145 or (resid 146 and (name N \ or name CA or name C or name O or name CB )) or (resid 150 and (name N or name C \ A or name C or name O or name CB )) or resid 151 through 152 or (resid 153 throu \ gh 155 and (name N or name CA or name C or name O or name CB )) or resid 156 or \ (resid 157 and (name N or name CA or name C or name O or name CB )) or resid 158 \ through 169 or (resid 170 and (name N or name CA or name C or name O or name CB \ )) or resid 171 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 200 or (resid 201 and (name N or name C \ A or name C or name O or name CB )) or resid 202 through 228 or (resid 229 and ( \ name N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 a \ nd (name N or name CA or name C or name O or name CB )) or resid 232 through 418 \ or (resid 419 and (name N or name CA or name C or name O or name CB )) or resid \ 420 through 421 or (resid 422 and (name N or name CA or name C or name O or nam \ e CB )) or resid 423 through 502)) selection = (chain 'Y' and (resid 15 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 203 or (resid 204 and (name N o \ r name CA or name C or name O or name CB )) or resid 205 through 207 or resid 22 \ 1 through 222 or (resid 223 and (name N or name CA or name C or name O or name C \ B )) or resid 224 through 225 or (resid 226 and (name N or name CA or name C or \ name O or name CB )) or resid 227 through 281 or (resid 282 and (name N or name \ CA or name C or name O or name CB )) or resid 283 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.490 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: 0.850 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 45.520 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 40755 Z= 0.285 Angle : 0.719 11.660 56100 Z= 0.475 Chirality : 0.044 0.209 6594 Planarity : 0.004 0.075 6344 Dihedral : 19.751 172.692 15734 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.42 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.72 (0.12), residues: 4460 helix: 0.06 (0.12), residues: 1913 sheet: -1.32 (0.25), residues: 438 loop : -2.29 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 381 TYR 0.028 0.001 TYR T 375 PHE 0.026 0.001 PHE X 125 TRP 0.022 0.001 TRP R 397 HIS 0.009 0.001 HIS V 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.28 (40742) covalent geometry : angle 0.71944 / 0.48 (56097) hydrogen bonds : bond 0.14545 / 9.27 ( 1711) hydrogen bonds : angle 6.31518 / 4.53 ( 4679) metal coordination : bond 0.00608 / 0.36 ( 7) metal coordination : angle 1.19065 / 0.61 ( 3) Misc. bond : bond 0.00134 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.309 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: M 723 MET cc_start: 0.1832 (tmm) cc_final: 0.0783 (tmm) REVERT: R 237 ASN cc_start: 0.7937 (p0) cc_final: 0.7689 (p0) REVERT: R 403 PHE cc_start: 0.6281 (t80) cc_final: 0.5847 (t80) REVERT: S 211 PHE cc_start: -0.0173 (m-10) cc_final: -0.0523 (m-80) REVERT: T 344 MET cc_start: -0.1844 (mmt) cc_final: -0.4593 (ttm) REVERT: V 268 MET cc_start: 0.8766 (tmm) cc_final: 0.8404 (tmm) REVERT: V 269 MET cc_start: 0.6816 (mpp) cc_final: 0.6491 (mpp) REVERT: V 376 ASP cc_start: 0.8191 (t0) cc_final: 0.7917 (t0) REVERT: W 86 MET cc_start: 0.8535 (ppp) cc_final: 0.7893 (ppp) REVERT: W 302 ASP cc_start: 0.9163 (t0) cc_final: 0.8809 (t0) REVERT: W 379 LEU cc_start: 0.7267 (mt) cc_final: 0.6880 (mt) REVERT: X 315 MET cc_start: 0.7736 (tpt) cc_final: 0.7434 (tpp) REVERT: X 414 TYR cc_start: 0.5164 (t80) cc_final: 0.4379 (t80) REVERT: Z 220 ILE cc_start: 0.8937 (tp) cc_final: 0.8712 (tp) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2390 time to fit residues: 96.6785 Evaluate side-chains 183 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN M1036 ASN R 280 GLN R 364 ASN R 367 GLN ** U 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN V 94 GLN ** V 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN W 237 HIS W 373 GLN Y 223 GLN Y 230 GLN ** Y 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 279 GLN Z 587 GLN ** Z 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.137296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.127402 restraints weight = 401562.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.127752 restraints weight = 292716.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.127938 restraints weight = 261707.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.128415 restraints weight = 212265.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.128459 restraints weight = 182541.561| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4509 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40755 Z= 0.170 Angle : 0.701 10.586 56100 Z= 0.372 Chirality : 0.047 0.306 6594 Planarity : 0.005 0.080 6344 Dihedral : 21.514 171.262 7349 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.95 % Favored : 90.87 % Rotamer: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.91 (0.12), residues: 4460 helix: -0.13 (0.12), residues: 1962 sheet: -1.41 (0.24), residues: 459 loop : -2.40 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 73 TYR 0.021 0.002 TYR M 950 PHE 0.018 0.002 PHE M1008 TRP 0.017 0.002 TRP R 397 HIS 0.006 0.001 HIS R 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (40742) covalent geometry : angle 0.70131 / 0.37 (56097) hydrogen bonds : bond 0.06313 / 4.14 ( 1711) hydrogen bonds : angle 5.48252 / 3.92 ( 4679) metal coordination : bond 0.00786 / 0.45 ( 7) metal coordination : angle 1.14045 / 0.60 ( 3) Misc. bond : bond 0.00134 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 1.507 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: M 723 MET cc_start: 0.2192 (tmm) cc_final: 0.1122 (tmm) REVERT: M 1347 MET cc_start: -0.4941 (tpt) cc_final: -0.5149 (tpt) REVERT: R 106 MET cc_start: 0.6699 (mmt) cc_final: 0.6280 (mmt) REVERT: R 237 ASN cc_start: 0.7825 (p0) cc_final: 0.7536 (p0) REVERT: T 344 MET cc_start: -0.1673 (mmt) cc_final: -0.4637 (ttm) REVERT: V 268 MET cc_start: 0.8902 (tmm) cc_final: 0.8526 (tmm) REVERT: V 269 MET cc_start: 0.7014 (mpp) cc_final: 0.6644 (mpp) REVERT: W 302 ASP cc_start: 0.9007 (t0) cc_final: 0.8559 (t0) REVERT: W 379 LEU cc_start: 0.7050 (mt) cc_final: 0.6675 (mt) REVERT: X 315 MET cc_start: 0.7765 (tpt) cc_final: 0.7444 (tpp) REVERT: X 414 TYR cc_start: 0.4550 (t80) cc_final: 0.4058 (t80) REVERT: Y 292 VAL cc_start: 0.4497 (OUTLIER) cc_final: 0.4279 (t) REVERT: Z 220 ILE cc_start: 0.9020 (tp) cc_final: 0.8590 (tp) outliers start: 3 outliers final: 0 residues processed: 243 average time/residue: 0.2332 time to fit residues: 94.8778 Evaluate side-chains 183 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 428 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 455 optimal weight: 0.6980 chunk 431 optimal weight: 7.9990 chunk 392 optimal weight: 1.9990 chunk 343 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 210 optimal weight: 0.0020 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 HIS ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN V 94 GLN ** V 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN ** W 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 373 GLN Y 223 GLN ** Y 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.141353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.124309 restraints weight = 361111.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.123543 restraints weight = 321602.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.123733 restraints weight = 298910.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.123795 restraints weight = 267929.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.123992 restraints weight = 253292.220| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5102 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40755 Z= 0.135 Angle : 0.671 10.530 56100 Z= 0.352 Chirality : 0.046 0.301 6594 Planarity : 0.004 0.080 6344 Dihedral : 21.498 171.267 7349 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.58 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.86 (0.12), residues: 4460 helix: -0.08 (0.12), residues: 1950 sheet: -1.30 (0.24), residues: 447 loop : -2.40 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M1023 TYR 0.019 0.001 TYR M 776 PHE 0.027 0.001 PHE W 254 TRP 0.015 0.001 TRP R 397 HIS 0.015 0.001 HIS W 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (40742) covalent geometry : angle 0.67069 / 0.35 (56097) hydrogen bonds : bond 0.05456 / 3.56 ( 1711) hydrogen bonds : angle 5.23215 / 3.74 ( 4679) metal coordination : bond 0.00735 / 0.41 ( 7) metal coordination : angle 1.53114 / 0.83 ( 3) Misc. bond : bond 0.00523 / 0.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.271 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: G 62 MET cc_start: 0.3459 (tpt) cc_final: 0.3102 (mpp) REVERT: M 723 MET cc_start: 0.2155 (tmm) cc_final: 0.1497 (tmm) REVERT: M 1256 GLN cc_start: 0.8396 (tp40) cc_final: 0.8182 (mp10) REVERT: R 237 ASN cc_start: 0.7879 (p0) cc_final: 0.7459 (p0) REVERT: R 238 MET cc_start: 0.2071 (mmt) cc_final: 0.1295 (mmt) REVERT: R 286 TYR cc_start: 0.8500 (p90) cc_final: 0.8004 (p90) REVERT: S 211 PHE cc_start: -0.0402 (m-10) cc_final: -0.0670 (m-80) REVERT: T 344 MET cc_start: -0.1987 (mmt) cc_final: -0.4701 (ttm) REVERT: U 175 MET cc_start: 0.4809 (mpp) cc_final: 0.4485 (mpp) REVERT: V 268 MET cc_start: 0.8827 (tmm) cc_final: 0.8402 (tmm) REVERT: V 269 MET cc_start: 0.7159 (mpp) cc_final: 0.6789 (mpp) REVERT: V 376 ASP cc_start: 0.7824 (t0) cc_final: 0.7380 (t0) REVERT: W 86 MET cc_start: 0.8571 (ppp) cc_final: 0.8158 (ppp) REVERT: W 302 ASP cc_start: 0.9197 (t0) cc_final: 0.8687 (t0) REVERT: W 379 LEU cc_start: 0.7164 (mt) cc_final: 0.6773 (mt) REVERT: X 414 TYR cc_start: 0.4948 (t80) cc_final: 0.3993 (t80) REVERT: X 451 ARG cc_start: 0.4757 (mtm180) cc_final: 0.3708 (ttt180) REVERT: Y 72 LEU cc_start: 0.7872 (tp) cc_final: 0.7503 (tt) REVERT: Z 220 ILE cc_start: 0.8977 (tp) cc_final: 0.8591 (tp) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2425 time to fit residues: 102.5415 Evaluate side-chains 189 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 455 optimal weight: 0.6980 chunk 371 optimal weight: 8.9990 chunk 364 optimal weight: 0.7980 chunk 352 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 447 optimal weight: 3.9990 chunk 329 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 349 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN ** M 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS ** U 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN V 94 GLN ** V 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN W 237 HIS W 373 GLN X 238 HIS Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 279 GLN ** Z 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.139257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.123443 restraints weight = 362229.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.122693 restraints weight = 357100.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.123048 restraints weight = 296478.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.123302 restraints weight = 250049.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.123417 restraints weight = 237743.960| |-----------------------------------------------------------------------------| r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4986 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 40755 Z= 0.175 Angle : 0.712 9.890 56100 Z= 0.376 Chirality : 0.048 0.308 6594 Planarity : 0.005 0.076 6344 Dihedral : 21.535 170.220 7349 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.13 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.12), residues: 4460 helix: -0.22 (0.11), residues: 1944 sheet: -1.50 (0.24), residues: 438 loop : -2.49 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 346 TYR 0.020 0.002 TYR M 776 PHE 0.036 0.002 PHE V 321 TRP 0.017 0.002 TRP R 397 HIS 0.008 0.001 HIS W 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (40742) covalent geometry : angle 0.71217 / 0.38 (56097) hydrogen bonds : bond 0.05815 / 3.88 ( 1711) hydrogen bonds : angle 5.30599 / 3.78 ( 4679) metal coordination : bond 0.01242 / 0.57 ( 7) metal coordination : angle 1.89387 / 1.01 ( 3) Misc. bond : bond 0.00557 / 0.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.409 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: G 62 MET cc_start: 0.3546 (tpt) cc_final: 0.3151 (mpp) REVERT: M 723 MET cc_start: 0.2252 (tmm) cc_final: 0.1414 (tmm) REVERT: R 237 ASN cc_start: 0.7920 (p0) cc_final: 0.7436 (p0) REVERT: R 238 MET cc_start: 0.1976 (mmt) cc_final: 0.1085 (mmt) REVERT: R 286 TYR cc_start: 0.8584 (p90) cc_final: 0.7945 (p90) REVERT: S 211 PHE cc_start: -0.0621 (m-10) cc_final: -0.0860 (m-80) REVERT: T 344 MET cc_start: -0.1573 (mmt) cc_final: -0.4595 (ttm) REVERT: V 268 MET cc_start: 0.8875 (tmm) cc_final: 0.8458 (tmm) REVERT: V 269 MET cc_start: 0.7200 (mpp) cc_final: 0.6800 (mpp) REVERT: V 376 ASP cc_start: 0.8043 (t0) cc_final: 0.7582 (t0) REVERT: W 86 MET cc_start: 0.8413 (ppp) cc_final: 0.8038 (ppp) REVERT: W 302 ASP cc_start: 0.9151 (t0) cc_final: 0.8644 (t0) REVERT: W 379 LEU cc_start: 0.7324 (mt) cc_final: 0.6904 (mt) REVERT: X 291 VAL cc_start: 0.6334 (t) cc_final: 0.5986 (t) REVERT: X 315 MET cc_start: 0.7501 (mpp) cc_final: 0.6156 (tpp) REVERT: X 414 TYR cc_start: 0.5060 (t80) cc_final: 0.4047 (t80) REVERT: X 451 ARG cc_start: 0.4813 (mtm180) cc_final: 0.3414 (ttt180) REVERT: Y 72 LEU cc_start: 0.8226 (tp) cc_final: 0.7921 (tt) REVERT: Z 220 ILE cc_start: 0.9083 (tp) cc_final: 0.8809 (tp) REVERT: Z 226 LYS cc_start: 0.9477 (mtmm) cc_final: 0.9269 (mttt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2446 time to fit residues: 98.8871 Evaluate side-chains 180 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 441 optimal weight: 10.0000 chunk 260 optimal weight: 2.9990 chunk 56 optimal weight: 40.0000 chunk 117 optimal weight: 7.9990 chunk 351 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 389 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 344 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN ** U 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN ** V 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 94 GLN ** V 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN W 237 HIS W 373 GLN Y 223 GLN ** Z 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.136355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.126705 restraints weight = 395886.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.126968 restraints weight = 303686.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.126994 restraints weight = 258693.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.127261 restraints weight = 227380.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.127385 restraints weight = 203157.315| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4517 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 40755 Z= 0.182 Angle : 0.736 9.906 56100 Z= 0.387 Chirality : 0.048 0.300 6594 Planarity : 0.005 0.075 6344 Dihedral : 21.619 171.490 7349 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.44 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.12), residues: 4460 helix: -0.41 (0.11), residues: 1958 sheet: -1.62 (0.23), residues: 441 loop : -2.57 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG R 288 TYR 0.030 0.002 TYR R 274 PHE 0.020 0.002 PHE W 254 TRP 0.019 0.002 TRP R 397 HIS 0.009 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (40742) covalent geometry : angle 0.73574 / 0.39 (56097) hydrogen bonds : bond 0.05820 / 3.89 ( 1711) hydrogen bonds : angle 5.37175 / 3.84 ( 4679) metal coordination : bond 0.01168 / 0.53 ( 7) metal coordination : angle 1.87450 / 0.99 ( 3) Misc. bond : bond 0.00509 / 0.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.343 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: G 62 MET cc_start: 0.3276 (tpt) cc_final: 0.2937 (mpp) REVERT: M 723 MET cc_start: 0.2215 (tmm) cc_final: 0.1422 (tmm) REVERT: R 106 MET cc_start: 0.7191 (mmt) cc_final: 0.6568 (mmt) REVERT: R 237 ASN cc_start: 0.7838 (p0) cc_final: 0.7514 (p0) REVERT: T 344 MET cc_start: -0.1603 (mmt) cc_final: -0.4692 (ttm) REVERT: V 268 MET cc_start: 0.8847 (tmm) cc_final: 0.8492 (tmm) REVERT: V 269 MET cc_start: 0.7224 (mpp) cc_final: 0.6762 (mpp) REVERT: V 376 ASP cc_start: 0.8094 (t0) cc_final: 0.7735 (t0) REVERT: W 86 MET cc_start: 0.8727 (ppp) cc_final: 0.8409 (ppp) REVERT: W 302 ASP cc_start: 0.8975 (t0) cc_final: 0.8495 (t0) REVERT: W 379 LEU cc_start: 0.7009 (mt) cc_final: 0.6613 (mt) REVERT: X 291 VAL cc_start: 0.6218 (t) cc_final: 0.5922 (t) REVERT: X 315 MET cc_start: 0.7425 (mpp) cc_final: 0.6093 (tpp) REVERT: X 414 TYR cc_start: 0.4631 (t80) cc_final: 0.4031 (t80) REVERT: Z 220 ILE cc_start: 0.9061 (tp) cc_final: 0.8656 (tp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2443 time to fit residues: 94.7331 Evaluate side-chains 174 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 207 optimal weight: 0.0980 chunk 313 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 420 optimal weight: 3.9990 chunk 53 optimal weight: 40.0000 chunk 289 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 375 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1225 HIS ** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN V 94 GLN ** V 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN W 237 HIS W 373 GLN Y 223 GLN ** Y 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 279 GLN ** Z 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.137306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.127409 restraints weight = 400772.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.127595 restraints weight = 293139.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.127796 restraints weight = 251265.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.128425 restraints weight = 217907.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.128449 restraints weight = 179744.453| |-----------------------------------------------------------------------------| r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4472 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40755 Z= 0.147 Angle : 0.706 10.216 56100 Z= 0.369 Chirality : 0.047 0.299 6594 Planarity : 0.005 0.085 6344 Dihedral : 21.602 172.118 7349 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.83 % Favored : 90.99 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.12), residues: 4460 helix: -0.31 (0.11), residues: 1958 sheet: -1.57 (0.23), residues: 437 loop : -2.56 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M1023 TYR 0.025 0.002 TYR R 286 PHE 0.036 0.002 PHE M1121 TRP 0.016 0.001 TRP R 397 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (40742) covalent geometry : angle 0.70622 / 0.37 (56097) hydrogen bonds : bond 0.05404 / 3.59 ( 1711) hydrogen bonds : angle 5.25545 / 3.76 ( 4679) metal coordination : bond 0.00841 / 0.42 ( 7) metal coordination : angle 1.65317 / 0.87 ( 3) Misc. bond : bond 0.00239 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.225 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: G 62 MET cc_start: 0.3297 (tpt) cc_final: 0.2935 (mpp) REVERT: M 723 MET cc_start: 0.1618 (tmm) cc_final: 0.1060 (tmm) REVERT: M 820 TYR cc_start: 0.4022 (m-10) cc_final: 0.3780 (m-80) REVERT: R 237 ASN cc_start: 0.7786 (p0) cc_final: 0.7449 (p0) REVERT: T 344 MET cc_start: -0.1806 (mmt) cc_final: -0.4776 (ttm) REVERT: V 268 MET cc_start: 0.8800 (tmm) cc_final: 0.8456 (tmm) REVERT: V 269 MET cc_start: 0.7064 (mpp) cc_final: 0.6668 (mpp) REVERT: V 376 ASP cc_start: 0.8039 (t0) cc_final: 0.7727 (t0) REVERT: W 302 ASP cc_start: 0.9006 (t0) cc_final: 0.8497 (t0) REVERT: W 379 LEU cc_start: 0.6863 (mt) cc_final: 0.6456 (mt) REVERT: X 291 VAL cc_start: 0.6188 (t) cc_final: 0.5901 (t) REVERT: X 414 TYR cc_start: 0.4487 (t80) cc_final: 0.3925 (t80) REVERT: Z 220 ILE cc_start: 0.9006 (tp) cc_final: 0.8641 (tp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2377 time to fit residues: 93.9250 Evaluate side-chains 175 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 351 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 53 optimal weight: 40.0000 chunk 389 optimal weight: 0.0370 chunk 16 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 381 optimal weight: 9.9990 chunk 426 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 overall best weight: 2.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN ** M 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1350 GLN ** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN V 94 GLN ** V 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN W 237 HIS W 373 GLN Y 223 GLN ** Y 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 279 GLN ** Z 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.141673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.128021 restraints weight = 316273.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.128176 restraints weight = 287458.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.128699 restraints weight = 255306.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.129256 restraints weight = 221019.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.129396 restraints weight = 203536.119| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4516 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40755 Z= 0.169 Angle : 0.728 10.007 56100 Z= 0.382 Chirality : 0.048 0.309 6594 Planarity : 0.005 0.074 6344 Dihedral : 21.623 171.436 7349 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.71 % Favored : 90.13 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.12), residues: 4460 helix: -0.39 (0.11), residues: 1957 sheet: -1.67 (0.23), residues: 441 loop : -2.60 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Z 223 TYR 0.024 0.002 TYR S 179 PHE 0.029 0.002 PHE M1121 TRP 0.034 0.002 TRP R 381 HIS 0.010 0.001 HIS U 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (40742) covalent geometry : angle 0.72761 / 0.38 (56097) hydrogen bonds : bond 0.05673 / 3.81 ( 1711) hydrogen bonds : angle 5.31905 / 3.81 ( 4679) metal coordination : bond 0.01174 / 0.53 ( 7) metal coordination : angle 1.18125 / 0.65 ( 3) Misc. bond : bond 0.00153 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.349 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: G 57 ILE cc_start: 0.5883 (mm) cc_final: 0.5378 (mm) REVERT: G 62 MET cc_start: 0.3250 (tpt) cc_final: 0.2881 (mpp) REVERT: M 723 MET cc_start: 0.1613 (tmm) cc_final: 0.1083 (tmm) REVERT: R 106 MET cc_start: 0.7447 (mmt) cc_final: 0.7004 (mmt) REVERT: R 237 ASN cc_start: 0.7749 (p0) cc_final: 0.7276 (p0) REVERT: R 238 MET cc_start: 0.2177 (mmt) cc_final: 0.1184 (mmt) REVERT: R 286 TYR cc_start: 0.8464 (p90) cc_final: 0.7662 (p90) REVERT: T 344 MET cc_start: -0.1719 (mmt) cc_final: -0.4502 (ttm) REVERT: U 175 MET cc_start: 0.4456 (mpp) cc_final: 0.4249 (mpp) REVERT: V 268 MET cc_start: 0.8831 (tmm) cc_final: 0.8462 (tmm) REVERT: V 269 MET cc_start: 0.7141 (mpp) cc_final: 0.6634 (mpp) REVERT: V 376 ASP cc_start: 0.8068 (t0) cc_final: 0.7751 (t0) REVERT: W 302 ASP cc_start: 0.9043 (t0) cc_final: 0.8545 (t0) REVERT: W 379 LEU cc_start: 0.6815 (mt) cc_final: 0.6370 (mt) REVERT: X 291 VAL cc_start: 0.6212 (t) cc_final: 0.5928 (t) REVERT: X 414 TYR cc_start: 0.4829 (t80) cc_final: 0.4068 (t80) REVERT: Z 220 ILE cc_start: 0.8739 (tp) cc_final: 0.8073 (tp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2435 time to fit residues: 96.3154 Evaluate side-chains 172 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 465 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 324 optimal weight: 0.3980 chunk 450 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 366 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 0.0970 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN V 94 GLN ** V 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN W 237 HIS W 373 GLN Y 223 GLN ** Y 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 279 GLN ** Z 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.139885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.121777 restraints weight = 357206.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.121368 restraints weight = 306789.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.121439 restraints weight = 298177.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.121578 restraints weight = 251997.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.121753 restraints weight = 238354.908| |-----------------------------------------------------------------------------| r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5297 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40755 Z= 0.137 Angle : 0.700 10.416 56100 Z= 0.365 Chirality : 0.047 0.304 6594 Planarity : 0.004 0.072 6344 Dihedral : 21.573 171.872 7349 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.34 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.12), residues: 4460 helix: -0.27 (0.11), residues: 1961 sheet: -1.53 (0.24), residues: 441 loop : -2.53 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 288 TYR 0.022 0.002 TYR R 286 PHE 0.028 0.002 PHE M1121 TRP 0.027 0.002 TRP R 381 HIS 0.007 0.001 HIS U 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (40742) covalent geometry : angle 0.69973 / 0.36 (56097) hydrogen bonds : bond 0.05197 / 3.45 ( 1711) hydrogen bonds : angle 5.16462 / 3.71 ( 4679) metal coordination : bond 0.01104 / 0.47 ( 7) metal coordination : angle 2.13118 / 1.10 ( 3) Misc. bond : bond 0.00125 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.489 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: G 57 ILE cc_start: 0.6237 (mm) cc_final: 0.5224 (mm) REVERT: G 62 MET cc_start: 0.3175 (tpt) cc_final: 0.2785 (mpp) REVERT: M 723 MET cc_start: 0.1812 (tmm) cc_final: 0.1602 (tmm) REVERT: R 237 ASN cc_start: 0.7647 (p0) cc_final: 0.7283 (p0) REVERT: R 238 MET cc_start: 0.2635 (mmt) cc_final: 0.1711 (mmt) REVERT: T 344 MET cc_start: -0.1612 (mmt) cc_final: -0.4586 (ttm) REVERT: U 175 MET cc_start: 0.5091 (mpp) cc_final: 0.4724 (mpp) REVERT: V 268 MET cc_start: 0.8768 (tmm) cc_final: 0.8397 (tmm) REVERT: V 269 MET cc_start: 0.7350 (mpp) cc_final: 0.6808 (mpp) REVERT: V 376 ASP cc_start: 0.8137 (t0) cc_final: 0.7735 (t0) REVERT: W 86 MET cc_start: 0.8702 (ppp) cc_final: 0.8269 (ppp) REVERT: W 302 ASP cc_start: 0.9199 (t0) cc_final: 0.8652 (t0) REVERT: W 379 LEU cc_start: 0.7221 (mt) cc_final: 0.6777 (mt) REVERT: X 291 VAL cc_start: 0.6413 (t) cc_final: 0.6081 (t) REVERT: X 414 TYR cc_start: 0.5029 (t80) cc_final: 0.4201 (t80) REVERT: Z 220 ILE cc_start: 0.9091 (tp) cc_final: 0.8827 (tp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2413 time to fit residues: 96.5142 Evaluate side-chains 182 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 96 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 403 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 chunk 312 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 412 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN ** M 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN V 94 GLN ** V 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN W 237 HIS W 373 GLN Y 223 GLN ** Y 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 279 GLN ** Z 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.138487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.121642 restraints weight = 360527.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.121279 restraints weight = 321881.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.121148 restraints weight = 307593.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.121403 restraints weight = 269447.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.121554 restraints weight = 242497.440| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5173 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 40755 Z= 0.161 Angle : 0.716 10.387 56100 Z= 0.375 Chirality : 0.048 0.318 6594 Planarity : 0.005 0.072 6344 Dihedral : 21.565 170.781 7349 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.35 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.12), residues: 4460 helix: -0.35 (0.11), residues: 1968 sheet: -1.62 (0.23), residues: 436 loop : -2.57 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 126 TYR 0.018 0.002 TYR V 201 PHE 0.027 0.002 PHE M1121 TRP 0.022 0.002 TRP R 381 HIS 0.008 0.001 HIS U 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (40742) covalent geometry : angle 0.71561 / 0.37 (56097) hydrogen bonds : bond 0.05470 / 3.68 ( 1711) hydrogen bonds : angle 5.21037 / 3.74 ( 4679) metal coordination : bond 0.01100 / 0.50 ( 7) metal coordination : angle 1.92359 / 1.01 ( 3) Misc. bond : bond 0.00122 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.104 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: G 57 ILE cc_start: 0.6324 (mm) cc_final: 0.5543 (mm) REVERT: G 62 MET cc_start: 0.3194 (tpt) cc_final: 0.2805 (mpp) REVERT: M 723 MET cc_start: 0.1966 (tmm) cc_final: 0.1655 (tmm) REVERT: R 106 MET cc_start: 0.7378 (mmt) cc_final: 0.6855 (mmt) REVERT: R 237 ASN cc_start: 0.7848 (p0) cc_final: 0.7442 (p0) REVERT: R 238 MET cc_start: 0.2587 (mmt) cc_final: 0.1701 (mmt) REVERT: T 344 MET cc_start: -0.1580 (mmt) cc_final: -0.4572 (ttm) REVERT: U 175 MET cc_start: 0.4819 (mpp) cc_final: 0.4494 (mpp) REVERT: U 215 MET cc_start: 0.0007 (tmm) cc_final: -0.0195 (tmm) REVERT: V 268 MET cc_start: 0.8779 (tmm) cc_final: 0.8414 (tmm) REVERT: V 269 MET cc_start: 0.7254 (mpp) cc_final: 0.6716 (mpp) REVERT: V 376 ASP cc_start: 0.8032 (t0) cc_final: 0.7658 (t0) REVERT: W 86 MET cc_start: 0.8686 (ppp) cc_final: 0.8266 (ppp) REVERT: W 302 ASP cc_start: 0.9171 (t0) cc_final: 0.8661 (t0) REVERT: W 379 LEU cc_start: 0.7148 (mt) cc_final: 0.6699 (mt) REVERT: X 291 VAL cc_start: 0.6328 (t) cc_final: 0.6006 (t) REVERT: X 414 TYR cc_start: 0.4844 (t80) cc_final: 0.4110 (t80) REVERT: Z 220 ILE cc_start: 0.9084 (tp) cc_final: 0.8691 (tp) REVERT: Z 226 LYS cc_start: 0.9455 (mtmm) cc_final: 0.9221 (mttt) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2586 time to fit residues: 102.8253 Evaluate side-chains 179 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 286 optimal weight: 10.0000 chunk 348 optimal weight: 3.9990 chunk 46 optimal weight: 40.0000 chunk 374 optimal weight: 0.1980 chunk 209 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 406 optimal weight: 8.9990 chunk 22 optimal weight: 0.2980 chunk 136 optimal weight: 3.9990 chunk 347 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN V 94 GLN ** V 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN W 237 HIS W 373 GLN Y 223 GLN ** Y 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 279 GLN ** Z 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.139364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.122341 restraints weight = 358519.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.121767 restraints weight = 315584.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.121917 restraints weight = 315130.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.122058 restraints weight = 259666.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.122162 restraints weight = 236495.218| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5149 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40755 Z= 0.142 Angle : 0.711 10.478 56100 Z= 0.369 Chirality : 0.047 0.311 6594 Planarity : 0.005 0.071 6344 Dihedral : 21.544 171.449 7349 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.45 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.12), residues: 4460 helix: -0.30 (0.11), residues: 1970 sheet: -1.58 (0.24), residues: 428 loop : -2.55 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 288 TYR 0.030 0.002 TYR W 359 PHE 0.023 0.002 PHE M1121 TRP 0.022 0.002 TRP R 381 HIS 0.006 0.001 HIS U 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (40742) covalent geometry : angle 0.71059 / 0.37 (56097) hydrogen bonds : bond 0.05209 / 3.47 ( 1711) hydrogen bonds : angle 5.14173 / 3.69 ( 4679) metal coordination : bond 0.00920 / 0.43 ( 7) metal coordination : angle 1.79769 / 0.93 ( 3) Misc. bond : bond 0.00207 / 0.13 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8920 Ramachandran restraints generated. 4460 Oldfield, 0 Emsley, 4460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.423 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: G 57 ILE cc_start: 0.6217 (mm) cc_final: 0.5412 (mm) REVERT: G 62 MET cc_start: 0.3212 (tpt) cc_final: 0.2906 (mpp) REVERT: M 723 MET cc_start: 0.1895 (tmm) cc_final: 0.1595 (tmm) REVERT: R 106 MET cc_start: 0.7390 (mmt) cc_final: 0.6904 (mmt) REVERT: R 237 ASN cc_start: 0.7831 (p0) cc_final: 0.7429 (p0) REVERT: R 238 MET cc_start: 0.2486 (mmt) cc_final: 0.1569 (mmt) REVERT: R 286 TYR cc_start: 0.8418 (p90) cc_final: 0.7983 (p90) REVERT: T 344 MET cc_start: -0.1524 (mmt) cc_final: -0.4498 (ttm) REVERT: U 175 MET cc_start: 0.4883 (mpp) cc_final: 0.4552 (mpp) REVERT: V 268 MET cc_start: 0.8750 (tmm) cc_final: 0.8398 (tmm) REVERT: V 269 MET cc_start: 0.7266 (mpp) cc_final: 0.6678 (mpp) REVERT: V 376 ASP cc_start: 0.8083 (t0) cc_final: 0.7713 (t0) REVERT: W 86 MET cc_start: 0.8317 (ppp) cc_final: 0.7900 (ppp) REVERT: W 302 ASP cc_start: 0.9181 (t0) cc_final: 0.8659 (t0) REVERT: W 379 LEU cc_start: 0.7091 (mt) cc_final: 0.6649 (mt) REVERT: X 291 VAL cc_start: 0.6243 (t) cc_final: 0.5932 (t) REVERT: X 414 TYR cc_start: 0.4935 (t80) cc_final: 0.4235 (t80) REVERT: Z 220 ILE cc_start: 0.9020 (tp) cc_final: 0.8660 (tp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2460 time to fit residues: 95.9584 Evaluate side-chains 178 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 429 optimal weight: 0.7980 chunk 257 optimal weight: 20.0000 chunk 329 optimal weight: 0.4980 chunk 78 optimal weight: 20.0000 chunk 446 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 112 optimal weight: 0.0970 chunk 211 optimal weight: 4.9990 chunk 331 optimal weight: 8.9990 chunk 198 optimal weight: 0.7980 chunk 222 optimal weight: 6.9990 overall best weight: 1.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN ** U 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN V 94 GLN ** V 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN W 237 HIS W 373 GLN Y 223 GLN Z 279 GLN ** Z 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.140230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.122935 restraints weight = 359871.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.122767 restraints weight = 319543.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.122770 restraints weight = 290344.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.122828 restraints weight = 249551.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.123130 restraints weight = 230032.087| |-----------------------------------------------------------------------------| r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5121 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40755 Z= 0.134 Angle : 0.690 10.801 56100 Z= 0.357 Chirality : 0.046 0.324 6594 Planarity : 0.004 0.071 6344 Dihedral : 21.436 170.179 7349 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.52 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.12), residues: 4460 helix: -0.21 (0.11), residues: 1972 sheet: -1.46 (0.24), residues: 435 loop : -2.50 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 288 TYR 0.018 0.001 TYR M 776 PHE 0.028 0.002 PHE T 102 TRP 0.024 0.002 TRP R 397 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (40742) covalent geometry : angle 0.68990 / 0.36 (56097) hydrogen bonds : bond 0.05059 / 3.38 ( 1711) hydrogen bonds : angle 5.01533 / 3.60 ( 4679) metal coordination : bond 0.00881 / 0.41 ( 7) metal coordination : angle 1.66052 / 0.87 ( 3) Misc. bond : bond 0.00171 / 0.10 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6793.22 seconds wall clock time: 119 minutes 2.76 seconds (7142.76 seconds total)