Starting phenix.real_space_refine on Tue Aug 26 18:06:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fbw_50297/08_2025/9fbw_50297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fbw_50297/08_2025/9fbw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fbw_50297/08_2025/9fbw_50297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fbw_50297/08_2025/9fbw_50297.map" model { file = "/net/cci-nas-00/data/ceres_data/9fbw_50297/08_2025/9fbw_50297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fbw_50297/08_2025/9fbw_50297.cif" } 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-2.0-5787/lib/python3.9/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: 10.09, per 1000 atoms: 0.25 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: 4.07 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 6.01 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: 11.75 Time building geometry restraints manager: 5.20 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=" C3' DC J 24 " pdb=" O3' DC J 24 " ideal model delta sigma weight residual 1.422 1.469 -0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" C3' DC I -56 " pdb=" O3' DC I -56 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" C LYS C 31 " pdb=" N PRO C 32 " ideal model delta sigma weight residual 1.334 1.365 -0.032 2.34e-02 1.83e+03 1.82e+00 bond pdb=" C VAL R 137 " pdb=" N PRO R 138 " ideal model delta sigma weight residual 1.334 1.364 -0.031 2.34e-02 1.83e+03 1.70e+00 bond pdb=" C1' DC I -75 " pdb=" N1 DC I -75 " ideal model delta sigma weight residual 1.490 1.528 -0.038 3.00e-02 1.11e+03 1.60e+00 ... (remaining 40737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 55258 2.33 - 4.66: 713 4.66 - 7.00: 111 7.00 - 9.33: 11 9.33 - 11.66: 4 Bond angle restraints: 56097 Sorted by residual: 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=" N PHE M 979 " pdb=" CA PHE M 979 " pdb=" C PHE M 979 " ideal model delta sigma weight residual 111.69 117.34 -5.65 1.23e+00 6.61e-01 2.11e+01 angle pdb=" C GLU Z 222 " pdb=" N ARG Z 223 " pdb=" CA ARG Z 223 " ideal model delta sigma weight residual 121.66 114.14 7.52 1.76e+00 3.23e-01 1.83e+01 angle pdb=" N GLY D 41 " pdb=" CA GLY D 41 " pdb=" C GLY D 41 " ideal model delta sigma weight residual 113.18 123.11 -9.93 2.37e+00 1.78e-01 1.76e+01 angle pdb=" N THR C 30 " pdb=" CA THR C 30 " pdb=" C THR C 30 " ideal model delta sigma weight residual 110.80 119.30 -8.50 2.13e+00 2.20e-01 1.59e+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: 4735 0.042 - 0.084: 1407 0.084 - 0.126: 401 0.126 - 0.168: 47 0.168 - 0.209: 4 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: 10.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.740 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 50.990 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 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:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4970 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 : 0.003 0.047 40755 Z= 0.139 Angle : 0.675 11.660 56100 Z= 0.356 Chirality : 0.043 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 aren 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 covalent geometry : bond 0.00285 (40742) covalent geometry : angle 0.67522 (56097) hydrogen bonds : bond 0.14545 ( 1711) hydrogen bonds : angle 6.31518 ( 4679) metal coordination : bond 0.00608 ( 7) metal coordination : angle 1.19065 ( 3) Misc. bond : bond 0.00134 ( 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 : 1.483 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: 0.2591 time to fit residues: 104.0367 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 : 1.565 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN M1036 ASN R 280 GLN ** R 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 X 238 HIS Y 223 GLN Y 230 GLN ** Y 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 587 GLN ** Z 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.136802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.126592 restraints weight = 401747.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.127030 restraints weight = 301880.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.127310 restraints weight = 274228.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.128115 restraints weight = 210901.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.128128 restraints weight = 166637.401| |-----------------------------------------------------------------------------| r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4503 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 40755 Z= 0.180 Angle : 0.698 10.317 56100 Z= 0.366 Chirality : 0.045 0.205 6594 Planarity : 0.005 0.075 6344 Dihedral : 21.486 170.333 7349 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.04 % Favored : 90.78 % Rotamer: Outliers : 0.11 % Allowed : 7.56 % Favored : 92.34 % 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 aren not related in a simple way. whole: -1.95 (0.12), residues: 4460 helix: -0.16 (0.12), residues: 1949 sheet: -1.46 (0.23), residues: 464 loop : -2.41 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W 413 TYR 0.022 0.002 TYR V 201 PHE 0.016 0.002 PHE X 125 TRP 0.018 0.002 TRP R 397 HIS 0.007 0.001 HIS V 27 Details of bonding type rmsd covalent geometry : bond 0.00384 (40742) covalent geometry : angle 0.69769 (56097) hydrogen bonds : bond 0.05634 ( 1711) hydrogen bonds : angle 5.38018 ( 4679) metal coordination : bond 0.00873 ( 7) metal coordination : angle 1.50259 ( 3) Misc. bond : bond 0.00140 ( 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 242 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 238 time to evaluate : 1.598 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: M 723 MET cc_start: 0.2292 (tmm) cc_final: 0.1186 (tmm) REVERT: R 106 MET cc_start: 0.6907 (mmt) cc_final: 0.6487 (mmt) REVERT: R 237 ASN cc_start: 0.7769 (p0) cc_final: 0.7470 (p0) REVERT: R 238 MET cc_start: 0.2273 (mmt) cc_final: 0.1939 (mmt) REVERT: T 344 MET cc_start: -0.1583 (mmt) cc_final: -0.4570 (ttm) REVERT: V 268 MET cc_start: 0.8944 (tmm) cc_final: 0.8507 (tmm) REVERT: V 269 MET cc_start: 0.7141 (mpp) cc_final: 0.6751 (mpp) REVERT: W 86 MET cc_start: 0.7477 (ppp) cc_final: 0.7269 (ppp) REVERT: W 302 ASP cc_start: 0.9000 (t0) cc_final: 0.8559 (t0) REVERT: W 379 LEU cc_start: 0.7117 (mt) cc_final: 0.6695 (mt) REVERT: X 315 MET cc_start: 0.7770 (tpt) cc_final: 0.7448 (tpp) REVERT: X 414 TYR cc_start: 0.4607 (t80) cc_final: 0.4063 (t80) REVERT: Z 220 ILE cc_start: 0.9108 (tp) cc_final: 0.8654 (tp) outliers start: 4 outliers final: 0 residues processed: 242 average time/residue: 0.2541 time to fit residues: 102.4418 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 : 1.508 ------------------------------------------------------------------------------- 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: 2.9990 chunk 8 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 428 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 455 optimal weight: 0.6980 chunk 431 optimal weight: 7.9990 chunk 392 optimal weight: 10.0000 chunk 343 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 210 optimal weight: 0.0980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 100 ASN R 270 HIS ** R 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 W 453 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.141523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.128278 restraints weight = 316820.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.128052 restraints weight = 281280.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.128344 restraints weight = 265578.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.128387 restraints weight = 247055.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.128421 restraints weight = 236246.284| |-----------------------------------------------------------------------------| r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4522 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40755 Z= 0.187 Angle : 0.715 9.646 56100 Z= 0.373 Chirality : 0.045 0.225 6594 Planarity : 0.005 0.079 6344 Dihedral : 21.606 170.778 7349 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.13 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % 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 aren not related in a simple way. whole: -2.18 (0.12), residues: 4460 helix: -0.38 (0.11), residues: 1946 sheet: -1.52 (0.24), residues: 437 loop : -2.52 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M1387 TYR 0.019 0.002 TYR M 776 PHE 0.039 0.002 PHE W 254 TRP 0.019 0.002 TRP R 397 HIS 0.019 0.002 HIS V 250 Details of bonding type rmsd covalent geometry : bond 0.00406 (40742) covalent geometry : angle 0.71452 (56097) hydrogen bonds : bond 0.05600 ( 1711) hydrogen bonds : angle 5.44442 ( 4679) metal coordination : bond 0.01650 ( 7) metal coordination : angle 1.92094 ( 3) Misc. bond : bond 0.00551 ( 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 241 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.455 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: G 62 MET cc_start: 0.3384 (tpt) cc_final: 0.3065 (mpp) REVERT: M 723 MET cc_start: 0.2098 (tmm) cc_final: 0.1289 (tmm) REVERT: R 237 ASN cc_start: 0.7727 (p0) cc_final: 0.7418 (p0) REVERT: R 286 TYR cc_start: 0.8478 (p90) cc_final: 0.7693 (p90) REVERT: T 344 MET cc_start: -0.1696 (mmt) cc_final: -0.4617 (ttm) REVERT: V 268 MET cc_start: 0.8864 (tmm) cc_final: 0.8457 (tmm) REVERT: V 269 MET cc_start: 0.7303 (mpp) cc_final: 0.6835 (mpp) REVERT: V 376 ASP cc_start: 0.7982 (t0) cc_final: 0.7571 (t0) REVERT: W 302 ASP cc_start: 0.9050 (t0) cc_final: 0.8544 (t0) REVERT: W 379 LEU cc_start: 0.6984 (mt) cc_final: 0.6587 (mt) REVERT: X 291 VAL cc_start: 0.6186 (t) cc_final: 0.5915 (t) REVERT: X 315 MET cc_start: 0.7697 (tpt) cc_final: 0.7401 (tpp) REVERT: X 414 TYR cc_start: 0.4832 (t80) cc_final: 0.4165 (t80) REVERT: Z 220 ILE cc_start: 0.9101 (tp) cc_final: 0.8465 (tp) REVERT: Z 235 MET cc_start: 0.2933 (mmt) cc_final: 0.2688 (mmt) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2480 time to fit residues: 98.4827 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 : 1.368 ------------------------------------------------------------------------------- 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: 0.5980 chunk 371 optimal weight: 10.0000 chunk 364 optimal weight: 9.9990 chunk 352 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 447 optimal weight: 0.9990 chunk 329 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 349 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN ** M 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1225 HIS ** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 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 = 0.4731 r_free = 0.4731 target = 0.137864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.121577 restraints weight = 360788.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.121128 restraints weight = 322356.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.120943 restraints weight = 298150.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.121125 restraints weight = 272616.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.121186 restraints weight = 242455.307| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5094 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 40755 Z= 0.175 Angle : 0.705 10.203 56100 Z= 0.369 Chirality : 0.045 0.245 6594 Planarity : 0.005 0.078 6344 Dihedral : 21.658 171.824 7349 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.33 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % 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 aren not related in a simple way. whole: -2.27 (0.12), residues: 4460 helix: -0.42 (0.11), residues: 1950 sheet: -1.68 (0.23), residues: 432 loop : -2.57 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 346 TYR 0.019 0.002 TYR M 737 PHE 0.036 0.002 PHE B 104 TRP 0.017 0.002 TRP R 397 HIS 0.010 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00380 (40742) covalent geometry : angle 0.70512 (56097) hydrogen bonds : bond 0.05401 ( 1711) hydrogen bonds : angle 5.36911 ( 4679) metal coordination : bond 0.01191 ( 7) metal coordination : angle 2.28192 ( 3) Misc. bond : bond 0.00124 ( 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 233 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.472 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: G 62 MET cc_start: 0.3351 (tpt) cc_final: 0.2994 (mpp) REVERT: M 723 MET cc_start: 0.2561 (tmm) cc_final: 0.1840 (tmm) REVERT: R 237 ASN cc_start: 0.7895 (p0) cc_final: 0.7557 (p0) REVERT: R 286 TYR cc_start: 0.8606 (p90) cc_final: 0.8121 (p90) REVERT: U 175 MET cc_start: 0.4818 (mpp) cc_final: 0.4559 (mpp) REVERT: V 268 MET cc_start: 0.8808 (tmm) cc_final: 0.8431 (tmm) REVERT: V 269 MET cc_start: 0.7191 (mpp) cc_final: 0.6765 (mpp) REVERT: V 376 ASP cc_start: 0.7984 (t0) cc_final: 0.7645 (t0) REVERT: W 86 MET cc_start: 0.8683 (ppp) cc_final: 0.8268 (ppp) REVERT: W 302 ASP cc_start: 0.9158 (t0) cc_final: 0.8645 (t0) REVERT: W 379 LEU cc_start: 0.7398 (mt) cc_final: 0.6939 (mt) REVERT: X 291 VAL cc_start: 0.6213 (t) cc_final: 0.5948 (t) REVERT: X 414 TYR cc_start: 0.5089 (t80) cc_final: 0.4307 (t80) REVERT: Z 220 ILE cc_start: 0.9097 (tp) cc_final: 0.8700 (tp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2314 time to fit residues: 88.8929 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 : 1.278 ------------------------------------------------------------------------------- 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: 9.9990 chunk 56 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 351 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 389 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 344 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 367 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 ** 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 = 0.4744 r_free = 0.4744 target = 0.138637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.121719 restraints weight = 359097.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.121220 restraints weight = 321884.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.121403 restraints weight = 289860.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.121472 restraints weight = 253561.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.121495 restraints weight = 236595.482| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5142 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40755 Z= 0.156 Angle : 0.689 10.032 56100 Z= 0.358 Chirality : 0.045 0.233 6594 Planarity : 0.005 0.071 6344 Dihedral : 21.610 171.175 7349 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.72 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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 aren not related in a simple way. whole: -2.18 (0.12), residues: 4460 helix: -0.32 (0.11), residues: 1950 sheet: -1.57 (0.24), residues: 418 loop : -2.56 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 346 TYR 0.018 0.002 TYR M 777 PHE 0.024 0.002 PHE M1121 TRP 0.015 0.002 TRP M 745 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00337 (40742) covalent geometry : angle 0.68930 (56097) hydrogen bonds : bond 0.05093 ( 1711) hydrogen bonds : angle 5.23115 ( 4679) metal coordination : bond 0.01027 ( 7) metal coordination : angle 1.82876 ( 3) Misc. bond : bond 0.00155 ( 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 240 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.573 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: 0.3180 (tpt) cc_final: 0.2790 (mpp) REVERT: M 723 MET cc_start: 0.2156 (tmm) cc_final: 0.1622 (tmm) REVERT: R 237 ASN cc_start: 0.7831 (p0) cc_final: 0.7476 (p0) REVERT: R 286 TYR cc_start: 0.8678 (p90) cc_final: 0.8052 (p90) REVERT: T 344 MET cc_start: -0.1146 (mmt) cc_final: -0.4458 (ttm) REVERT: U 175 MET cc_start: 0.4919 (mpp) cc_final: 0.4589 (mpp) REVERT: V 268 MET cc_start: 0.8792 (tmm) cc_final: 0.8439 (tmm) REVERT: V 269 MET cc_start: 0.7353 (mpp) cc_final: 0.6843 (mpp) REVERT: V 376 ASP cc_start: 0.8095 (t0) cc_final: 0.7784 (t0) REVERT: W 86 MET cc_start: 0.8773 (ppp) cc_final: 0.8433 (ppp) REVERT: W 302 ASP cc_start: 0.9176 (t0) cc_final: 0.8645 (t0) REVERT: W 379 LEU cc_start: 0.7368 (mt) cc_final: 0.6896 (mt) REVERT: X 291 VAL cc_start: 0.6264 (t) cc_final: 0.5991 (t) REVERT: X 414 TYR cc_start: 0.5050 (t80) cc_final: 0.4223 (t80) REVERT: Z 220 ILE cc_start: 0.9102 (tp) cc_final: 0.8618 (tp) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2326 time to fit residues: 93.3422 Evaluate side-chains 176 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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: 20.0000 chunk 313 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 420 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 375 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 367 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** W 237 HIS W 373 GLN Y 223 GLN ** 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 = 0.4718 r_free = 0.4718 target = 0.136951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.119912 restraints weight = 363267.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.119645 restraints weight = 333866.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.119636 restraints weight = 290855.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.119853 restraints weight = 267736.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.119843 restraints weight = 246868.036| |-----------------------------------------------------------------------------| r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5204 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 40755 Z= 0.190 Angle : 0.733 9.876 56100 Z= 0.384 Chirality : 0.046 0.247 6594 Planarity : 0.005 0.072 6344 Dihedral : 21.662 170.482 7349 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.45 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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 aren not related in a simple way. whole: -2.41 (0.12), residues: 4460 helix: -0.52 (0.11), residues: 1961 sheet: -1.68 (0.23), residues: 419 loop : -2.70 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 311 TYR 0.021 0.002 TYR V 201 PHE 0.021 0.002 PHE W 308 TRP 0.036 0.002 TRP R 381 HIS 0.009 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00412 (40742) covalent geometry : angle 0.73315 (56097) hydrogen bonds : bond 0.05552 ( 1711) hydrogen bonds : angle 5.39429 ( 4679) metal coordination : bond 0.01429 ( 7) metal coordination : angle 2.33246 ( 3) Misc. bond : bond 0.00121 ( 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 237 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.030 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: M 723 MET cc_start: 0.2067 (tmm) cc_final: 0.1477 (tmm) REVERT: R 106 MET cc_start: 0.7447 (mmt) cc_final: 0.6838 (mmt) REVERT: R 237 ASN cc_start: 0.8014 (p0) cc_final: 0.7689 (p0) REVERT: R 286 TYR cc_start: 0.8510 (p90) cc_final: 0.8118 (p90) REVERT: S 103 MET cc_start: 0.2243 (mmt) cc_final: 0.2017 (mmp) REVERT: T 344 MET cc_start: -0.0704 (mmt) cc_final: -0.4084 (ttm) REVERT: U 175 MET cc_start: 0.5113 (mpp) cc_final: 0.4766 (mpp) REVERT: V 268 MET cc_start: 0.8717 (tmm) cc_final: 0.8318 (tmm) REVERT: V 269 MET cc_start: 0.7014 (mpp) cc_final: 0.6558 (mpp) REVERT: V 376 ASP cc_start: 0.8019 (t0) cc_final: 0.7688 (t0) REVERT: W 86 MET cc_start: 0.8766 (ppp) cc_final: 0.8431 (ppp) REVERT: W 302 ASP cc_start: 0.9135 (t0) cc_final: 0.8629 (t0) REVERT: W 379 LEU cc_start: 0.7360 (mt) cc_final: 0.6902 (mt) REVERT: X 291 VAL cc_start: 0.6276 (t) cc_final: 0.6016 (t) REVERT: X 414 TYR cc_start: 0.5117 (t80) cc_final: 0.4313 (t80) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2224 time to fit residues: 87.1587 Evaluate side-chains 168 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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: 8.9990 chunk 133 optimal weight: 0.9990 chunk 232 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 389 optimal weight: 0.0370 chunk 16 optimal weight: 1.9990 chunk 385 optimal weight: 10.0000 chunk 381 optimal weight: 1.9990 chunk 426 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** R 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 242 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 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 = 0.4747 r_free = 0.4747 target = 0.138664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.121699 restraints weight = 360326.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.121818 restraints weight = 331117.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.121650 restraints weight = 266796.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.121863 restraints weight = 261486.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.121855 restraints weight = 237023.314| |-----------------------------------------------------------------------------| r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5091 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40755 Z= 0.149 Angle : 0.689 10.191 56100 Z= 0.358 Chirality : 0.045 0.245 6594 Planarity : 0.004 0.073 6344 Dihedral : 21.591 170.837 7349 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.36 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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 aren not related in a simple way. whole: -2.20 (0.12), residues: 4460 helix: -0.36 (0.11), residues: 1966 sheet: -1.53 (0.24), residues: 422 loop : -2.58 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 51 TYR 0.021 0.002 TYR W 359 PHE 0.021 0.002 PHE T 102 TRP 0.021 0.002 TRP R 381 HIS 0.008 0.001 HIS R 319 Details of bonding type rmsd covalent geometry : bond 0.00323 (40742) covalent geometry : angle 0.68879 (56097) hydrogen bonds : bond 0.04977 ( 1711) hydrogen bonds : angle 5.17930 ( 4679) metal coordination : bond 0.01069 ( 7) metal coordination : angle 2.12964 ( 3) Misc. bond : bond 0.00134 ( 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 : 1.434 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 62 MET cc_start: 0.3306 (tpt) cc_final: 0.2896 (mpp) REVERT: M 723 MET cc_start: 0.2043 (tmm) cc_final: 0.1667 (tmm) REVERT: R 237 ASN cc_start: 0.8071 (p0) cc_final: 0.7749 (p0) REVERT: R 238 MET cc_start: 0.2646 (mmt) cc_final: 0.2226 (mmt) REVERT: R 286 TYR cc_start: 0.8471 (p90) cc_final: 0.8113 (p90) REVERT: T 344 MET cc_start: -0.1209 (mmt) cc_final: -0.4535 (ttm) REVERT: U 175 MET cc_start: 0.4861 (mpp) cc_final: 0.4622 (mpp) REVERT: V 268 MET cc_start: 0.8726 (tmm) cc_final: 0.8341 (tmm) REVERT: V 269 MET cc_start: 0.7209 (mpp) cc_final: 0.6682 (mpp) REVERT: V 376 ASP cc_start: 0.7854 (t0) cc_final: 0.7478 (t0) REVERT: W 86 MET cc_start: 0.8654 (ppp) cc_final: 0.8293 (ppp) REVERT: W 302 ASP cc_start: 0.9182 (t0) cc_final: 0.8653 (t0) REVERT: W 379 LEU cc_start: 0.7309 (mt) cc_final: 0.6837 (mt) REVERT: X 291 VAL cc_start: 0.6346 (t) cc_final: 0.6057 (t) REVERT: X 414 TYR cc_start: 0.4829 (t80) cc_final: 0.4074 (t80) REVERT: Z 220 ILE cc_start: 0.9053 (tp) cc_final: 0.8509 (tp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2285 time to fit residues: 89.9145 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 : 1.572 ------------------------------------------------------------------------------- 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: 6.9990 chunk 274 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 267 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 324 optimal weight: 6.9990 chunk 450 optimal weight: 0.1980 chunk 118 optimal weight: 0.9980 chunk 366 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** R 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 367 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 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 = 0.4739 r_free = 0.4739 target = 0.138157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.121279 restraints weight = 360030.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.120749 restraints weight = 317395.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.121173 restraints weight = 283720.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.121291 restraints weight = 243984.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.121240 restraints weight = 227005.422| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5142 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40755 Z= 0.160 Angle : 0.701 10.246 56100 Z= 0.363 Chirality : 0.045 0.225 6594 Planarity : 0.005 0.073 6344 Dihedral : 21.555 168.604 7349 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.44 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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 aren not related in a simple way. whole: -2.24 (0.12), residues: 4460 helix: -0.37 (0.11), residues: 1965 sheet: -1.53 (0.24), residues: 426 loop : -2.63 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 223 TYR 0.025 0.002 TYR M 776 PHE 0.025 0.002 PHE S 269 TRP 0.021 0.002 TRP R 397 HIS 0.007 0.001 HIS R 319 Details of bonding type rmsd covalent geometry : bond 0.00347 (40742) covalent geometry : angle 0.70091 (56097) hydrogen bonds : bond 0.05087 ( 1711) hydrogen bonds : angle 5.16768 ( 4679) metal coordination : bond 0.00938 ( 7) metal coordination : angle 1.73865 ( 3) Misc. bond : bond 0.00120 ( 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 236 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.494 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: M 723 MET cc_start: 0.1962 (tmm) cc_final: 0.1628 (tmm) REVERT: R 237 ASN cc_start: 0.8081 (p0) cc_final: 0.7722 (p0) REVERT: R 238 MET cc_start: 0.2465 (mmt) cc_final: 0.1704 (mmt) REVERT: R 286 TYR cc_start: 0.8441 (p90) cc_final: 0.8104 (p90) REVERT: S 103 MET cc_start: 0.2196 (mmt) cc_final: 0.1971 (mmp) REVERT: T 344 MET cc_start: -0.1364 (mmt) cc_final: -0.4623 (ttm) REVERT: U 175 MET cc_start: 0.4949 (mpp) cc_final: 0.4654 (mpp) REVERT: V 268 MET cc_start: 0.8738 (tmm) cc_final: 0.8351 (tmm) REVERT: V 269 MET cc_start: 0.7302 (mpp) cc_final: 0.6742 (mpp) REVERT: V 376 ASP cc_start: 0.8006 (t0) cc_final: 0.7622 (t0) REVERT: W 86 MET cc_start: 0.8511 (ppp) cc_final: 0.8147 (ppp) REVERT: W 302 ASP cc_start: 0.9178 (t0) cc_final: 0.8667 (t0) REVERT: W 379 LEU cc_start: 0.7163 (mt) cc_final: 0.6689 (mt) REVERT: X 291 VAL cc_start: 0.6273 (t) cc_final: 0.5974 (t) REVERT: X 414 TYR cc_start: 0.4902 (t80) cc_final: 0.4164 (t80) REVERT: Z 220 ILE cc_start: 0.9092 (tp) cc_final: 0.8481 (tp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2250 time to fit residues: 89.3780 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 : 1.154 ------------------------------------------------------------------------------- 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: 0.0980 chunk 205 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 403 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 312 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 412 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 367 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.137848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.120196 restraints weight = 361710.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.120478 restraints weight = 311073.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.120030 restraints weight = 269279.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.120472 restraints weight = 249006.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.120279 restraints weight = 231386.298| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5262 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40755 Z= 0.163 Angle : 0.712 10.450 56100 Z= 0.370 Chirality : 0.045 0.221 6594 Planarity : 0.005 0.071 6344 Dihedral : 21.540 168.579 7349 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.08 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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 aren not related in a simple way. whole: -2.24 (0.12), residues: 4460 helix: -0.38 (0.11), residues: 1952 sheet: -1.51 (0.24), residues: 429 loop : -2.63 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 223 TYR 0.024 0.002 TYR M 776 PHE 0.022 0.002 PHE T 102 TRP 0.022 0.002 TRP R 397 HIS 0.005 0.001 HIS U 242 Details of bonding type rmsd covalent geometry : bond 0.00355 (40742) covalent geometry : angle 0.71193 (56097) hydrogen bonds : bond 0.05104 ( 1711) hydrogen bonds : angle 5.20860 ( 4679) metal coordination : bond 0.01444 ( 7) metal coordination : angle 1.86329 ( 3) Misc. bond : bond 0.00127 ( 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 229 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.035 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: M 723 MET cc_start: 0.1794 (tmm) cc_final: 0.1579 (tmm) REVERT: M 1271 MET cc_start: 0.3189 (tpt) cc_final: 0.2988 (tpt) REVERT: R 106 MET cc_start: 0.7386 (mmt) cc_final: 0.7119 (mmt) REVERT: R 237 ASN cc_start: 0.8025 (p0) cc_final: 0.7699 (p0) REVERT: R 238 MET cc_start: 0.2637 (mmt) cc_final: 0.1909 (mmt) REVERT: R 286 TYR cc_start: 0.8322 (p90) cc_final: 0.8046 (p90) REVERT: T 344 MET cc_start: -0.1363 (mmt) cc_final: -0.4615 (ttm) REVERT: U 175 MET cc_start: 0.5130 (mpp) cc_final: 0.4780 (mpp) REVERT: V 268 MET cc_start: 0.8772 (tmm) cc_final: 0.8347 (tmm) REVERT: V 269 MET cc_start: 0.7399 (mpp) cc_final: 0.6782 (mpp) REVERT: V 376 ASP cc_start: 0.8062 (t0) cc_final: 0.7668 (t0) REVERT: V 406 MET cc_start: 0.8767 (mpp) cc_final: 0.8220 (mpp) REVERT: W 302 ASP cc_start: 0.9204 (t0) cc_final: 0.8689 (t0) REVERT: W 379 LEU cc_start: 0.7205 (mt) cc_final: 0.6757 (mt) REVERT: X 291 VAL cc_start: 0.6274 (t) cc_final: 0.5992 (t) REVERT: X 414 TYR cc_start: 0.4948 (t80) cc_final: 0.4153 (t80) REVERT: Z 220 ILE cc_start: 0.9169 (tp) cc_final: 0.8489 (tp) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2135 time to fit residues: 81.0401 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 : 1.262 ------------------------------------------------------------------------------- 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: 6.9990 chunk 348 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 374 optimal weight: 0.9980 chunk 209 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 406 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 347 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 ASN R 367 GLN 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 373 GLN X 245 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.139533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.122208 restraints weight = 358286.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.121952 restraints weight = 305036.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.122027 restraints weight = 282681.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.122514 restraints weight = 243083.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.122384 restraints weight = 224489.488| |-----------------------------------------------------------------------------| r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5108 moved from start: 0.2349 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= 0.142 Angle : 0.683 10.822 56100 Z= 0.353 Chirality : 0.044 0.206 6594 Planarity : 0.004 0.070 6344 Dihedral : 21.405 167.520 7349 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.34 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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 aren not related in a simple way. whole: -2.10 (0.12), residues: 4460 helix: -0.24 (0.11), residues: 1970 sheet: -1.56 (0.24), residues: 449 loop : -2.55 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 51 TYR 0.022 0.001 TYR X 218 PHE 0.025 0.002 PHE T 102 TRP 0.022 0.001 TRP R 397 HIS 0.004 0.001 HIS M1285 Details of bonding type rmsd covalent geometry : bond 0.00303 (40742) covalent geometry : angle 0.68292 (56097) hydrogen bonds : bond 0.04768 ( 1711) hydrogen bonds : angle 4.97748 ( 4679) metal coordination : bond 0.00926 ( 7) metal coordination : angle 1.51026 ( 3) Misc. bond : bond 0.00117 ( 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 239 residues out of total 3947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.079 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: M 723 MET cc_start: 0.1817 (tmm) cc_final: 0.1565 (tmm) REVERT: R 237 ASN cc_start: 0.8029 (p0) cc_final: 0.7665 (p0) REVERT: R 238 MET cc_start: 0.2244 (mmt) cc_final: 0.1455 (mmt) REVERT: R 286 TYR cc_start: 0.8378 (p90) cc_final: 0.8022 (p90) REVERT: S 103 MET cc_start: 0.1825 (mmp) cc_final: 0.1612 (mmt) REVERT: T 344 MET cc_start: -0.1790 (mmt) cc_final: -0.4873 (ttm) REVERT: U 175 MET cc_start: 0.4947 (mpp) cc_final: 0.4648 (mpp) REVERT: V 269 MET cc_start: 0.7381 (mpp) cc_final: 0.6958 (mpp) REVERT: V 376 ASP cc_start: 0.8034 (t0) cc_final: 0.7660 (t0) REVERT: W 86 MET cc_start: 0.7963 (ppp) cc_final: 0.7717 (ppp) REVERT: W 302 ASP cc_start: 0.9177 (t0) cc_final: 0.8656 (t0) REVERT: W 379 LEU cc_start: 0.7015 (mt) cc_final: 0.6557 (mt) REVERT: X 291 VAL cc_start: 0.6327 (t) cc_final: 0.5987 (t) REVERT: X 414 TYR cc_start: 0.4871 (t80) cc_final: 0.4113 (t80) REVERT: Z 220 ILE cc_start: 0.9060 (tp) cc_final: 0.8362 (tp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2110 time to fit residues: 83.5311 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 : 1.076 ------------------------------------------------------------------------------- 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: 8.9990 chunk 257 optimal weight: 20.0000 chunk 329 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 446 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 331 optimal weight: 8.9990 chunk 198 optimal weight: 0.4980 chunk 222 optimal weight: 7.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN ** M 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 797 HIS ** M 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Y 223 GLN Z 587 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 = 0.4690 r_free = 0.4690 target = 0.134957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.117899 restraints weight = 365721.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.117509 restraints weight = 326241.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.117429 restraints weight = 320197.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.117616 restraints weight = 273968.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.117738 restraints weight = 250577.118| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5302 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 40755 Z= 0.249 Angle : 0.835 10.853 56100 Z= 0.438 Chirality : 0.049 0.338 6594 Planarity : 0.006 0.068 6344 Dihedral : 21.598 166.691 7349 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 27.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.28 % Favored : 88.54 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.65 % 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 aren not related in a simple way. whole: -2.70 (0.12), residues: 4460 helix: -0.77 (0.11), residues: 1939 sheet: -1.97 (0.23), residues: 442 loop : -2.78 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 416 TYR 0.024 0.003 TYR M 777 PHE 0.023 0.003 PHE W 254 TRP 0.024 0.003 TRP R 397 HIS 0.011 0.002 HIS U 23 Details of bonding type rmsd covalent geometry : bond 0.00544 (40742) covalent geometry : angle 0.83449 (56097) hydrogen bonds : bond 0.06371 ( 1711) hydrogen bonds : angle 5.57029 ( 4679) metal coordination : bond 0.01732 ( 7) metal coordination : angle 2.28947 ( 3) Misc. bond : bond 0.00156 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6716.05 seconds wall clock time: 117 minutes 28.37 seconds (7048.37 seconds total)