Starting phenix.real_space_refine on Tue Feb 13 12:42:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4p_32311/02_2024/7w4p_32311_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4p_32311/02_2024/7w4p_32311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4p_32311/02_2024/7w4p_32311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4p_32311/02_2024/7w4p_32311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4p_32311/02_2024/7w4p_32311_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w4p_32311/02_2024/7w4p_32311_updated.pdb" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.173 sd= 0.331 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 28 5.49 5 Mg 8 5.21 5 S 312 5.16 5 Cl 4 4.86 5 C 35240 2.51 5 N 9220 2.21 5 O 9596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 1354": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 54408 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2512 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 10986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1401, 10986 Classifications: {'peptide': 1401} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 45, 'TRANS': 1355} Chain breaks: 8 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2512 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 10986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1401, 10986 Classifications: {'peptide': 1401} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 45, 'TRANS': 1355} Chain breaks: 8 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "E" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2512 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 10986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1401, 10986 Classifications: {'peptide': 1401} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 45, 'TRANS': 1355} Chain breaks: 8 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "G" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2512 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 10986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1401, 10986 Classifications: {'peptide': 1401} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 45, 'TRANS': 1355} Chain breaks: 8 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 77 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'E2H': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 77 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'E2H': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 77 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'E2H': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 77 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'E2H': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 21.20, per 1000 atoms: 0.39 Number of scatterers: 54408 At special positions: 0 Unit cell: (202.572, 202.572, 146.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 312 16.00 P 28 15.00 Mg 8 11.99 O 9596 8.00 N 9220 7.00 C 35240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 26 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 142 " distance=2.03 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.05 Conformation dependent library (CDL) restraints added in 8.0 seconds 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 248 helices and 44 sheets defined 57.6% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.74 Creating SS restraints... Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 68 through 97 removed outlier: 3.647A pdb=" N PHE A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 266 through 269 removed outlier: 4.536A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 28 through 49 removed outlier: 3.796A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) Proline residue: B 35 - end of helix Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 71 through 97 removed outlier: 3.636A pdb=" N GLY B 97 " --> pdb=" O ILE B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 108 through 130 Processing helix chain 'B' and resid 133 through 159 removed outlier: 3.797A pdb=" N ILE B 137 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE B 152 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 192 Processing helix chain 'B' and resid 208 through 211 No H-bonds generated for 'chain 'B' and resid 208 through 211' Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.985A pdb=" N ALA B 235 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA B 240 " --> pdb=" O ILE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 328 removed outlier: 5.934A pdb=" N ARG B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 356 through 400 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.932A pdb=" N VAL B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 455 Proline residue: B 436 - end of helix Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 458 through 504 removed outlier: 3.919A pdb=" N LEU B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix removed outlier: 3.591A pdb=" N GLU B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 515 through 561 Proline residue: B 551 - end of helix Processing helix chain 'B' and resid 573 through 614 Proline residue: B 589 - end of helix removed outlier: 4.532A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 593 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 784 through 789 Processing helix chain 'B' and resid 796 through 806 removed outlier: 3.514A pdb=" N MET B 801 " --> pdb=" O GLN B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 812 No H-bonds generated for 'chain 'B' and resid 809 through 812' Processing helix chain 'B' and resid 832 through 845 Processing helix chain 'B' and resid 862 through 870 Processing helix chain 'B' and resid 891 through 896 Proline residue: B 895 - end of helix Processing helix chain 'B' and resid 914 through 917 No H-bonds generated for 'chain 'B' and resid 914 through 917' Processing helix chain 'B' and resid 922 through 931 Processing helix chain 'B' and resid 1003 through 1008 Processing helix chain 'B' and resid 1010 through 1038 Processing helix chain 'B' and resid 1061 through 1106 removed outlier: 3.789A pdb=" N GLU B1087 " --> pdb=" O SER B1083 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS B1098 " --> pdb=" O ALA B1094 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1115 Processing helix chain 'B' and resid 1118 through 1126 removed outlier: 4.012A pdb=" N ARG B1124 " --> pdb=" O SER B1120 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1160 removed outlier: 4.551A pdb=" N ILE B1136 " --> pdb=" O ILE B1132 " (cutoff:3.500A) Proline residue: B1137 - end of helix removed outlier: 3.576A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B1151 " --> pdb=" O THR B1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 1162 through 1209 removed outlier: 3.829A pdb=" N LEU B1169 " --> pdb=" O VAL B1166 " (cutoff:3.500A) Proline residue: B1170 - end of helix removed outlier: 4.106A pdb=" N CYS B1175 " --> pdb=" O ALA B1172 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE B1182 " --> pdb=" O GLN B1179 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG B1183 " --> pdb=" O LYS B1180 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B1184 " --> pdb=" O TYR B1181 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B1186 " --> pdb=" O ARG B1183 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B1187 " --> pdb=" O VAL B1184 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B1190 " --> pdb=" O ARG B1187 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B1192 " --> pdb=" O LEU B1189 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR B1195 " --> pdb=" O LEU B1192 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B1196 " --> pdb=" O ASP B1193 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU B1198 " --> pdb=" O THR B1195 " (cutoff:3.500A) Proline residue: B1199 - end of helix removed outlier: 4.291A pdb=" N SER B1202 " --> pdb=" O PRO B1199 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B1206 " --> pdb=" O HIS B1203 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B1208 " --> pdb=" O ALA B1205 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU B1209 " --> pdb=" O GLU B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1216 Processing helix chain 'B' and resid 1220 through 1273 Processing helix chain 'B' and resid 1280 through 1319 removed outlier: 3.658A pdb=" N MET B1290 " --> pdb=" O THR B1286 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASN B1296 " --> pdb=" O SER B1292 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP B1297 " --> pdb=" O ASN B1293 " (cutoff:3.500A) Processing helix chain 'B' and resid 1385 through 1393 removed outlier: 3.657A pdb=" N SER B1389 " --> pdb=" O LYS B1385 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B1392 " --> pdb=" O PHE B1388 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE B1393 " --> pdb=" O SER B1389 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1412 No H-bonds generated for 'chain 'B' and resid 1410 through 1412' Processing helix chain 'B' and resid 1415 through 1420 Processing helix chain 'B' and resid 1436 through 1440 Processing helix chain 'B' and resid 1448 through 1457 Processing helix chain 'B' and resid 1461 through 1466 Processing helix chain 'B' and resid 1470 through 1472 No H-bonds generated for 'chain 'B' and resid 1470 through 1472' Processing helix chain 'B' and resid 1484 through 1498 removed outlier: 4.280A pdb=" N ARG B1498 " --> pdb=" O ARG B1494 " (cutoff:3.500A) Processing helix chain 'B' and resid 1508 through 1511 removed outlier: 4.465A pdb=" N SER B1511 " --> pdb=" O ALA B1508 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1508 through 1511' Processing helix chain 'B' and resid 1514 through 1527 removed outlier: 3.684A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1543 Processing helix chain 'B' and resid 1563 through 1568 Processing helix chain 'B' and resid 1573 through 1579 Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 68 through 97 removed outlier: 3.647A pdb=" N PHE C 79 " --> pdb=" O PHE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 171 Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 266 through 269 removed outlier: 4.536A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 269' Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'D' and resid 13 through 15 No H-bonds generated for 'chain 'D' and resid 13 through 15' Processing helix chain 'D' and resid 28 through 49 removed outlier: 3.796A pdb=" N VAL D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Proline residue: D 35 - end of helix Proline residue: D 45 - end of helix Processing helix chain 'D' and resid 71 through 97 removed outlier: 3.636A pdb=" N GLY D 97 " --> pdb=" O ILE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 108 through 130 Processing helix chain 'D' and resid 133 through 159 removed outlier: 3.797A pdb=" N ILE D 137 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE D 152 " --> pdb=" O THR D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 192 Processing helix chain 'D' and resid 208 through 211 No H-bonds generated for 'chain 'D' and resid 208 through 211' Processing helix chain 'D' and resid 218 through 221 Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 231 through 242 removed outlier: 3.985A pdb=" N ALA D 235 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA D 240 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 284 through 328 removed outlier: 5.934A pdb=" N ARG D 297 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'D' and resid 356 through 400 Processing helix chain 'D' and resid 404 through 408 Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.932A pdb=" N VAL D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 455 Proline residue: D 436 - end of helix Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 458 through 504 removed outlier: 3.919A pdb=" N LEU D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Proline residue: D 472 - end of helix removed outlier: 3.591A pdb=" N GLU D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 511 Processing helix chain 'D' and resid 515 through 561 Proline residue: D 551 - end of helix Processing helix chain 'D' and resid 573 through 614 Proline residue: D 589 - end of helix removed outlier: 4.532A pdb=" N LEU D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 726 Processing helix chain 'D' and resid 784 through 789 Processing helix chain 'D' and resid 796 through 806 removed outlier: 3.514A pdb=" N MET D 801 " --> pdb=" O GLN D 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 812 No H-bonds generated for 'chain 'D' and resid 809 through 812' Processing helix chain 'D' and resid 832 through 845 Processing helix chain 'D' and resid 862 through 870 Processing helix chain 'D' and resid 891 through 896 Proline residue: D 895 - end of helix Processing helix chain 'D' and resid 914 through 917 No H-bonds generated for 'chain 'D' and resid 914 through 917' Processing helix chain 'D' and resid 922 through 931 Processing helix chain 'D' and resid 1003 through 1008 Processing helix chain 'D' and resid 1010 through 1038 Processing helix chain 'D' and resid 1061 through 1106 removed outlier: 3.789A pdb=" N GLU D1087 " --> pdb=" O SER D1083 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS D1098 " --> pdb=" O ALA D1094 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D1106 " --> pdb=" O LEU D1102 " (cutoff:3.500A) Processing helix chain 'D' and resid 1110 through 1115 Processing helix chain 'D' and resid 1118 through 1126 removed outlier: 4.012A pdb=" N ARG D1124 " --> pdb=" O SER D1120 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1128 through 1160 removed outlier: 4.551A pdb=" N ILE D1136 " --> pdb=" O ILE D1132 " (cutoff:3.500A) Proline residue: D1137 - end of helix removed outlier: 3.576A pdb=" N GLU D1141 " --> pdb=" O PRO D1137 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D1151 " --> pdb=" O THR D1147 " (cutoff:3.500A) Processing helix chain 'D' and resid 1162 through 1209 removed outlier: 3.829A pdb=" N LEU D1169 " --> pdb=" O VAL D1166 " (cutoff:3.500A) Proline residue: D1170 - end of helix removed outlier: 4.106A pdb=" N CYS D1175 " --> pdb=" O ALA D1172 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE D1182 " --> pdb=" O GLN D1179 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG D1183 " --> pdb=" O LYS D1180 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL D1184 " --> pdb=" O TYR D1181 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER D1186 " --> pdb=" O ARG D1183 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG D1187 " --> pdb=" O VAL D1184 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D1190 " --> pdb=" O ARG D1187 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU D1192 " --> pdb=" O LEU D1189 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR D1195 " --> pdb=" O LEU D1192 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR D1196 " --> pdb=" O ASP D1193 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU D1198 " --> pdb=" O THR D1195 " (cutoff:3.500A) Proline residue: D1199 - end of helix removed outlier: 4.291A pdb=" N SER D1202 " --> pdb=" O PRO D1199 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU D1206 " --> pdb=" O HIS D1203 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL D1208 " --> pdb=" O ALA D1205 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU D1209 " --> pdb=" O GLU D1206 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1216 Processing helix chain 'D' and resid 1220 through 1273 Processing helix chain 'D' and resid 1280 through 1319 removed outlier: 3.658A pdb=" N MET D1290 " --> pdb=" O THR D1286 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASN D1296 " --> pdb=" O SER D1292 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP D1297 " --> pdb=" O ASN D1293 " (cutoff:3.500A) Processing helix chain 'D' and resid 1385 through 1393 removed outlier: 3.657A pdb=" N SER D1389 " --> pdb=" O LYS D1385 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D1392 " --> pdb=" O PHE D1388 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE D1393 " --> pdb=" O SER D1389 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1412 No H-bonds generated for 'chain 'D' and resid 1410 through 1412' Processing helix chain 'D' and resid 1415 through 1420 Processing helix chain 'D' and resid 1436 through 1440 Processing helix chain 'D' and resid 1448 through 1457 Processing helix chain 'D' and resid 1461 through 1466 Processing helix chain 'D' and resid 1470 through 1472 No H-bonds generated for 'chain 'D' and resid 1470 through 1472' Processing helix chain 'D' and resid 1484 through 1498 removed outlier: 4.280A pdb=" N ARG D1498 " --> pdb=" O ARG D1494 " (cutoff:3.500A) Processing helix chain 'D' and resid 1508 through 1511 removed outlier: 4.465A pdb=" N SER D1511 " --> pdb=" O ALA D1508 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1508 through 1511' Processing helix chain 'D' and resid 1514 through 1527 removed outlier: 3.684A pdb=" N ILE D1519 " --> pdb=" O ALA D1515 " (cutoff:3.500A) Processing helix chain 'D' and resid 1540 through 1543 Processing helix chain 'D' and resid 1563 through 1568 Processing helix chain 'D' and resid 1573 through 1579 Processing helix chain 'E' and resid 59 through 65 Processing helix chain 'E' and resid 68 through 97 removed outlier: 3.647A pdb=" N PHE E 79 " --> pdb=" O PHE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 143 through 171 Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 266 through 269 removed outlier: 4.536A pdb=" N ASP E 269 " --> pdb=" O PRO E 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 266 through 269' Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 346 through 355 Processing helix chain 'F' and resid 13 through 15 No H-bonds generated for 'chain 'F' and resid 13 through 15' Processing helix chain 'F' and resid 28 through 49 removed outlier: 3.796A pdb=" N VAL F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Proline residue: F 35 - end of helix Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 71 through 97 removed outlier: 3.636A pdb=" N GLY F 97 " --> pdb=" O ILE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 108 through 130 Processing helix chain 'F' and resid 133 through 159 removed outlier: 3.797A pdb=" N ILE F 137 " --> pdb=" O LYS F 134 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE F 152 " --> pdb=" O THR F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 192 Processing helix chain 'F' and resid 208 through 211 No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 218 through 221 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 231 through 242 removed outlier: 3.985A pdb=" N ALA F 235 " --> pdb=" O TRP F 232 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA F 240 " --> pdb=" O ILE F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 274 Processing helix chain 'F' and resid 284 through 328 removed outlier: 5.934A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE F 314 " --> pdb=" O ASP F 310 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 348 through 352 Processing helix chain 'F' and resid 356 through 400 Processing helix chain 'F' and resid 404 through 408 Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.932A pdb=" N VAL F 421 " --> pdb=" O ILE F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 455 Proline residue: F 436 - end of helix Proline residue: F 442 - end of helix Processing helix chain 'F' and resid 458 through 504 removed outlier: 3.919A pdb=" N LEU F 470 " --> pdb=" O VAL F 466 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA F 471 " --> pdb=" O ILE F 467 " (cutoff:3.500A) Proline residue: F 472 - end of helix removed outlier: 3.591A pdb=" N GLU F 494 " --> pdb=" O GLU F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 511 Processing helix chain 'F' and resid 515 through 561 Proline residue: F 551 - end of helix Processing helix chain 'F' and resid 573 through 614 Proline residue: F 589 - end of helix removed outlier: 4.532A pdb=" N LEU F 592 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU F 593 " --> pdb=" O PRO F 589 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 726 Processing helix chain 'F' and resid 784 through 789 Processing helix chain 'F' and resid 796 through 806 removed outlier: 3.514A pdb=" N MET F 801 " --> pdb=" O GLN F 797 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 812 No H-bonds generated for 'chain 'F' and resid 809 through 812' Processing helix chain 'F' and resid 832 through 845 Processing helix chain 'F' and resid 862 through 870 Processing helix chain 'F' and resid 891 through 896 Proline residue: F 895 - end of helix Processing helix chain 'F' and resid 914 through 917 No H-bonds generated for 'chain 'F' and resid 914 through 917' Processing helix chain 'F' and resid 922 through 931 Processing helix chain 'F' and resid 1003 through 1008 Processing helix chain 'F' and resid 1010 through 1038 Processing helix chain 'F' and resid 1061 through 1106 removed outlier: 3.789A pdb=" N GLU F1087 " --> pdb=" O SER F1083 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS F1098 " --> pdb=" O ALA F1094 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE F1106 " --> pdb=" O LEU F1102 " (cutoff:3.500A) Processing helix chain 'F' and resid 1110 through 1115 Processing helix chain 'F' and resid 1118 through 1126 removed outlier: 4.012A pdb=" N ARG F1124 " --> pdb=" O SER F1120 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE F1125 " --> pdb=" O ILE F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1128 through 1160 removed outlier: 4.551A pdb=" N ILE F1136 " --> pdb=" O ILE F1132 " (cutoff:3.500A) Proline residue: F1137 - end of helix removed outlier: 3.576A pdb=" N GLU F1141 " --> pdb=" O PRO F1137 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL F1151 " --> pdb=" O THR F1147 " (cutoff:3.500A) Processing helix chain 'F' and resid 1162 through 1209 removed outlier: 3.829A pdb=" N LEU F1169 " --> pdb=" O VAL F1166 " (cutoff:3.500A) Proline residue: F1170 - end of helix removed outlier: 4.106A pdb=" N CYS F1175 " --> pdb=" O ALA F1172 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE F1182 " --> pdb=" O GLN F1179 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG F1183 " --> pdb=" O LYS F1180 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL F1184 " --> pdb=" O TYR F1181 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER F1186 " --> pdb=" O ARG F1183 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG F1187 " --> pdb=" O VAL F1184 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN F1190 " --> pdb=" O ARG F1187 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU F1192 " --> pdb=" O LEU F1189 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR F1195 " --> pdb=" O LEU F1192 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR F1196 " --> pdb=" O ASP F1193 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU F1198 " --> pdb=" O THR F1195 " (cutoff:3.500A) Proline residue: F1199 - end of helix removed outlier: 4.291A pdb=" N SER F1202 " --> pdb=" O PRO F1199 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU F1206 " --> pdb=" O HIS F1203 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL F1208 " --> pdb=" O ALA F1205 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU F1209 " --> pdb=" O GLU F1206 " (cutoff:3.500A) Processing helix chain 'F' and resid 1211 through 1216 Processing helix chain 'F' and resid 1220 through 1273 Processing helix chain 'F' and resid 1280 through 1319 removed outlier: 3.658A pdb=" N MET F1290 " --> pdb=" O THR F1286 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASN F1296 " --> pdb=" O SER F1292 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP F1297 " --> pdb=" O ASN F1293 " (cutoff:3.500A) Processing helix chain 'F' and resid 1385 through 1393 removed outlier: 3.657A pdb=" N SER F1389 " --> pdb=" O LYS F1385 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE F1392 " --> pdb=" O PHE F1388 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE F1393 " --> pdb=" O SER F1389 " (cutoff:3.500A) Processing helix chain 'F' and resid 1410 through 1412 No H-bonds generated for 'chain 'F' and resid 1410 through 1412' Processing helix chain 'F' and resid 1415 through 1420 Processing helix chain 'F' and resid 1436 through 1440 Processing helix chain 'F' and resid 1448 through 1457 Processing helix chain 'F' and resid 1461 through 1466 Processing helix chain 'F' and resid 1470 through 1472 No H-bonds generated for 'chain 'F' and resid 1470 through 1472' Processing helix chain 'F' and resid 1484 through 1498 removed outlier: 4.280A pdb=" N ARG F1498 " --> pdb=" O ARG F1494 " (cutoff:3.500A) Processing helix chain 'F' and resid 1508 through 1511 removed outlier: 4.465A pdb=" N SER F1511 " --> pdb=" O ALA F1508 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1508 through 1511' Processing helix chain 'F' and resid 1514 through 1527 removed outlier: 3.684A pdb=" N ILE F1519 " --> pdb=" O ALA F1515 " (cutoff:3.500A) Processing helix chain 'F' and resid 1540 through 1543 Processing helix chain 'F' and resid 1563 through 1568 Processing helix chain 'F' and resid 1573 through 1579 Processing helix chain 'G' and resid 59 through 65 Processing helix chain 'G' and resid 68 through 97 removed outlier: 3.647A pdb=" N PHE G 79 " --> pdb=" O PHE G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 128 Processing helix chain 'G' and resid 143 through 171 Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 266 through 269 removed outlier: 4.536A pdb=" N ASP G 269 " --> pdb=" O PRO G 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 266 through 269' Processing helix chain 'G' and resid 330 through 332 No H-bonds generated for 'chain 'G' and resid 330 through 332' Processing helix chain 'G' and resid 346 through 355 Processing helix chain 'H' and resid 13 through 15 No H-bonds generated for 'chain 'H' and resid 13 through 15' Processing helix chain 'H' and resid 28 through 49 removed outlier: 3.796A pdb=" N VAL H 33 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) Proline residue: H 35 - end of helix Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 71 through 97 removed outlier: 3.636A pdb=" N GLY H 97 " --> pdb=" O ILE H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 106 No H-bonds generated for 'chain 'H' and resid 104 through 106' Processing helix chain 'H' and resid 108 through 130 Processing helix chain 'H' and resid 133 through 159 removed outlier: 3.797A pdb=" N ILE H 137 " --> pdb=" O LYS H 134 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE H 152 " --> pdb=" O THR H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 192 Processing helix chain 'H' and resid 208 through 211 No H-bonds generated for 'chain 'H' and resid 208 through 211' Processing helix chain 'H' and resid 218 through 221 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 231 through 242 removed outlier: 3.985A pdb=" N ALA H 235 " --> pdb=" O TRP H 232 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA H 240 " --> pdb=" O ILE H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 274 Processing helix chain 'H' and resid 284 through 328 removed outlier: 5.934A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE H 314 " --> pdb=" O ASP H 310 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA H 315 " --> pdb=" O LEU H 311 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY H 316 " --> pdb=" O LEU H 312 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 348 through 352 Processing helix chain 'H' and resid 356 through 400 Processing helix chain 'H' and resid 404 through 408 Processing helix chain 'H' and resid 414 through 422 removed outlier: 3.932A pdb=" N VAL H 421 " --> pdb=" O ILE H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 424 through 455 Proline residue: H 436 - end of helix Proline residue: H 442 - end of helix Processing helix chain 'H' and resid 458 through 504 removed outlier: 3.919A pdb=" N LEU H 470 " --> pdb=" O VAL H 466 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Proline residue: H 472 - end of helix removed outlier: 3.591A pdb=" N GLU H 494 " --> pdb=" O GLU H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 506 through 511 Processing helix chain 'H' and resid 515 through 561 Proline residue: H 551 - end of helix Processing helix chain 'H' and resid 573 through 614 Proline residue: H 589 - end of helix removed outlier: 4.532A pdb=" N LEU H 592 " --> pdb=" O THR H 588 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU H 593 " --> pdb=" O PRO H 589 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 719 through 726 Processing helix chain 'H' and resid 784 through 789 Processing helix chain 'H' and resid 796 through 806 removed outlier: 3.514A pdb=" N MET H 801 " --> pdb=" O GLN H 797 " (cutoff:3.500A) Processing helix chain 'H' and resid 809 through 812 No H-bonds generated for 'chain 'H' and resid 809 through 812' Processing helix chain 'H' and resid 832 through 845 Processing helix chain 'H' and resid 862 through 870 Processing helix chain 'H' and resid 891 through 896 Proline residue: H 895 - end of helix Processing helix chain 'H' and resid 914 through 917 No H-bonds generated for 'chain 'H' and resid 914 through 917' Processing helix chain 'H' and resid 922 through 931 Processing helix chain 'H' and resid 1003 through 1008 Processing helix chain 'H' and resid 1010 through 1038 Processing helix chain 'H' and resid 1061 through 1106 removed outlier: 3.789A pdb=" N GLU H1087 " --> pdb=" O SER H1083 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS H1098 " --> pdb=" O ALA H1094 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE H1106 " --> pdb=" O LEU H1102 " (cutoff:3.500A) Processing helix chain 'H' and resid 1110 through 1115 Processing helix chain 'H' and resid 1118 through 1126 removed outlier: 4.012A pdb=" N ARG H1124 " --> pdb=" O SER H1120 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE H1125 " --> pdb=" O ILE H1121 " (cutoff:3.500A) Processing helix chain 'H' and resid 1128 through 1160 removed outlier: 4.551A pdb=" N ILE H1136 " --> pdb=" O ILE H1132 " (cutoff:3.500A) Proline residue: H1137 - end of helix removed outlier: 3.576A pdb=" N GLU H1141 " --> pdb=" O PRO H1137 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL H1151 " --> pdb=" O THR H1147 " (cutoff:3.500A) Processing helix chain 'H' and resid 1162 through 1209 removed outlier: 3.829A pdb=" N LEU H1169 " --> pdb=" O VAL H1166 " (cutoff:3.500A) Proline residue: H1170 - end of helix removed outlier: 4.106A pdb=" N CYS H1175 " --> pdb=" O ALA H1172 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE H1182 " --> pdb=" O GLN H1179 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG H1183 " --> pdb=" O LYS H1180 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL H1184 " --> pdb=" O TYR H1181 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER H1186 " --> pdb=" O ARG H1183 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG H1187 " --> pdb=" O VAL H1184 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN H1190 " --> pdb=" O ARG H1187 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU H1192 " --> pdb=" O LEU H1189 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR H1195 " --> pdb=" O LEU H1192 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR H1196 " --> pdb=" O ASP H1193 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU H1198 " --> pdb=" O THR H1195 " (cutoff:3.500A) Proline residue: H1199 - end of helix removed outlier: 4.291A pdb=" N SER H1202 " --> pdb=" O PRO H1199 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU H1206 " --> pdb=" O HIS H1203 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL H1208 " --> pdb=" O ALA H1205 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU H1209 " --> pdb=" O GLU H1206 " (cutoff:3.500A) Processing helix chain 'H' and resid 1211 through 1216 Processing helix chain 'H' and resid 1220 through 1273 Processing helix chain 'H' and resid 1280 through 1319 removed outlier: 3.658A pdb=" N MET H1290 " --> pdb=" O THR H1286 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASN H1296 " --> pdb=" O SER H1292 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP H1297 " --> pdb=" O ASN H1293 " (cutoff:3.500A) Processing helix chain 'H' and resid 1385 through 1393 removed outlier: 3.657A pdb=" N SER H1389 " --> pdb=" O LYS H1385 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE H1392 " --> pdb=" O PHE H1388 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE H1393 " --> pdb=" O SER H1389 " (cutoff:3.500A) Processing helix chain 'H' and resid 1410 through 1412 No H-bonds generated for 'chain 'H' and resid 1410 through 1412' Processing helix chain 'H' and resid 1415 through 1420 Processing helix chain 'H' and resid 1436 through 1440 Processing helix chain 'H' and resid 1448 through 1457 Processing helix chain 'H' and resid 1461 through 1466 Processing helix chain 'H' and resid 1470 through 1472 No H-bonds generated for 'chain 'H' and resid 1470 through 1472' Processing helix chain 'H' and resid 1484 through 1498 removed outlier: 4.280A pdb=" N ARG H1498 " --> pdb=" O ARG H1494 " (cutoff:3.500A) Processing helix chain 'H' and resid 1508 through 1511 removed outlier: 4.465A pdb=" N SER H1511 " --> pdb=" O ALA H1508 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1508 through 1511' Processing helix chain 'H' and resid 1514 through 1527 removed outlier: 3.684A pdb=" N ILE H1519 " --> pdb=" O ALA H1515 " (cutoff:3.500A) Processing helix chain 'H' and resid 1540 through 1543 Processing helix chain 'H' and resid 1563 through 1568 Processing helix chain 'H' and resid 1573 through 1579 Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.168A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 234 through 238 removed outlier: 3.612A pdb=" N ARG A 221 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 319 through 321 Processing sheet with id= F, first strand: chain 'B' and resid 736 through 739 removed outlier: 6.915A pdb=" N ILE B 703 " --> pdb=" O CYS B 678 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN B 680 " --> pdb=" O ILE B 701 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 701 " --> pdb=" O GLN B 680 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 908 through 912 removed outlier: 6.928A pdb=" N ALA B 902 " --> pdb=" O GLN B 909 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU B 911 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 900 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL B 884 " --> pdb=" O THR B 709 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE B 711 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 886 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLY B 713 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA B 771 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP B 854 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA B 773 " --> pdb=" O ASP B 854 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 1367 through 1369 Processing sheet with id= I, first strand: chain 'B' and resid 1556 through 1561 removed outlier: 6.760A pdb=" N VAL B1551 " --> pdb=" O LEU B1558 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE B1560 " --> pdb=" O VAL B1549 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B1549 " --> pdb=" O PHE B1560 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B1533 " --> pdb=" O ILE B1375 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE B1377 " --> pdb=" O VAL B1533 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B1535 " --> pdb=" O ILE B1377 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N GLY B1379 " --> pdb=" O THR B1535 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 685 through 687 removed outlier: 6.245A pdb=" N THR B 687 " --> pdb=" O LYS B 732 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LYS B 732 " --> pdb=" O THR B 687 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 1351 through 1353 removed outlier: 3.633A pdb=" N GLU B1400 " --> pdb=" O SER B1351 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ARG B1353 " --> pdb=" O MET B1398 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N MET B1398 " --> pdb=" O ARG B1353 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= M, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.168A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 234 through 238 removed outlier: 3.612A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= P, first strand: chain 'C' and resid 319 through 321 Processing sheet with id= Q, first strand: chain 'D' and resid 736 through 739 removed outlier: 6.915A pdb=" N ILE D 703 " --> pdb=" O CYS D 678 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN D 680 " --> pdb=" O ILE D 701 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE D 701 " --> pdb=" O GLN D 680 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 908 through 912 removed outlier: 6.928A pdb=" N ALA D 902 " --> pdb=" O GLN D 909 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU D 911 " --> pdb=" O ILE D 900 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE D 900 " --> pdb=" O GLU D 911 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL D 884 " --> pdb=" O THR D 709 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE D 711 " --> pdb=" O VAL D 884 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU D 886 " --> pdb=" O ILE D 711 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLY D 713 " --> pdb=" O LEU D 886 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA D 771 " --> pdb=" O PHE D 852 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP D 854 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA D 773 " --> pdb=" O ASP D 854 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 1367 through 1369 Processing sheet with id= T, first strand: chain 'D' and resid 1556 through 1561 removed outlier: 6.760A pdb=" N VAL D1551 " --> pdb=" O LEU D1558 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE D1560 " --> pdb=" O VAL D1549 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL D1549 " --> pdb=" O PHE D1560 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D1533 " --> pdb=" O ILE D1375 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE D1377 " --> pdb=" O VAL D1533 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR D1535 " --> pdb=" O ILE D1377 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N GLY D1379 " --> pdb=" O THR D1535 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 685 through 687 removed outlier: 6.245A pdb=" N THR D 687 " --> pdb=" O LYS D 732 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LYS D 732 " --> pdb=" O THR D 687 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 1351 through 1353 removed outlier: 3.633A pdb=" N GLU D1400 " --> pdb=" O SER D1351 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ARG D1353 " --> pdb=" O MET D1398 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N MET D1398 " --> pdb=" O ARG D1353 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= X, first strand: chain 'E' and resid 309 through 311 removed outlier: 6.168A pdb=" N ALA E 187 " --> pdb=" O LEU E 310 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 234 through 238 removed outlier: 3.612A pdb=" N ARG E 221 " --> pdb=" O HIS E 234 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET E 217 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 313 through 315 Processing sheet with id= AA, first strand: chain 'E' and resid 319 through 321 Processing sheet with id= AB, first strand: chain 'F' and resid 736 through 739 removed outlier: 6.915A pdb=" N ILE F 703 " --> pdb=" O CYS F 678 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN F 680 " --> pdb=" O ILE F 701 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE F 701 " --> pdb=" O GLN F 680 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 908 through 912 removed outlier: 6.928A pdb=" N ALA F 902 " --> pdb=" O GLN F 909 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU F 911 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE F 900 " --> pdb=" O GLU F 911 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL F 884 " --> pdb=" O THR F 709 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE F 711 " --> pdb=" O VAL F 884 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU F 886 " --> pdb=" O ILE F 711 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLY F 713 " --> pdb=" O LEU F 886 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA F 771 " --> pdb=" O PHE F 852 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP F 854 " --> pdb=" O ALA F 771 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA F 773 " --> pdb=" O ASP F 854 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 1367 through 1369 Processing sheet with id= AE, first strand: chain 'F' and resid 1556 through 1561 removed outlier: 6.760A pdb=" N VAL F1551 " --> pdb=" O LEU F1558 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE F1560 " --> pdb=" O VAL F1549 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL F1549 " --> pdb=" O PHE F1560 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL F1533 " --> pdb=" O ILE F1375 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE F1377 " --> pdb=" O VAL F1533 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR F1535 " --> pdb=" O ILE F1377 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N GLY F1379 " --> pdb=" O THR F1535 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 685 through 687 removed outlier: 6.245A pdb=" N THR F 687 " --> pdb=" O LYS F 732 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LYS F 732 " --> pdb=" O THR F 687 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 1351 through 1353 removed outlier: 3.633A pdb=" N GLU F1400 " --> pdb=" O SER F1351 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ARG F1353 " --> pdb=" O MET F1398 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N MET F1398 " --> pdb=" O ARG F1353 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 181 through 183 Processing sheet with id= AI, first strand: chain 'G' and resid 309 through 311 removed outlier: 6.168A pdb=" N ALA G 187 " --> pdb=" O LEU G 310 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 234 through 238 removed outlier: 3.612A pdb=" N ARG G 221 " --> pdb=" O HIS G 234 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET G 217 " --> pdb=" O ILE G 238 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 313 through 315 Processing sheet with id= AL, first strand: chain 'G' and resid 319 through 321 Processing sheet with id= AM, first strand: chain 'H' and resid 736 through 739 removed outlier: 6.915A pdb=" N ILE H 703 " --> pdb=" O CYS H 678 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN H 680 " --> pdb=" O ILE H 701 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE H 701 " --> pdb=" O GLN H 680 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 908 through 912 removed outlier: 6.928A pdb=" N ALA H 902 " --> pdb=" O GLN H 909 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU H 911 " --> pdb=" O ILE H 900 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE H 900 " --> pdb=" O GLU H 911 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL H 884 " --> pdb=" O THR H 709 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE H 711 " --> pdb=" O VAL H 884 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU H 886 " --> pdb=" O ILE H 711 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N GLY H 713 " --> pdb=" O LEU H 886 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA H 771 " --> pdb=" O PHE H 852 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP H 854 " --> pdb=" O ALA H 771 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA H 773 " --> pdb=" O ASP H 854 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'H' and resid 1367 through 1369 Processing sheet with id= AP, first strand: chain 'H' and resid 1556 through 1561 removed outlier: 6.760A pdb=" N VAL H1551 " --> pdb=" O LEU H1558 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE H1560 " --> pdb=" O VAL H1549 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL H1549 " --> pdb=" O PHE H1560 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL H1533 " --> pdb=" O ILE H1375 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE H1377 " --> pdb=" O VAL H1533 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR H1535 " --> pdb=" O ILE H1377 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N GLY H1379 " --> pdb=" O THR H1535 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 685 through 687 removed outlier: 6.245A pdb=" N THR H 687 " --> pdb=" O LYS H 732 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LYS H 732 " --> pdb=" O THR H 687 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 1351 through 1353 removed outlier: 3.633A pdb=" N GLU H1400 " --> pdb=" O SER H1351 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ARG H1353 " --> pdb=" O MET H1398 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N MET H1398 " --> pdb=" O ARG H1353 " (cutoff:3.500A) 2972 hydrogen bonds defined for protein. 8100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.15 Time building geometry restraints manager: 18.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16816 1.34 - 1.46: 12252 1.46 - 1.58: 25960 1.58 - 1.70: 52 1.70 - 1.82: 484 Bond restraints: 55564 Sorted by residual: bond pdb=" C13 E2H H1604 " pdb=" N07 E2H H1604 " ideal model delta sigma weight residual 1.363 1.568 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C13 E2H B1604 " pdb=" N07 E2H B1604 " ideal model delta sigma weight residual 1.363 1.568 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C13 E2H F1604 " pdb=" N07 E2H F1604 " ideal model delta sigma weight residual 1.363 1.568 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C13 E2H D1604 " pdb=" N07 E2H D1604 " ideal model delta sigma weight residual 1.363 1.568 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C14 E2H B1604 " pdb=" N07 E2H B1604 " ideal model delta sigma weight residual 1.371 1.552 -0.181 2.00e-02 2.50e+03 8.21e+01 ... (remaining 55559 not shown) Histogram of bond angle deviations from ideal: 59.47 - 75.58: 12 75.58 - 91.68: 0 91.68 - 107.79: 2200 107.79 - 123.90: 71672 123.90 - 140.01: 1632 Bond angle restraints: 75516 Sorted by residual: angle pdb=" C15 E2H B1604 " pdb=" S03 E2H B1604 " pdb=" C17 E2H B1604 " ideal model delta sigma weight residual 90.00 107.43 -17.43 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C15 E2H H1604 " pdb=" S03 E2H H1604 " pdb=" C17 E2H H1604 " ideal model delta sigma weight residual 90.00 107.43 -17.43 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C15 E2H F1604 " pdb=" S03 E2H F1604 " pdb=" C17 E2H F1604 " ideal model delta sigma weight residual 90.00 107.43 -17.43 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C15 E2H D1604 " pdb=" S03 E2H D1604 " pdb=" C17 E2H D1604 " ideal model delta sigma weight residual 90.00 107.43 -17.43 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C15 E2H B1604 " pdb=" S02 E2H B1604 " pdb=" N08 E2H B1604 " ideal model delta sigma weight residual 102.15 117.07 -14.92 3.00e+00 1.11e-01 2.47e+01 ... (remaining 75511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.63: 31808 23.63 - 47.26: 1108 47.26 - 70.88: 116 70.88 - 94.51: 16 94.51 - 118.14: 16 Dihedral angle restraints: 33064 sinusoidal: 13000 harmonic: 20064 Sorted by residual: dihedral pdb=" O1B ADP B1601 " pdb=" O3A ADP B1601 " pdb=" PB ADP B1601 " pdb=" PA ADP B1601 " ideal model delta sinusoidal sigma weight residual -60.00 -178.14 118.14 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" O1B ADP D1601 " pdb=" O3A ADP D1601 " pdb=" PB ADP D1601 " pdb=" PA ADP D1601 " ideal model delta sinusoidal sigma weight residual -60.00 -178.14 118.14 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" O1B ADP H1601 " pdb=" O3A ADP H1601 " pdb=" PB ADP H1601 " pdb=" PA ADP H1601 " ideal model delta sinusoidal sigma weight residual -60.00 -178.14 118.14 1 2.00e+01 2.50e-03 3.53e+01 ... (remaining 33061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 7548 0.061 - 0.121: 1248 0.121 - 0.182: 172 0.182 - 0.242: 12 0.242 - 0.303: 4 Chirality restraints: 8984 Sorted by residual: chirality pdb=" CG LEU F1227 " pdb=" CB LEU F1227 " pdb=" CD1 LEU F1227 " pdb=" CD2 LEU F1227 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU D1227 " pdb=" CB LEU D1227 " pdb=" CD1 LEU D1227 " pdb=" CD2 LEU D1227 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU H1227 " pdb=" CB LEU H1227 " pdb=" CD1 LEU H1227 " pdb=" CD2 LEU H1227 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 8981 not shown) Planarity restraints: 9276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 377 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C TYR F 377 " 0.058 2.00e-02 2.50e+03 pdb=" O TYR F 377 " -0.022 2.00e-02 2.50e+03 pdb=" N TYR F 378 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 377 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C TYR D 377 " -0.058 2.00e-02 2.50e+03 pdb=" O TYR D 377 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR D 378 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 377 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C TYR B 377 " -0.058 2.00e-02 2.50e+03 pdb=" O TYR B 377 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR B 378 " 0.020 2.00e-02 2.50e+03 ... (remaining 9273 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1472 2.71 - 3.26: 53196 3.26 - 3.81: 91488 3.81 - 4.35: 116696 4.35 - 4.90: 196178 Nonbonded interactions: 459030 Sorted by model distance: nonbonded pdb=" OE1 GLN B 775 " pdb="MG MG B1602 " model vdw 2.166 2.170 nonbonded pdb=" OE1 GLN D 775 " pdb="MG MG D1602 " model vdw 2.166 2.170 nonbonded pdb=" OE1 GLN H 775 " pdb="MG MG H1602 " model vdw 2.166 2.170 nonbonded pdb=" OE1 GLN F 775 " pdb="MG MG F1602 " model vdw 2.166 2.170 nonbonded pdb=" O GLY H1282 " pdb=" OG1 THR H1286 " model vdw 2.236 2.440 ... (remaining 459025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 3.690 Check model and map are aligned: 0.580 Set scattering table: 0.360 Process input model: 112.330 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.205 55564 Z= 0.366 Angle : 0.755 17.427 75516 Z= 0.407 Chirality : 0.046 0.303 8984 Planarity : 0.007 0.057 9276 Dihedral : 12.283 118.138 20008 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 2.18 % Allowed : 5.73 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.09), residues: 6824 helix: 0.26 (0.07), residues: 4032 sheet: 0.17 (0.23), residues: 460 loop : -0.78 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F1247 HIS 0.005 0.001 HIS F 105 PHE 0.020 0.002 PHE G 183 TYR 0.018 0.001 TYR F 356 ARG 0.005 0.000 ARG F1215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1138 time to evaluate : 4.758 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: A 77 MET cc_start: 0.7844 (tpp) cc_final: 0.7629 (mmt) REVERT: B 506 MET cc_start: 0.8975 (tpt) cc_final: 0.8740 (tpt) REVERT: B 546 MET cc_start: 0.7380 (ttp) cc_final: 0.7153 (ttm) REVERT: B 592 LEU cc_start: 0.8267 (mt) cc_final: 0.7927 (mp) REVERT: B 869 MET cc_start: 0.8407 (tpt) cc_final: 0.8196 (tpt) REVERT: B 1026 VAL cc_start: 0.7681 (t) cc_final: 0.7057 (t) REVERT: B 1147 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8404 (m) REVERT: B 1169 LEU cc_start: 0.8136 (tt) cc_final: 0.7650 (mm) REVERT: B 1192 LEU cc_start: 0.8253 (tp) cc_final: 0.8002 (tp) REVERT: B 1273 HIS cc_start: 0.7285 (m-70) cc_final: 0.6831 (m90) REVERT: B 1342 GLN cc_start: 0.6626 (pt0) cc_final: 0.6324 (mt0) REVERT: C 77 MET cc_start: 0.7848 (tpp) cc_final: 0.7622 (mmt) REVERT: C 204 ASP cc_start: 0.8600 (t0) cc_final: 0.8355 (t70) REVERT: D 506 MET cc_start: 0.8992 (tpt) cc_final: 0.8755 (tpt) REVERT: D 555 VAL cc_start: 0.9000 (t) cc_final: 0.8362 (m) REVERT: D 592 LEU cc_start: 0.8247 (mt) cc_final: 0.7885 (mp) REVERT: D 862 VAL cc_start: 0.8168 (t) cc_final: 0.7918 (p) REVERT: D 1026 VAL cc_start: 0.7638 (t) cc_final: 0.7049 (t) REVERT: D 1110 MET cc_start: 0.8048 (mmm) cc_final: 0.7818 (tpt) REVERT: D 1147 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8430 (p) REVERT: D 1169 LEU cc_start: 0.8132 (tt) cc_final: 0.7713 (mm) REVERT: D 1192 LEU cc_start: 0.8264 (tp) cc_final: 0.8006 (tp) REVERT: D 1273 HIS cc_start: 0.7174 (m-70) cc_final: 0.6806 (m90) REVERT: D 1342 GLN cc_start: 0.6666 (pt0) cc_final: 0.6457 (mt0) REVERT: D 1499 LYS cc_start: 0.7591 (mtpm) cc_final: 0.7387 (mtpp) REVERT: E 77 MET cc_start: 0.7845 (tpp) cc_final: 0.7615 (mmt) REVERT: F 506 MET cc_start: 0.8986 (tpt) cc_final: 0.8738 (tpt) REVERT: F 546 MET cc_start: 0.7354 (ttp) cc_final: 0.7152 (ttm) REVERT: F 592 LEU cc_start: 0.8280 (mt) cc_final: 0.7925 (mp) REVERT: F 862 VAL cc_start: 0.8191 (t) cc_final: 0.7953 (p) REVERT: F 1026 VAL cc_start: 0.7663 (t) cc_final: 0.7004 (t) REVERT: F 1078 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7985 (mt) REVERT: F 1110 MET cc_start: 0.8059 (mmm) cc_final: 0.7842 (tpt) REVERT: F 1147 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8401 (p) REVERT: F 1169 LEU cc_start: 0.8166 (tt) cc_final: 0.7690 (mm) REVERT: F 1192 LEU cc_start: 0.8315 (tp) cc_final: 0.8055 (tp) REVERT: F 1273 HIS cc_start: 0.7247 (m-70) cc_final: 0.6875 (m90) REVERT: G 77 MET cc_start: 0.7844 (tpp) cc_final: 0.7629 (mmt) REVERT: H 506 MET cc_start: 0.8986 (tpt) cc_final: 0.8732 (tpt) REVERT: H 555 VAL cc_start: 0.8993 (t) cc_final: 0.8360 (m) REVERT: H 592 LEU cc_start: 0.8253 (mt) cc_final: 0.7887 (mp) REVERT: H 862 VAL cc_start: 0.8156 (t) cc_final: 0.7933 (p) REVERT: H 1026 VAL cc_start: 0.7648 (t) cc_final: 0.7065 (t) REVERT: H 1110 MET cc_start: 0.8032 (mmm) cc_final: 0.7805 (tpt) REVERT: H 1147 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8432 (p) REVERT: H 1169 LEU cc_start: 0.8123 (tt) cc_final: 0.7699 (mm) REVERT: H 1192 LEU cc_start: 0.8261 (tp) cc_final: 0.8006 (tp) REVERT: H 1273 HIS cc_start: 0.7172 (m-70) cc_final: 0.6800 (m90) REVERT: H 1342 GLN cc_start: 0.6659 (pt0) cc_final: 0.6350 (mt0) REVERT: H 1499 LYS cc_start: 0.7594 (mtpm) cc_final: 0.7389 (mtpp) outliers start: 128 outliers final: 25 residues processed: 1230 average time/residue: 0.6340 time to fit residues: 1248.6417 Evaluate side-chains 753 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 723 time to evaluate : 4.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 1147 THR Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 1147 THR Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 237 ASP Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 1078 LEU Chi-restraints excluded: chain F residue 1147 THR Chi-restraints excluded: chain F residue 1271 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 237 ASP Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 354 ASN Chi-restraints excluded: chain H residue 1147 THR Chi-restraints excluded: chain H residue 1271 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 580 optimal weight: 5.9990 chunk 521 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 178 optimal weight: 0.9990 chunk 351 optimal weight: 20.0000 chunk 278 optimal weight: 10.0000 chunk 539 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 327 optimal weight: 3.9990 chunk 401 optimal weight: 9.9990 chunk 624 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 241 HIS ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN B 493 ASN B1134 GLN B1225 GLN B1541 HIS C 46 HIS C 70 HIS ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D 241 HIS ** D 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 GLN D 493 ASN D 562 HIS D1134 GLN D1225 GLN D1541 HIS E 46 HIS E 70 HIS E 279 GLN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 241 HIS ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 GLN F 493 ASN F 562 HIS F 863 HIS F1134 GLN F1225 GLN F1541 HIS G 46 HIS G 70 HIS ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN H 241 HIS H 339 GLN ** H 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 GLN H 493 ASN H 562 HIS H 863 HIS H1134 GLN H1225 GLN H1541 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 55564 Z= 0.320 Angle : 0.592 7.574 75516 Z= 0.292 Chirality : 0.043 0.199 8984 Planarity : 0.004 0.039 9276 Dihedral : 8.479 109.632 7687 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 2.28 % Allowed : 10.96 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.10), residues: 6824 helix: 1.15 (0.08), residues: 4084 sheet: 0.00 (0.23), residues: 504 loop : -0.61 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1247 HIS 0.012 0.001 HIS B 584 PHE 0.017 0.002 PHE B 685 TYR 0.024 0.002 TYR F 123 ARG 0.009 0.001 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 781 time to evaluate : 4.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8682 (t80) cc_final: 0.8371 (t80) REVERT: A 77 MET cc_start: 0.7912 (tpp) cc_final: 0.7611 (mmt) REVERT: A 330 TYR cc_start: 0.9112 (m-80) cc_final: 0.8400 (m-80) REVERT: B 102 ARG cc_start: 0.7044 (mtp180) cc_final: 0.6844 (mmm-85) REVERT: B 108 MET cc_start: 0.8265 (tmm) cc_final: 0.8039 (ttt) REVERT: B 506 MET cc_start: 0.9037 (tpt) cc_final: 0.8731 (tpt) REVERT: B 530 MET cc_start: 0.8179 (mmm) cc_final: 0.7752 (mmm) REVERT: B 555 VAL cc_start: 0.8902 (t) cc_final: 0.8355 (m) REVERT: B 592 LEU cc_start: 0.8328 (mt) cc_final: 0.7999 (mp) REVERT: B 1018 PHE cc_start: 0.7084 (t80) cc_final: 0.6840 (t80) REVERT: B 1169 LEU cc_start: 0.8225 (tt) cc_final: 0.7699 (mm) REVERT: B 1273 HIS cc_start: 0.7553 (m-70) cc_final: 0.7215 (m90) REVERT: B 1342 GLN cc_start: 0.6913 (pt0) cc_final: 0.6507 (mt0) REVERT: C 35 PHE cc_start: 0.8682 (t80) cc_final: 0.8380 (t80) REVERT: C 77 MET cc_start: 0.7916 (tpp) cc_final: 0.7607 (mmt) REVERT: C 330 TYR cc_start: 0.9108 (m-80) cc_final: 0.8429 (m-80) REVERT: D 108 MET cc_start: 0.8270 (tmm) cc_final: 0.8025 (ttt) REVERT: D 506 MET cc_start: 0.9053 (tpt) cc_final: 0.8849 (tpt) REVERT: D 530 MET cc_start: 0.8126 (mmm) cc_final: 0.7680 (mmm) REVERT: D 555 VAL cc_start: 0.8913 (t) cc_final: 0.8389 (m) REVERT: D 592 LEU cc_start: 0.8301 (mt) cc_final: 0.7964 (mp) REVERT: D 862 VAL cc_start: 0.8251 (t) cc_final: 0.8022 (p) REVERT: D 1018 PHE cc_start: 0.7091 (t80) cc_final: 0.6853 (t80) REVERT: D 1169 LEU cc_start: 0.8263 (tt) cc_final: 0.7776 (mm) REVERT: D 1273 HIS cc_start: 0.7457 (m-70) cc_final: 0.7113 (m90) REVERT: D 1342 GLN cc_start: 0.6925 (pt0) cc_final: 0.6563 (mt0) REVERT: E 35 PHE cc_start: 0.8678 (t80) cc_final: 0.8375 (t80) REVERT: E 77 MET cc_start: 0.7915 (tpp) cc_final: 0.7602 (mmt) REVERT: E 330 TYR cc_start: 0.9108 (m-80) cc_final: 0.8392 (m-80) REVERT: F 102 ARG cc_start: 0.7052 (mtp180) cc_final: 0.6852 (mmm-85) REVERT: F 108 MET cc_start: 0.8272 (tmm) cc_final: 0.8029 (ttt) REVERT: F 555 VAL cc_start: 0.8887 (t) cc_final: 0.8378 (m) REVERT: F 592 LEU cc_start: 0.8334 (mt) cc_final: 0.8006 (mp) REVERT: F 862 VAL cc_start: 0.8292 (t) cc_final: 0.8029 (p) REVERT: F 1018 PHE cc_start: 0.7077 (t80) cc_final: 0.6831 (t80) REVERT: F 1169 LEU cc_start: 0.8250 (tt) cc_final: 0.7734 (mm) REVERT: F 1273 HIS cc_start: 0.7517 (m-70) cc_final: 0.7171 (m90) REVERT: F 1342 GLN cc_start: 0.7087 (pt0) cc_final: 0.6709 (mt0) REVERT: G 35 PHE cc_start: 0.8679 (t80) cc_final: 0.8380 (t80) REVERT: G 77 MET cc_start: 0.7913 (tpp) cc_final: 0.7612 (mmt) REVERT: G 330 TYR cc_start: 0.9112 (m-80) cc_final: 0.8400 (m-80) REVERT: H 108 MET cc_start: 0.8275 (tmm) cc_final: 0.8027 (ttt) REVERT: H 506 MET cc_start: 0.9055 (tpt) cc_final: 0.8841 (tpt) REVERT: H 530 MET cc_start: 0.8130 (mmm) cc_final: 0.7700 (mmm) REVERT: H 555 VAL cc_start: 0.8901 (t) cc_final: 0.8381 (m) REVERT: H 592 LEU cc_start: 0.8306 (mt) cc_final: 0.7957 (mp) REVERT: H 862 VAL cc_start: 0.8267 (t) cc_final: 0.8013 (p) REVERT: H 1018 PHE cc_start: 0.7086 (t80) cc_final: 0.6849 (t80) REVERT: H 1169 LEU cc_start: 0.8251 (tt) cc_final: 0.7760 (mm) REVERT: H 1273 HIS cc_start: 0.7451 (m-70) cc_final: 0.7110 (m90) REVERT: H 1342 GLN cc_start: 0.6913 (pt0) cc_final: 0.6504 (mt0) outliers start: 134 outliers final: 65 residues processed: 858 average time/residue: 0.5826 time to fit residues: 811.7337 Evaluate side-chains 770 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 705 time to evaluate : 4.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1290 MET Chi-restraints excluded: chain B residue 1302 LEU Chi-restraints excluded: chain B residue 1571 ASP Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 1176 TYR Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1571 ASP Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 1176 TYR Chi-restraints excluded: chain F residue 1271 SER Chi-restraints excluded: chain F residue 1290 MET Chi-restraints excluded: chain F residue 1302 LEU Chi-restraints excluded: chain F residue 1571 ASP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 1176 TYR Chi-restraints excluded: chain H residue 1271 SER Chi-restraints excluded: chain H residue 1290 MET Chi-restraints excluded: chain H residue 1571 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 347 optimal weight: 0.0020 chunk 193 optimal weight: 4.9990 chunk 519 optimal weight: 0.0980 chunk 425 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 625 optimal weight: 9.9990 chunk 676 optimal weight: 3.9990 chunk 557 optimal weight: 8.9990 chunk 620 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 502 optimal weight: 7.9990 overall best weight: 3.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN B 131 ASN B 562 HIS B1123 ASN B1191 GLN B1541 HIS ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN D 131 ASN D1541 HIS ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN F 131 ASN F1123 ASN F1191 GLN F1541 HIS ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 ASN H 131 ASN H 339 GLN H1123 ASN H1541 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 55564 Z= 0.242 Angle : 0.545 7.933 75516 Z= 0.270 Chirality : 0.042 0.211 8984 Planarity : 0.004 0.041 9276 Dihedral : 8.254 109.483 7660 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.77 % Favored : 97.08 % Rotamer: Outliers : 2.49 % Allowed : 11.52 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.10), residues: 6824 helix: 1.50 (0.08), residues: 4072 sheet: 0.07 (0.23), residues: 484 loop : -0.58 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1339 HIS 0.008 0.001 HIS B 584 PHE 0.012 0.001 PHE F 794 TYR 0.019 0.001 TYR F 123 ARG 0.004 0.000 ARG E 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 713 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8263 (ptpt) cc_final: 0.8006 (ptpt) REVERT: A 77 MET cc_start: 0.7941 (tpp) cc_final: 0.7639 (mmt) REVERT: A 330 TYR cc_start: 0.9134 (m-80) cc_final: 0.8374 (m-80) REVERT: B 329 LYS cc_start: 0.6130 (tmtt) cc_final: 0.5569 (tmtt) REVERT: B 506 MET cc_start: 0.9021 (tpt) cc_final: 0.8745 (tpt) REVERT: B 555 VAL cc_start: 0.8900 (t) cc_final: 0.8365 (m) REVERT: B 592 LEU cc_start: 0.8280 (mt) cc_final: 0.7991 (mp) REVERT: B 1018 PHE cc_start: 0.6874 (t80) cc_final: 0.6647 (t80) REVERT: B 1169 LEU cc_start: 0.8316 (tt) cc_final: 0.7792 (mm) REVERT: B 1342 GLN cc_start: 0.6925 (pt0) cc_final: 0.6543 (mt0) REVERT: C 77 MET cc_start: 0.7943 (tpp) cc_final: 0.7630 (mmt) REVERT: C 330 TYR cc_start: 0.9116 (m-80) cc_final: 0.8381 (m-80) REVERT: D 530 MET cc_start: 0.8098 (mmm) cc_final: 0.7685 (mmm) REVERT: D 555 VAL cc_start: 0.8894 (t) cc_final: 0.8401 (m) REVERT: D 592 LEU cc_start: 0.8256 (mt) cc_final: 0.7963 (mp) REVERT: D 862 VAL cc_start: 0.8264 (t) cc_final: 0.8036 (p) REVERT: D 1013 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8669 (mp) REVERT: D 1018 PHE cc_start: 0.7042 (t80) cc_final: 0.6778 (t80) REVERT: D 1169 LEU cc_start: 0.8302 (tt) cc_final: 0.7831 (mm) REVERT: D 1187 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7681 (mtm-85) REVERT: D 1342 GLN cc_start: 0.6938 (pt0) cc_final: 0.6602 (mt0) REVERT: E 77 MET cc_start: 0.7940 (tpp) cc_final: 0.7627 (mmt) REVERT: E 330 TYR cc_start: 0.9131 (m-80) cc_final: 0.8354 (m-80) REVERT: F 530 MET cc_start: 0.8116 (mmm) cc_final: 0.7701 (mmm) REVERT: F 555 VAL cc_start: 0.8892 (t) cc_final: 0.8399 (m) REVERT: F 592 LEU cc_start: 0.8295 (mt) cc_final: 0.7992 (mp) REVERT: F 1018 PHE cc_start: 0.6850 (t80) cc_final: 0.6617 (t80) REVERT: F 1169 LEU cc_start: 0.8335 (tt) cc_final: 0.7822 (mm) REVERT: F 1342 GLN cc_start: 0.7149 (pt0) cc_final: 0.6804 (mt0) REVERT: G 47 LYS cc_start: 0.8255 (ptpt) cc_final: 0.8002 (ptpt) REVERT: G 77 MET cc_start: 0.7934 (tpp) cc_final: 0.7638 (mmt) REVERT: G 330 TYR cc_start: 0.9135 (m-80) cc_final: 0.8363 (m-80) REVERT: H 530 MET cc_start: 0.8098 (mmm) cc_final: 0.7702 (mmm) REVERT: H 555 VAL cc_start: 0.8893 (t) cc_final: 0.8415 (m) REVERT: H 592 LEU cc_start: 0.8253 (mt) cc_final: 0.7955 (mp) REVERT: H 862 VAL cc_start: 0.8250 (t) cc_final: 0.8023 (p) REVERT: H 1018 PHE cc_start: 0.6869 (t80) cc_final: 0.6622 (t80) REVERT: H 1169 LEU cc_start: 0.8295 (tt) cc_final: 0.7819 (mm) REVERT: H 1187 ARG cc_start: 0.7886 (mtt90) cc_final: 0.7675 (mtm-85) REVERT: H 1342 GLN cc_start: 0.6926 (pt0) cc_final: 0.6547 (mt0) outliers start: 146 outliers final: 72 residues processed: 809 average time/residue: 0.5809 time to fit residues: 759.8084 Evaluate side-chains 734 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 661 time to evaluate : 4.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1290 MET Chi-restraints excluded: chain B residue 1302 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1571 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 1013 LEU Chi-restraints excluded: chain D residue 1250 VAL Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1276 LEU Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain D residue 1309 LEU Chi-restraints excluded: chain D residue 1315 ILE Chi-restraints excluded: chain D residue 1571 ASP Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1271 SER Chi-restraints excluded: chain F residue 1290 MET Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1571 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 563 VAL Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1271 SER Chi-restraints excluded: chain H residue 1276 LEU Chi-restraints excluded: chain H residue 1290 MET Chi-restraints excluded: chain H residue 1302 LEU Chi-restraints excluded: chain H residue 1309 LEU Chi-restraints excluded: chain H residue 1571 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 618 optimal weight: 3.9990 chunk 470 optimal weight: 9.9990 chunk 324 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 chunk 420 optimal weight: 8.9990 chunk 628 optimal weight: 6.9990 chunk 665 optimal weight: 2.9990 chunk 328 optimal weight: 8.9990 chunk 595 optimal weight: 9.9990 chunk 179 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 23 ASN B1191 GLN B1225 GLN B1349 ASN B1541 HIS C 153 ASN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 23 ASN D 131 ASN D1541 HIS ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN F 23 ASN F 131 ASN F1191 GLN F1541 HIS G 279 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN H 131 ASN H1541 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 55564 Z= 0.239 Angle : 0.532 7.272 75516 Z= 0.262 Chirality : 0.041 0.218 8984 Planarity : 0.004 0.037 9276 Dihedral : 8.149 108.702 7660 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.70 % Favored : 97.16 % Rotamer: Outliers : 2.81 % Allowed : 11.49 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.10), residues: 6824 helix: 1.68 (0.08), residues: 4080 sheet: 0.00 (0.24), residues: 484 loop : -0.53 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1247 HIS 0.006 0.001 HIS B 584 PHE 0.012 0.001 PHE A 198 TYR 0.020 0.001 TYR D 123 ARG 0.004 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 717 time to evaluate : 4.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 TYR cc_start: 0.9140 (m-80) cc_final: 0.8321 (m-80) REVERT: B 329 LYS cc_start: 0.6365 (tmtt) cc_final: 0.5723 (tmtt) REVERT: B 506 MET cc_start: 0.8984 (tpt) cc_final: 0.8748 (tpt) REVERT: B 555 VAL cc_start: 0.8925 (t) cc_final: 0.8424 (m) REVERT: B 592 LEU cc_start: 0.8304 (mt) cc_final: 0.8021 (mp) REVERT: B 1018 PHE cc_start: 0.6675 (t80) cc_final: 0.6446 (t80) REVERT: B 1169 LEU cc_start: 0.8336 (tt) cc_final: 0.7777 (mm) REVERT: B 1225 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7820 (tp-100) REVERT: B 1342 GLN cc_start: 0.7003 (pt0) cc_final: 0.6565 (mt0) REVERT: C 330 TYR cc_start: 0.9127 (m-80) cc_final: 0.8423 (m-80) REVERT: D 329 LYS cc_start: 0.6587 (tmtt) cc_final: 0.5947 (tmtt) REVERT: D 555 VAL cc_start: 0.8904 (t) cc_final: 0.8425 (m) REVERT: D 592 LEU cc_start: 0.8284 (mt) cc_final: 0.8005 (mp) REVERT: D 862 VAL cc_start: 0.8257 (t) cc_final: 0.8024 (p) REVERT: D 1013 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8776 (mp) REVERT: D 1018 PHE cc_start: 0.6721 (t80) cc_final: 0.6477 (t80) REVERT: D 1169 LEU cc_start: 0.8320 (tt) cc_final: 0.7826 (mm) REVERT: D 1187 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7784 (mtm-85) REVERT: D 1342 GLN cc_start: 0.6974 (pt0) cc_final: 0.6593 (mt0) REVERT: E 330 TYR cc_start: 0.9139 (m-80) cc_final: 0.8415 (m-80) REVERT: F 530 MET cc_start: 0.8189 (mmm) cc_final: 0.7539 (tpp) REVERT: F 555 VAL cc_start: 0.8915 (t) cc_final: 0.8453 (m) REVERT: F 592 LEU cc_start: 0.8315 (mt) cc_final: 0.8027 (mp) REVERT: F 815 LEU cc_start: 0.8514 (mt) cc_final: 0.8200 (mp) REVERT: F 1018 PHE cc_start: 0.6693 (t80) cc_final: 0.6464 (t80) REVERT: F 1169 LEU cc_start: 0.8349 (tt) cc_final: 0.7806 (mm) REVERT: F 1342 GLN cc_start: 0.7201 (pt0) cc_final: 0.6864 (mt0) REVERT: F 1505 MET cc_start: 0.8329 (mtp) cc_final: 0.8093 (mtp) REVERT: G 330 TYR cc_start: 0.9138 (m-80) cc_final: 0.8434 (m-80) REVERT: H 329 LYS cc_start: 0.6589 (tmtt) cc_final: 0.5945 (tmtt) REVERT: H 555 VAL cc_start: 0.8906 (t) cc_final: 0.8434 (m) REVERT: H 592 LEU cc_start: 0.8283 (mt) cc_final: 0.7999 (mp) REVERT: H 862 VAL cc_start: 0.8255 (t) cc_final: 0.8023 (p) REVERT: H 1018 PHE cc_start: 0.6710 (t80) cc_final: 0.6477 (t80) REVERT: H 1169 LEU cc_start: 0.8314 (tt) cc_final: 0.7812 (mm) REVERT: H 1187 ARG cc_start: 0.7989 (mtt90) cc_final: 0.7786 (mtm-85) REVERT: H 1342 GLN cc_start: 0.6979 (pt0) cc_final: 0.6539 (mt0) outliers start: 165 outliers final: 88 residues processed: 842 average time/residue: 0.5782 time to fit residues: 793.0006 Evaluate side-chains 748 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 659 time to evaluate : 4.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1571 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 1013 LEU Chi-restraints excluded: chain D residue 1250 VAL Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1276 LEU Chi-restraints excluded: chain D residue 1309 LEU Chi-restraints excluded: chain D residue 1315 ILE Chi-restraints excluded: chain D residue 1571 ASP Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1271 SER Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1302 LEU Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1571 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 279 GLN Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 563 VAL Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1271 SER Chi-restraints excluded: chain H residue 1276 LEU Chi-restraints excluded: chain H residue 1309 LEU Chi-restraints excluded: chain H residue 1571 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 553 optimal weight: 10.0000 chunk 377 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 495 optimal weight: 10.0000 chunk 274 optimal weight: 7.9990 chunk 567 optimal weight: 40.0000 chunk 459 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 596 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1541 HIS C 173 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D1296 ASN D1427 GLN D1541 HIS E 153 ASN E 173 GLN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F1225 GLN F1541 HIS G 153 ASN G 173 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN H1541 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 55564 Z= 0.486 Angle : 0.657 9.317 75516 Z= 0.324 Chirality : 0.046 0.193 8984 Planarity : 0.005 0.043 9276 Dihedral : 8.587 118.407 7660 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.37 % Favored : 96.47 % Rotamer: Outliers : 3.08 % Allowed : 12.12 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.10), residues: 6824 helix: 1.39 (0.08), residues: 4060 sheet: -0.30 (0.23), residues: 508 loop : -0.57 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1247 HIS 0.009 0.002 HIS D1024 PHE 0.024 0.002 PHE H 685 TYR 0.024 0.002 TYR H 123 ARG 0.005 0.001 ARG B 526 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 694 time to evaluate : 4.598 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: A 70 HIS cc_start: 0.8021 (m170) cc_final: 0.7799 (m90) REVERT: A 330 TYR cc_start: 0.9185 (m-80) cc_final: 0.8266 (m-80) REVERT: B 88 GLU cc_start: 0.7952 (tp30) cc_final: 0.7706 (tp30) REVERT: B 108 MET cc_start: 0.8330 (tmm) cc_final: 0.8111 (ttt) REVERT: B 329 LYS cc_start: 0.6311 (tmtt) cc_final: 0.5618 (tmtt) REVERT: B 555 VAL cc_start: 0.8975 (t) cc_final: 0.8459 (m) REVERT: B 592 LEU cc_start: 0.8331 (mt) cc_final: 0.8041 (mp) REVERT: B 1169 LEU cc_start: 0.8377 (tt) cc_final: 0.7806 (mm) REVERT: B 1342 GLN cc_start: 0.7170 (pt0) cc_final: 0.6715 (mt0) REVERT: C 70 HIS cc_start: 0.7976 (m170) cc_final: 0.7742 (m90) REVERT: C 330 TYR cc_start: 0.9181 (m-80) cc_final: 0.8276 (m-80) REVERT: D 88 GLU cc_start: 0.8020 (tp30) cc_final: 0.7743 (tp30) REVERT: D 91 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8295 (tm-30) REVERT: D 108 MET cc_start: 0.8327 (tmm) cc_final: 0.8113 (ttt) REVERT: D 329 LYS cc_start: 0.6582 (tmtt) cc_final: 0.5856 (tmtt) REVERT: D 555 VAL cc_start: 0.8962 (t) cc_final: 0.8489 (m) REVERT: D 592 LEU cc_start: 0.8307 (mt) cc_final: 0.8013 (mp) REVERT: D 862 VAL cc_start: 0.8317 (t) cc_final: 0.8062 (p) REVERT: D 1013 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8782 (mp) REVERT: D 1110 MET cc_start: 0.8061 (tpp) cc_final: 0.7852 (tpt) REVERT: D 1169 LEU cc_start: 0.8380 (tt) cc_final: 0.7889 (mm) REVERT: D 1342 GLN cc_start: 0.7159 (pt0) cc_final: 0.6750 (mt0) REVERT: E 70 HIS cc_start: 0.7984 (m170) cc_final: 0.7751 (m90) REVERT: E 330 TYR cc_start: 0.9180 (m-80) cc_final: 0.8263 (m-80) REVERT: F 88 GLU cc_start: 0.7952 (tp30) cc_final: 0.7690 (tp30) REVERT: F 91 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: F 108 MET cc_start: 0.8324 (tmm) cc_final: 0.8108 (ttt) REVERT: F 329 LYS cc_start: 0.6567 (tmtt) cc_final: 0.5865 (tmtt) REVERT: F 530 MET cc_start: 0.8201 (mmm) cc_final: 0.7889 (tpp) REVERT: F 555 VAL cc_start: 0.8946 (t) cc_final: 0.8493 (m) REVERT: F 592 LEU cc_start: 0.8339 (mt) cc_final: 0.8035 (mp) REVERT: F 1110 MET cc_start: 0.8069 (tpp) cc_final: 0.7808 (tpt) REVERT: F 1169 LEU cc_start: 0.8384 (tt) cc_final: 0.7833 (mm) REVERT: F 1342 GLN cc_start: 0.7373 (pt0) cc_final: 0.7084 (mt0) REVERT: G 70 HIS cc_start: 0.7985 (m170) cc_final: 0.7754 (m90) REVERT: G 330 TYR cc_start: 0.9178 (m-80) cc_final: 0.8269 (m-80) REVERT: H 108 MET cc_start: 0.8325 (tmm) cc_final: 0.8110 (ttt) REVERT: H 329 LYS cc_start: 0.6582 (tmtt) cc_final: 0.5851 (tmtt) REVERT: H 555 VAL cc_start: 0.8957 (t) cc_final: 0.8486 (m) REVERT: H 592 LEU cc_start: 0.8311 (mt) cc_final: 0.8005 (mp) REVERT: H 1110 MET cc_start: 0.8048 (tpp) cc_final: 0.7794 (tpt) REVERT: H 1169 LEU cc_start: 0.8374 (tt) cc_final: 0.7876 (mm) REVERT: H 1342 GLN cc_start: 0.7180 (pt0) cc_final: 0.6737 (mt0) outliers start: 181 outliers final: 136 residues processed: 829 average time/residue: 0.5781 time to fit residues: 774.8101 Evaluate side-chains 791 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 652 time to evaluate : 4.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1290 MET Chi-restraints excluded: chain B residue 1302 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1465 LYS Chi-restraints excluded: chain B residue 1566 LEU Chi-restraints excluded: chain B residue 1571 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 1013 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1176 TYR Chi-restraints excluded: chain D residue 1250 VAL Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1276 LEU Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1302 LEU Chi-restraints excluded: chain D residue 1309 LEU Chi-restraints excluded: chain D residue 1315 ILE Chi-restraints excluded: chain D residue 1566 LEU Chi-restraints excluded: chain D residue 1571 ASP Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 158 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 689 THR Chi-restraints excluded: chain F residue 712 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 1105 ILE Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1259 VAL Chi-restraints excluded: chain F residue 1271 SER Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1290 MET Chi-restraints excluded: chain F residue 1302 LEU Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1465 LYS Chi-restraints excluded: chain F residue 1566 LEU Chi-restraints excluded: chain F residue 1571 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 158 TYR Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 563 VAL Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 689 THR Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 1105 ILE Chi-restraints excluded: chain H residue 1176 TYR Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1259 VAL Chi-restraints excluded: chain H residue 1271 SER Chi-restraints excluded: chain H residue 1276 LEU Chi-restraints excluded: chain H residue 1290 MET Chi-restraints excluded: chain H residue 1302 LEU Chi-restraints excluded: chain H residue 1309 LEU Chi-restraints excluded: chain H residue 1571 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 223 optimal weight: 2.9990 chunk 598 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 390 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 665 optimal weight: 2.9990 chunk 552 optimal weight: 6.9990 chunk 308 optimal weight: 0.4980 chunk 55 optimal weight: 0.0070 chunk 220 optimal weight: 8.9990 chunk 349 optimal weight: 0.8980 overall best weight: 1.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D1541 HIS ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN H1541 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 55564 Z= 0.171 Angle : 0.521 8.243 75516 Z= 0.258 Chirality : 0.040 0.184 8984 Planarity : 0.004 0.044 9276 Dihedral : 8.248 113.908 7659 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.48 % Favored : 97.39 % Rotamer: Outliers : 1.94 % Allowed : 13.82 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.10), residues: 6824 helix: 1.82 (0.08), residues: 4044 sheet: -0.29 (0.24), residues: 508 loop : -0.45 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1247 HIS 0.005 0.001 HIS B 584 PHE 0.016 0.001 PHE A 198 TYR 0.017 0.001 TYR F 123 ARG 0.006 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 692 time to evaluate : 4.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.7978 (m170) cc_final: 0.7770 (m-70) REVERT: A 141 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: A 330 TYR cc_start: 0.9138 (m-80) cc_final: 0.8210 (m-80) REVERT: B 108 MET cc_start: 0.8224 (tmm) cc_final: 0.7983 (ttt) REVERT: B 329 LYS cc_start: 0.6296 (tmtt) cc_final: 0.5596 (tmtt) REVERT: B 555 VAL cc_start: 0.8945 (t) cc_final: 0.8663 (p) REVERT: B 592 LEU cc_start: 0.8310 (mt) cc_final: 0.8049 (mp) REVERT: B 1169 LEU cc_start: 0.8325 (tt) cc_final: 0.7792 (mm) REVERT: B 1225 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7656 (tp-100) REVERT: B 1342 GLN cc_start: 0.7041 (pt0) cc_final: 0.6626 (mt0) REVERT: B 1505 MET cc_start: 0.8375 (mtp) cc_final: 0.8170 (mtp) REVERT: C 141 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: C 330 TYR cc_start: 0.9142 (m-80) cc_final: 0.8335 (m-80) REVERT: D 88 GLU cc_start: 0.7927 (tp30) cc_final: 0.7710 (tp30) REVERT: D 108 MET cc_start: 0.8218 (tmm) cc_final: 0.7983 (ttt) REVERT: D 329 LYS cc_start: 0.6462 (tmtt) cc_final: 0.5809 (tmtt) REVERT: D 555 VAL cc_start: 0.8942 (t) cc_final: 0.8474 (m) REVERT: D 565 PHE cc_start: 0.7340 (t80) cc_final: 0.7073 (m-10) REVERT: D 592 LEU cc_start: 0.8302 (mt) cc_final: 0.8036 (mp) REVERT: D 862 VAL cc_start: 0.8257 (t) cc_final: 0.8027 (p) REVERT: D 1169 LEU cc_start: 0.8304 (tt) cc_final: 0.7836 (mm) REVERT: D 1342 GLN cc_start: 0.7034 (pt0) cc_final: 0.6650 (mt0) REVERT: E 70 HIS cc_start: 0.7986 (m170) cc_final: 0.7774 (m-70) REVERT: E 141 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: E 330 TYR cc_start: 0.9135 (m-80) cc_final: 0.8205 (m-80) REVERT: F 88 GLU cc_start: 0.7903 (tp30) cc_final: 0.7690 (tp30) REVERT: F 108 MET cc_start: 0.8222 (tmm) cc_final: 0.7988 (ttt) REVERT: F 329 LYS cc_start: 0.6420 (tmtt) cc_final: 0.5743 (tmtt) REVERT: F 530 MET cc_start: 0.8081 (mmm) cc_final: 0.7512 (tpp) REVERT: F 555 VAL cc_start: 0.8938 (t) cc_final: 0.8465 (m) REVERT: F 592 LEU cc_start: 0.8325 (mt) cc_final: 0.8054 (mp) REVERT: F 1169 LEU cc_start: 0.8334 (tt) cc_final: 0.7819 (mm) REVERT: F 1342 GLN cc_start: 0.7302 (pt0) cc_final: 0.7018 (mt0) REVERT: F 1505 MET cc_start: 0.8401 (mtp) cc_final: 0.8117 (mtp) REVERT: G 70 HIS cc_start: 0.7982 (m170) cc_final: 0.7777 (m-70) REVERT: G 141 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: G 330 TYR cc_start: 0.9136 (m-80) cc_final: 0.8203 (m-80) REVERT: H 108 MET cc_start: 0.8236 (tmm) cc_final: 0.8002 (ttt) REVERT: H 329 LYS cc_start: 0.6469 (tmtt) cc_final: 0.5815 (tmtt) REVERT: H 550 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8111 (tt) REVERT: H 555 VAL cc_start: 0.8952 (t) cc_final: 0.8484 (m) REVERT: H 592 LEU cc_start: 0.8304 (mt) cc_final: 0.8042 (mp) REVERT: H 862 VAL cc_start: 0.8285 (t) cc_final: 0.8045 (p) REVERT: H 1169 LEU cc_start: 0.8298 (tt) cc_final: 0.7823 (mm) REVERT: H 1342 GLN cc_start: 0.7039 (pt0) cc_final: 0.6625 (mt0) REVERT: H 1505 MET cc_start: 0.8375 (mtp) cc_final: 0.8142 (mtp) outliers start: 114 outliers final: 77 residues processed: 765 average time/residue: 0.5781 time to fit residues: 718.4847 Evaluate side-chains 728 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 646 time to evaluate : 4.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1290 MET Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1571 ASP Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 1176 TYR Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1309 LEU Chi-restraints excluded: chain D residue 1315 ILE Chi-restraints excluded: chain D residue 1566 LEU Chi-restraints excluded: chain D residue 1568 SER Chi-restraints excluded: chain D residue 1571 ASP Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 158 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 712 VAL Chi-restraints excluded: chain F residue 1176 TYR Chi-restraints excluded: chain F residue 1271 SER Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1290 MET Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1566 LEU Chi-restraints excluded: chain F residue 1571 ASP Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 158 TYR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 550 ILE Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 1176 TYR Chi-restraints excluded: chain H residue 1271 SER Chi-restraints excluded: chain H residue 1290 MET Chi-restraints excluded: chain H residue 1309 LEU Chi-restraints excluded: chain H residue 1566 LEU Chi-restraints excluded: chain H residue 1571 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 641 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 379 optimal weight: 0.6980 chunk 486 optimal weight: 9.9990 chunk 376 optimal weight: 0.6980 chunk 560 optimal weight: 20.0000 chunk 371 optimal weight: 2.9990 chunk 663 optimal weight: 2.9990 chunk 414 optimal weight: 8.9990 chunk 404 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B1296 ASN B1541 HIS C 173 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D1225 GLN E 173 GLN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN F1296 ASN F1541 HIS G 173 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN H1296 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 55564 Z= 0.198 Angle : 0.528 9.039 75516 Z= 0.259 Chirality : 0.041 0.225 8984 Planarity : 0.004 0.044 9276 Dihedral : 8.093 110.959 7656 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Rotamer: Outliers : 2.30 % Allowed : 13.26 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.10), residues: 6824 helix: 1.94 (0.08), residues: 4040 sheet: -0.23 (0.24), residues: 508 loop : -0.42 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D1247 HIS 0.005 0.001 HIS D1541 PHE 0.017 0.001 PHE E 198 TYR 0.018 0.001 TYR B 123 ARG 0.006 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 655 time to evaluate : 4.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.8105 (m170) cc_final: 0.7885 (m-70) REVERT: A 141 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: A 330 TYR cc_start: 0.9134 (m-80) cc_final: 0.8400 (m-80) REVERT: B 108 MET cc_start: 0.8216 (tmm) cc_final: 0.7968 (ttt) REVERT: B 329 LYS cc_start: 0.6364 (tmtt) cc_final: 0.5625 (tmtt) REVERT: B 555 VAL cc_start: 0.8975 (t) cc_final: 0.8692 (p) REVERT: B 592 LEU cc_start: 0.8325 (mt) cc_final: 0.8043 (mp) REVERT: B 919 ARG cc_start: 0.7452 (ptt-90) cc_final: 0.7108 (ptt-90) REVERT: B 1084 VAL cc_start: 0.8798 (t) cc_final: 0.8430 (m) REVERT: B 1169 LEU cc_start: 0.8308 (tt) cc_final: 0.7794 (mm) REVERT: B 1225 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7593 (tp-100) REVERT: B 1342 GLN cc_start: 0.7068 (pt0) cc_final: 0.6654 (mt0) REVERT: B 1505 MET cc_start: 0.8378 (mtp) cc_final: 0.8175 (mtp) REVERT: C 141 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: C 330 TYR cc_start: 0.9139 (m-80) cc_final: 0.8452 (m-80) REVERT: D 108 MET cc_start: 0.8203 (tmm) cc_final: 0.7946 (ttt) REVERT: D 329 LYS cc_start: 0.6405 (tmtt) cc_final: 0.5769 (tmtt) REVERT: D 555 VAL cc_start: 0.8960 (t) cc_final: 0.8495 (m) REVERT: D 592 LEU cc_start: 0.8309 (mt) cc_final: 0.8019 (mp) REVERT: D 1169 LEU cc_start: 0.8280 (tt) cc_final: 0.7836 (mm) REVERT: D 1342 GLN cc_start: 0.7059 (pt0) cc_final: 0.6692 (mt0) REVERT: E 70 HIS cc_start: 0.8110 (m170) cc_final: 0.7889 (m-70) REVERT: E 141 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: E 330 TYR cc_start: 0.9135 (m-80) cc_final: 0.8292 (m-80) REVERT: F 108 MET cc_start: 0.8216 (tmm) cc_final: 0.7971 (ttt) REVERT: F 329 LYS cc_start: 0.6363 (tmtt) cc_final: 0.5700 (tmtt) REVERT: F 530 MET cc_start: 0.8098 (mmm) cc_final: 0.7515 (tpp) REVERT: F 555 VAL cc_start: 0.8950 (t) cc_final: 0.8482 (m) REVERT: F 592 LEU cc_start: 0.8336 (mt) cc_final: 0.8045 (mp) REVERT: F 1169 LEU cc_start: 0.8328 (tt) cc_final: 0.7825 (mm) REVERT: F 1505 MET cc_start: 0.8388 (mtp) cc_final: 0.8148 (mtp) REVERT: G 70 HIS cc_start: 0.8109 (m170) cc_final: 0.7890 (m-70) REVERT: G 141 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: G 330 TYR cc_start: 0.9129 (m-80) cc_final: 0.8272 (m-80) REVERT: H 108 MET cc_start: 0.8213 (tmm) cc_final: 0.7961 (ttt) REVERT: H 329 LYS cc_start: 0.6407 (tmtt) cc_final: 0.5752 (tmtt) REVERT: H 550 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8103 (tt) REVERT: H 555 VAL cc_start: 0.8971 (t) cc_final: 0.8506 (m) REVERT: H 592 LEU cc_start: 0.8313 (mt) cc_final: 0.8015 (mp) REVERT: H 862 VAL cc_start: 0.8281 (t) cc_final: 0.8041 (p) REVERT: H 1169 LEU cc_start: 0.8276 (tt) cc_final: 0.7827 (mm) REVERT: H 1342 GLN cc_start: 0.7058 (pt0) cc_final: 0.6658 (mt0) outliers start: 135 outliers final: 102 residues processed: 743 average time/residue: 0.5804 time to fit residues: 700.8919 Evaluate side-chains 744 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 637 time to evaluate : 4.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1290 MET Chi-restraints excluded: chain B residue 1302 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1566 LEU Chi-restraints excluded: chain B residue 1571 ASP Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 1176 TYR Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1276 LEU Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1309 LEU Chi-restraints excluded: chain D residue 1315 ILE Chi-restraints excluded: chain D residue 1566 LEU Chi-restraints excluded: chain D residue 1571 ASP Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 158 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 689 THR Chi-restraints excluded: chain F residue 712 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 1176 TYR Chi-restraints excluded: chain F residue 1271 SER Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1290 MET Chi-restraints excluded: chain F residue 1295 LEU Chi-restraints excluded: chain F residue 1302 LEU Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1566 LEU Chi-restraints excluded: chain F residue 1571 ASP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 237 ASP Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 158 TYR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 550 ILE Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 689 THR Chi-restraints excluded: chain H residue 723 LEU Chi-restraints excluded: chain H residue 1176 TYR Chi-restraints excluded: chain H residue 1271 SER Chi-restraints excluded: chain H residue 1276 LEU Chi-restraints excluded: chain H residue 1290 MET Chi-restraints excluded: chain H residue 1309 LEU Chi-restraints excluded: chain H residue 1566 LEU Chi-restraints excluded: chain H residue 1571 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 410 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 396 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 421 optimal weight: 9.9990 chunk 451 optimal weight: 9.9990 chunk 327 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 521 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 397 ASN B1427 GLN B1541 HIS C 173 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN E 173 GLN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN G 173 GLN H 397 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 55564 Z= 0.239 Angle : 0.544 9.709 75516 Z= 0.267 Chirality : 0.041 0.194 8984 Planarity : 0.004 0.044 9276 Dihedral : 8.012 110.728 7656 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.00 % Favored : 96.91 % Rotamer: Outliers : 2.18 % Allowed : 13.82 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.10), residues: 6824 helix: 1.92 (0.08), residues: 4044 sheet: -0.28 (0.24), residues: 508 loop : -0.42 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D1247 HIS 0.006 0.001 HIS F1541 PHE 0.022 0.001 PHE B 132 TYR 0.018 0.001 TYR D 123 ARG 0.008 0.000 ARG G 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 659 time to evaluate : 4.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.8102 (m170) cc_final: 0.7884 (m-70) REVERT: A 141 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: A 206 ARG cc_start: 0.8362 (mtp85) cc_final: 0.8115 (mtp180) REVERT: A 330 TYR cc_start: 0.9141 (m-80) cc_final: 0.8407 (m-80) REVERT: B 108 MET cc_start: 0.8226 (tmm) cc_final: 0.7980 (ttt) REVERT: B 329 LYS cc_start: 0.6385 (tmtt) cc_final: 0.5633 (tmtt) REVERT: B 555 VAL cc_start: 0.8982 (t) cc_final: 0.8707 (p) REVERT: B 592 LEU cc_start: 0.8323 (mt) cc_final: 0.8031 (mp) REVERT: B 919 ARG cc_start: 0.7429 (ptt-90) cc_final: 0.7076 (ptt-90) REVERT: B 1169 LEU cc_start: 0.8269 (tt) cc_final: 0.7745 (mm) REVERT: B 1225 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7657 (tp-100) REVERT: B 1342 GLN cc_start: 0.7095 (pt0) cc_final: 0.6671 (mt0) REVERT: C 141 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: C 206 ARG cc_start: 0.8322 (mtp85) cc_final: 0.8076 (mtp180) REVERT: C 330 TYR cc_start: 0.9147 (m-80) cc_final: 0.8448 (m-80) REVERT: D 108 MET cc_start: 0.8224 (tmm) cc_final: 0.7967 (ttt) REVERT: D 158 TYR cc_start: 0.6682 (OUTLIER) cc_final: 0.6377 (m-80) REVERT: D 329 LYS cc_start: 0.6426 (tmtt) cc_final: 0.5775 (tmtt) REVERT: D 555 VAL cc_start: 0.8966 (t) cc_final: 0.8500 (m) REVERT: D 592 LEU cc_start: 0.8304 (mt) cc_final: 0.8018 (mp) REVERT: D 1169 LEU cc_start: 0.8288 (tt) cc_final: 0.7839 (mm) REVERT: D 1342 GLN cc_start: 0.7102 (pt0) cc_final: 0.6732 (mt0) REVERT: E 70 HIS cc_start: 0.8105 (m170) cc_final: 0.7887 (m-70) REVERT: E 141 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: E 330 TYR cc_start: 0.9144 (m-80) cc_final: 0.8307 (m-80) REVERT: F 108 MET cc_start: 0.8224 (tmm) cc_final: 0.7968 (ttt) REVERT: F 329 LYS cc_start: 0.6457 (tmtt) cc_final: 0.5755 (tmtt) REVERT: F 530 MET cc_start: 0.8100 (mmm) cc_final: 0.7521 (tpp) REVERT: F 555 VAL cc_start: 0.8962 (t) cc_final: 0.8478 (m) REVERT: F 592 LEU cc_start: 0.8340 (mt) cc_final: 0.8043 (mp) REVERT: F 1169 LEU cc_start: 0.8327 (tt) cc_final: 0.7827 (mm) REVERT: F 1505 MET cc_start: 0.8413 (mtp) cc_final: 0.8167 (mtp) REVERT: G 70 HIS cc_start: 0.8108 (m170) cc_final: 0.7892 (m-70) REVERT: G 141 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: G 330 TYR cc_start: 0.9134 (m-80) cc_final: 0.8400 (m-80) REVERT: H 108 MET cc_start: 0.8221 (tmm) cc_final: 0.7980 (ttt) REVERT: H 158 TYR cc_start: 0.6594 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: H 329 LYS cc_start: 0.6426 (tmtt) cc_final: 0.5774 (tmtt) REVERT: H 550 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8113 (tt) REVERT: H 555 VAL cc_start: 0.8979 (t) cc_final: 0.8511 (m) REVERT: H 592 LEU cc_start: 0.8312 (mt) cc_final: 0.8015 (mp) REVERT: H 862 VAL cc_start: 0.8284 (t) cc_final: 0.8040 (p) REVERT: H 1169 LEU cc_start: 0.8284 (tt) cc_final: 0.7827 (mm) REVERT: H 1342 GLN cc_start: 0.7043 (pt0) cc_final: 0.6739 (mt0) outliers start: 128 outliers final: 103 residues processed: 742 average time/residue: 0.5811 time to fit residues: 698.6403 Evaluate side-chains 760 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 650 time to evaluate : 4.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1290 MET Chi-restraints excluded: chain B residue 1302 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1566 LEU Chi-restraints excluded: chain B residue 1571 ASP Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 1176 TYR Chi-restraints excluded: chain D residue 1250 VAL Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1276 LEU Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1295 LEU Chi-restraints excluded: chain D residue 1309 LEU Chi-restraints excluded: chain D residue 1315 ILE Chi-restraints excluded: chain D residue 1566 LEU Chi-restraints excluded: chain D residue 1571 ASP Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 237 ASP Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 158 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 1176 TYR Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1271 SER Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1290 MET Chi-restraints excluded: chain F residue 1295 LEU Chi-restraints excluded: chain F residue 1302 LEU Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1566 LEU Chi-restraints excluded: chain F residue 1568 SER Chi-restraints excluded: chain F residue 1571 ASP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 237 ASP Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 158 TYR Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 550 ILE Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 689 THR Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 1176 TYR Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1271 SER Chi-restraints excluded: chain H residue 1276 LEU Chi-restraints excluded: chain H residue 1290 MET Chi-restraints excluded: chain H residue 1309 LEU Chi-restraints excluded: chain H residue 1566 LEU Chi-restraints excluded: chain H residue 1571 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 603 optimal weight: 10.0000 chunk 635 optimal weight: 10.0000 chunk 579 optimal weight: 20.0000 chunk 617 optimal weight: 0.0980 chunk 371 optimal weight: 3.9990 chunk 269 optimal weight: 0.9990 chunk 485 optimal weight: 8.9990 chunk 189 optimal weight: 0.0470 chunk 558 optimal weight: 9.9990 chunk 584 optimal weight: 10.0000 chunk 615 optimal weight: 5.9990 overall best weight: 2.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 397 ASN C 173 GLN D 397 ASN E 173 GLN F 397 ASN F1191 GLN G 173 GLN H 397 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 55564 Z= 0.202 Angle : 0.530 8.524 75516 Z= 0.260 Chirality : 0.041 0.228 8984 Planarity : 0.004 0.045 9276 Dihedral : 7.859 108.094 7656 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.01 % Rotamer: Outliers : 2.03 % Allowed : 14.20 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.10), residues: 6824 helix: 1.99 (0.08), residues: 4044 sheet: -0.31 (0.24), residues: 508 loop : -0.39 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D1247 HIS 0.005 0.001 HIS F1541 PHE 0.017 0.001 PHE E 198 TYR 0.017 0.001 TYR B 123 ARG 0.006 0.000 ARG G 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 690 time to evaluate : 4.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.8090 (m170) cc_final: 0.7870 (m-70) REVERT: A 141 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: A 330 TYR cc_start: 0.9139 (m-80) cc_final: 0.8283 (m-80) REVERT: B 108 MET cc_start: 0.8215 (tmm) cc_final: 0.7950 (ttt) REVERT: B 158 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: B 329 LYS cc_start: 0.6444 (tmtt) cc_final: 0.5673 (tmtt) REVERT: B 555 VAL cc_start: 0.8980 (t) cc_final: 0.8705 (p) REVERT: B 592 LEU cc_start: 0.8305 (mt) cc_final: 0.8015 (mp) REVERT: B 919 ARG cc_start: 0.7428 (ptt-90) cc_final: 0.7079 (ptt-90) REVERT: B 1084 VAL cc_start: 0.8801 (t) cc_final: 0.8424 (m) REVERT: B 1169 LEU cc_start: 0.8275 (tt) cc_final: 0.7878 (mm) REVERT: B 1225 GLN cc_start: 0.7882 (tp-100) cc_final: 0.7567 (tp-100) REVERT: B 1342 GLN cc_start: 0.7085 (pt0) cc_final: 0.6681 (mt0) REVERT: B 1505 MET cc_start: 0.8308 (mtp) cc_final: 0.8003 (mtp) REVERT: C 141 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: C 330 TYR cc_start: 0.9137 (m-80) cc_final: 0.8334 (m-80) REVERT: D 108 MET cc_start: 0.8198 (tmm) cc_final: 0.7934 (ttt) REVERT: D 158 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.6275 (m-80) REVERT: D 329 LYS cc_start: 0.6481 (tmtt) cc_final: 0.5821 (tmtt) REVERT: D 555 VAL cc_start: 0.8968 (t) cc_final: 0.8505 (m) REVERT: D 592 LEU cc_start: 0.8297 (mt) cc_final: 0.8015 (mp) REVERT: D 1169 LEU cc_start: 0.8270 (tt) cc_final: 0.7815 (mm) REVERT: D 1342 GLN cc_start: 0.7028 (pt0) cc_final: 0.6765 (mt0) REVERT: E 70 HIS cc_start: 0.8100 (m170) cc_final: 0.7876 (m-70) REVERT: E 141 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: E 330 TYR cc_start: 0.9137 (m-80) cc_final: 0.8305 (m-80) REVERT: F 108 MET cc_start: 0.8206 (tmm) cc_final: 0.7943 (ttt) REVERT: F 158 TYR cc_start: 0.6525 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: F 329 LYS cc_start: 0.6518 (tmtt) cc_final: 0.5799 (tmtt) REVERT: F 530 MET cc_start: 0.8092 (mmm) cc_final: 0.7506 (tpp) REVERT: F 555 VAL cc_start: 0.9004 (t) cc_final: 0.8526 (m) REVERT: F 592 LEU cc_start: 0.8324 (mt) cc_final: 0.8039 (mp) REVERT: F 1078 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7850 (mt) REVERT: F 1169 LEU cc_start: 0.8259 (tt) cc_final: 0.7746 (mm) REVERT: F 1505 MET cc_start: 0.8400 (mtp) cc_final: 0.8174 (mtp) REVERT: G 70 HIS cc_start: 0.8094 (m170) cc_final: 0.7880 (m-70) REVERT: G 141 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: G 330 TYR cc_start: 0.9130 (m-80) cc_final: 0.8283 (m-80) REVERT: H 108 MET cc_start: 0.8197 (tmm) cc_final: 0.7944 (ttt) REVERT: H 158 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.6254 (m-80) REVERT: H 329 LYS cc_start: 0.6485 (tmtt) cc_final: 0.5821 (tmtt) REVERT: H 550 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8133 (tt) REVERT: H 555 VAL cc_start: 0.8978 (t) cc_final: 0.8511 (m) REVERT: H 592 LEU cc_start: 0.8300 (mt) cc_final: 0.8010 (mp) REVERT: H 862 VAL cc_start: 0.8336 (t) cc_final: 0.8100 (p) REVERT: H 1169 LEU cc_start: 0.8223 (tt) cc_final: 0.7751 (mm) REVERT: H 1342 GLN cc_start: 0.7012 (pt0) cc_final: 0.6705 (mt0) outliers start: 119 outliers final: 97 residues processed: 772 average time/residue: 0.5758 time to fit residues: 718.9573 Evaluate side-chains 757 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 650 time to evaluate : 4.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1290 MET Chi-restraints excluded: chain B residue 1302 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1566 LEU Chi-restraints excluded: chain B residue 1571 ASP Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 1176 TYR Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1276 LEU Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1295 LEU Chi-restraints excluded: chain D residue 1309 LEU Chi-restraints excluded: chain D residue 1315 ILE Chi-restraints excluded: chain D residue 1566 LEU Chi-restraints excluded: chain D residue 1571 ASP Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 158 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 1078 LEU Chi-restraints excluded: chain F residue 1176 TYR Chi-restraints excluded: chain F residue 1271 SER Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1290 MET Chi-restraints excluded: chain F residue 1302 LEU Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1566 LEU Chi-restraints excluded: chain F residue 1568 SER Chi-restraints excluded: chain F residue 1571 ASP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 158 TYR Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 550 ILE Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 1176 TYR Chi-restraints excluded: chain H residue 1271 SER Chi-restraints excluded: chain H residue 1276 LEU Chi-restraints excluded: chain H residue 1290 MET Chi-restraints excluded: chain H residue 1309 LEU Chi-restraints excluded: chain H residue 1566 LEU Chi-restraints excluded: chain H residue 1571 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 405 optimal weight: 20.0000 chunk 653 optimal weight: 0.9990 chunk 398 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 454 optimal weight: 0.7980 chunk 685 optimal weight: 10.0000 chunk 630 optimal weight: 8.9990 chunk 545 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 421 optimal weight: 10.0000 chunk 334 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 279 GLN B 397 ASN B1191 GLN C 153 ASN C 173 GLN C 279 GLN D 397 ASN E 173 GLN E 279 GLN F 397 ASN G 173 GLN H 397 ASN H1296 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 55564 Z= 0.254 Angle : 0.553 9.698 75516 Z= 0.271 Chirality : 0.041 0.211 8984 Planarity : 0.004 0.044 9276 Dihedral : 7.816 108.576 7656 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 2.10 % Allowed : 14.67 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.10), residues: 6824 helix: 1.94 (0.08), residues: 4044 sheet: -0.34 (0.24), residues: 508 loop : -0.38 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1247 HIS 0.006 0.001 HIS B1541 PHE 0.023 0.001 PHE B 132 TYR 0.018 0.001 TYR B 123 ARG 0.006 0.000 ARG C 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13648 Ramachandran restraints generated. 6824 Oldfield, 0 Emsley, 6824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 653 time to evaluate : 4.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.8091 (m170) cc_final: 0.7878 (m-70) REVERT: A 141 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: A 330 TYR cc_start: 0.9145 (m-80) cc_final: 0.8329 (m-80) REVERT: B 108 MET cc_start: 0.8230 (tmm) cc_final: 0.7994 (ttt) REVERT: B 158 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.6273 (m-80) REVERT: B 329 LYS cc_start: 0.6400 (tmtt) cc_final: 0.5629 (tmtt) REVERT: B 555 VAL cc_start: 0.8988 (t) cc_final: 0.8721 (p) REVERT: B 592 LEU cc_start: 0.8306 (mt) cc_final: 0.8015 (mp) REVERT: B 919 ARG cc_start: 0.7423 (ptt-90) cc_final: 0.7061 (ptt-90) REVERT: B 1169 LEU cc_start: 0.8299 (tt) cc_final: 0.7885 (mm) REVERT: B 1225 GLN cc_start: 0.7891 (tp-100) cc_final: 0.7587 (tp-100) REVERT: B 1342 GLN cc_start: 0.7139 (pt0) cc_final: 0.6728 (mt0) REVERT: B 1505 MET cc_start: 0.8339 (mtp) cc_final: 0.8083 (mtp) REVERT: C 141 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: C 330 TYR cc_start: 0.9147 (m-80) cc_final: 0.8374 (m-80) REVERT: D 108 MET cc_start: 0.8230 (tmm) cc_final: 0.7974 (ttt) REVERT: D 158 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.6444 (m-80) REVERT: D 329 LYS cc_start: 0.6622 (tmtt) cc_final: 0.5922 (tmtt) REVERT: D 555 VAL cc_start: 0.8975 (t) cc_final: 0.8505 (m) REVERT: D 592 LEU cc_start: 0.8307 (mt) cc_final: 0.8005 (mp) REVERT: D 1169 LEU cc_start: 0.8294 (tt) cc_final: 0.7926 (mm) REVERT: D 1342 GLN cc_start: 0.7078 (pt0) cc_final: 0.6809 (mt0) REVERT: E 70 HIS cc_start: 0.8098 (m170) cc_final: 0.7878 (m-70) REVERT: E 141 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: E 330 TYR cc_start: 0.9146 (m-80) cc_final: 0.8339 (m-80) REVERT: F 108 MET cc_start: 0.8234 (tmm) cc_final: 0.8006 (ttt) REVERT: F 158 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.6313 (m-80) REVERT: F 329 LYS cc_start: 0.6594 (tmtt) cc_final: 0.5873 (tmtt) REVERT: F 530 MET cc_start: 0.8099 (mmm) cc_final: 0.7676 (tpp) REVERT: F 555 VAL cc_start: 0.9009 (t) cc_final: 0.8524 (m) REVERT: F 592 LEU cc_start: 0.8329 (mt) cc_final: 0.8037 (mp) REVERT: F 1078 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7872 (mt) REVERT: F 1169 LEU cc_start: 0.8307 (tt) cc_final: 0.7901 (mm) REVERT: F 1505 MET cc_start: 0.8421 (mtp) cc_final: 0.8202 (mtp) REVERT: G 70 HIS cc_start: 0.8101 (m170) cc_final: 0.7883 (m-70) REVERT: G 141 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: G 330 TYR cc_start: 0.9139 (m-80) cc_final: 0.8317 (m-80) REVERT: H 108 MET cc_start: 0.8221 (tmm) cc_final: 0.7982 (ttt) REVERT: H 158 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.6294 (m-80) REVERT: H 329 LYS cc_start: 0.6547 (tmtt) cc_final: 0.5836 (tmtt) REVERT: H 550 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8090 (tt) REVERT: H 555 VAL cc_start: 0.8984 (t) cc_final: 0.8510 (m) REVERT: H 592 LEU cc_start: 0.8307 (mt) cc_final: 0.8006 (mp) REVERT: H 862 VAL cc_start: 0.8284 (t) cc_final: 0.8041 (p) REVERT: H 1169 LEU cc_start: 0.8288 (tt) cc_final: 0.7918 (mm) REVERT: H 1342 GLN cc_start: 0.7062 (pt0) cc_final: 0.6738 (mt0) outliers start: 123 outliers final: 106 residues processed: 736 average time/residue: 0.5809 time to fit residues: 693.8195 Evaluate side-chains 760 residues out of total 5996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 644 time to evaluate : 4.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1276 LEU Chi-restraints excluded: chain B residue 1290 MET Chi-restraints excluded: chain B residue 1302 LEU Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1566 LEU Chi-restraints excluded: chain B residue 1571 ASP Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 581 SER Chi-restraints excluded: chain D residue 850 VAL Chi-restraints excluded: chain D residue 1176 TYR Chi-restraints excluded: chain D residue 1250 VAL Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1276 LEU Chi-restraints excluded: chain D residue 1290 MET Chi-restraints excluded: chain D residue 1295 LEU Chi-restraints excluded: chain D residue 1309 LEU Chi-restraints excluded: chain D residue 1315 ILE Chi-restraints excluded: chain D residue 1566 LEU Chi-restraints excluded: chain D residue 1571 ASP Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 158 TYR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 1078 LEU Chi-restraints excluded: chain F residue 1176 TYR Chi-restraints excluded: chain F residue 1271 SER Chi-restraints excluded: chain F residue 1276 LEU Chi-restraints excluded: chain F residue 1290 MET Chi-restraints excluded: chain F residue 1295 LEU Chi-restraints excluded: chain F residue 1302 LEU Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1566 LEU Chi-restraints excluded: chain F residue 1568 SER Chi-restraints excluded: chain F residue 1571 ASP Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 163 MET Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 26 CYS Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 158 TYR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 437 ASN Chi-restraints excluded: chain H residue 550 ILE Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 1176 TYR Chi-restraints excluded: chain H residue 1271 SER Chi-restraints excluded: chain H residue 1276 LEU Chi-restraints excluded: chain H residue 1290 MET Chi-restraints excluded: chain H residue 1309 LEU Chi-restraints excluded: chain H residue 1566 LEU Chi-restraints excluded: chain H residue 1571 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 433 optimal weight: 9.9990 chunk 581 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 503 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 546 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 561 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN D 397 ASN ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN G 173 GLN H 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.097196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.084678 restraints weight = 104526.420| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.10 r_work: 0.3070 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.292 55564 Z= 0.330 Angle : 0.726 65.900 75516 Z= 0.396 Chirality : 0.042 0.283 8984 Planarity : 0.005 0.197 9276 Dihedral : 7.818 108.581 7656 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 2.10 % Allowed : 14.72 % Favored : 83.18 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.10), residues: 6824 helix: 1.94 (0.08), residues: 4044 sheet: -0.34 (0.24), residues: 508 loop : -0.39 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1247 HIS 0.005 0.001 HIS B1541 PHE 0.018 0.001 PHE B 132 TYR 0.018 0.001 TYR B 123 ARG 0.006 0.000 ARG C 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12731.05 seconds wall clock time: 224 minutes 42.51 seconds (13482.51 seconds total)