Starting phenix.real_space_refine on Tue Aug 26 06:34:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4o_17421/08_2025/8p4o_17421.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4o_17421/08_2025/8p4o_17421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p4o_17421/08_2025/8p4o_17421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4o_17421/08_2025/8p4o_17421.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4o_17421/08_2025/8p4o_17421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4o_17421/08_2025/8p4o_17421.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.157 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 7 8.98 5 P 14 5.49 5 Mg 7 5.21 5 S 160 5.16 5 Be 7 3.05 5 C 21486 2.51 5 N 6001 2.21 5 O 6902 1.98 5 F 21 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34605 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3847 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 644 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "P" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 644 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "Q" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 644 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "R" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 644 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "S" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 644 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "T" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 644 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "U" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 644 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "1" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2892 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 360} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 7.18, per 1000 atoms: 0.21 Number of scatterers: 34605 At special positions: 0 Unit cell: (155.87, 156.96, 141.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 7 19.00 S 160 16.00 P 14 15.00 Mg 7 11.99 F 21 9.00 O 6902 8.00 N 6001 7.00 C 21486 6.00 Be 7 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8516 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 61 sheets defined 50.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 4.159A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 4.158A pdb=" N GLU A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 85 removed outlier: 3.751A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 108 removed outlier: 3.671A pdb=" N ALA A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.936A pdb=" N ILE A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.698A pdb=" N THR A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 338 through 355 removed outlier: 3.510A pdb=" N ILE A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.552A pdb=" N ARG A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 364 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 409 Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.740A pdb=" N ILE A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.507A pdb=" N ARG A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 471 removed outlier: 3.513A pdb=" N VAL A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 497 through 515 removed outlier: 3.685A pdb=" N LEU A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 64 through 85 removed outlier: 3.877A pdb=" N GLU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 110 Processing helix chain 'B' and resid 112 through 135 removed outlier: 3.534A pdb=" N GLU B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.508A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.518A pdb=" N PHE B 204 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 205 " --> pdb=" O PRO B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 205' Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 233 through 244 removed outlier: 3.640A pdb=" N ALA B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 269 removed outlier: 4.106A pdb=" N THR B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 removed outlier: 3.529A pdb=" N LYS B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.588A pdb=" N LEU B 317 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 359 through 373 removed outlier: 3.514A pdb=" N GLU B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS B 364 " --> pdb=" O TYR B 360 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 410 Processing helix chain 'B' and resid 416 through 426 removed outlier: 3.827A pdb=" N ILE B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 447 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.677A pdb=" N ARG B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 471 removed outlier: 3.536A pdb=" N VAL B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.733A pdb=" N LEU B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 29 removed outlier: 4.196A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 Processing helix chain 'C' and resid 64 through 85 removed outlier: 3.885A pdb=" N GLU C 76 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 removed outlier: 3.725A pdb=" N LEU C 116 " --> pdb=" O ASN C 112 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 129 " --> pdb=" O THR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 151 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 201 through 205 removed outlier: 4.038A pdb=" N ILE C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 255 through 268 removed outlier: 3.744A pdb=" N THR C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 297 Processing helix chain 'C' and resid 308 through 312 removed outlier: 3.544A pdb=" N LYS C 311 " --> pdb=" O GLU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 338 through 356 removed outlier: 3.853A pdb=" N GLU C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU C 355 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 373 Processing helix chain 'C' and resid 385 through 409 Processing helix chain 'C' and resid 416 through 426 removed outlier: 3.979A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 447 Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.516A pdb=" N ARG C 452 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS C 458 " --> pdb=" O ILE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 472 removed outlier: 3.595A pdb=" N VAL C 465 " --> pdb=" O GLU C 461 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 516 removed outlier: 3.740A pdb=" N LEU C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 4.148A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 58 Processing helix chain 'D' and resid 64 through 85 removed outlier: 3.999A pdb=" N GLU D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 108 Processing helix chain 'D' and resid 112 through 135 removed outlier: 3.533A pdb=" N GLU D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 233 through 244 removed outlier: 3.623A pdb=" N ALA D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 338 through 355 removed outlier: 3.770A pdb=" N GLU D 355 " --> pdb=" O GLN D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 373 removed outlier: 3.651A pdb=" N LYS D 364 " --> pdb=" O TYR D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 410 Processing helix chain 'D' and resid 416 through 425 removed outlier: 3.669A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 447 Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.505A pdb=" N CYS D 458 " --> pdb=" O ILE D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 472 Processing helix chain 'D' and resid 497 through 515 removed outlier: 3.691A pdb=" N LEU D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 28 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 52 through 58 removed outlier: 3.696A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 85 removed outlier: 3.853A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 109 Processing helix chain 'E' and resid 112 through 135 removed outlier: 3.546A pdb=" N GLU E 129 " --> pdb=" O THR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 removed outlier: 3.562A pdb=" N GLY E 159 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 233 through 244 removed outlier: 3.610A pdb=" N LEU E 237 " --> pdb=" O MET E 233 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA E 243 " --> pdb=" O ALA E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 269 removed outlier: 4.372A pdb=" N THR E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 297 removed outlier: 3.531A pdb=" N LYS E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.627A pdb=" N ILE E 305 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY E 306 " --> pdb=" O GLU E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 338 through 354 Processing helix chain 'E' and resid 358 through 373 Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 426 removed outlier: 3.832A pdb=" N ILE E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.611A pdb=" N ARG E 452 " --> pdb=" O GLU E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.740A pdb=" N LEU E 513 " --> pdb=" O SER E 509 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 52 through 58 Processing helix chain 'F' and resid 64 through 85 removed outlier: 3.921A pdb=" N GLU F 76 " --> pdb=" O GLN F 72 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 108 Processing helix chain 'F' and resid 112 through 135 removed outlier: 3.519A pdb=" N GLU F 129 " --> pdb=" O THR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 removed outlier: 3.525A pdb=" N GLY F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 205 removed outlier: 3.766A pdb=" N ILE F 205 " --> pdb=" O PRO F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 244 removed outlier: 3.576A pdb=" N LYS F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 Processing helix chain 'F' and resid 282 through 297 removed outlier: 3.581A pdb=" N LYS F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.537A pdb=" N ILE F 305 " --> pdb=" O SER F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 312 Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 338 through 355 removed outlier: 3.760A pdb=" N GLU F 355 " --> pdb=" O GLN F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 373 removed outlier: 3.560A pdb=" N LYS F 364 " --> pdb=" O TYR F 360 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU F 365 " --> pdb=" O ASP F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 410 Processing helix chain 'F' and resid 416 through 425 removed outlier: 3.795A pdb=" N ILE F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.647A pdb=" N ARG F 452 " --> pdb=" O GLU F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 471 removed outlier: 3.924A pdb=" N VAL F 465 " --> pdb=" O GLU F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 497 through 516 removed outlier: 3.710A pdb=" N LEU F 513 " --> pdb=" O SER F 509 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 28 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 52 through 58 Processing helix chain 'G' and resid 64 through 85 removed outlier: 4.104A pdb=" N GLU G 76 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 108 removed outlier: 3.638A pdb=" N ALA G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 135 removed outlier: 3.543A pdb=" N GLU G 129 " --> pdb=" O THR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 151 Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 201 through 205 removed outlier: 4.161A pdb=" N ILE G 205 " --> pdb=" O PRO G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 232 removed outlier: 3.953A pdb=" N GLU G 232 " --> pdb=" O ASN G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 229 through 232' Processing helix chain 'G' and resid 233 through 242 Processing helix chain 'G' and resid 255 through 268 removed outlier: 3.595A pdb=" N THR G 261 " --> pdb=" O GLU G 257 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU G 262 " --> pdb=" O ALA G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 297 Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 338 through 355 Processing helix chain 'G' and resid 358 through 373 Processing helix chain 'G' and resid 385 through 409 Processing helix chain 'G' and resid 416 through 425 removed outlier: 3.658A pdb=" N ILE G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 447 Processing helix chain 'G' and resid 448 through 459 removed outlier: 3.501A pdb=" N ARG G 452 " --> pdb=" O GLU G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 472 removed outlier: 3.640A pdb=" N GLY G 472 " --> pdb=" O THR G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 516 removed outlier: 3.740A pdb=" N LEU G 513 " --> pdb=" O SER G 509 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 4.281A pdb=" N ALA O 31 " --> pdb=" O THR O 28 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA O 32 " --> pdb=" O GLY O 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 28 through 32' Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.936A pdb=" N ALA P 31 " --> pdb=" O THR P 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.540A pdb=" N ALA R 31 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA R 32 " --> pdb=" O GLY R 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 28 through 32' Processing helix chain 'S' and resid 28 through 32 removed outlier: 4.249A pdb=" N ALA S 31 " --> pdb=" O THR S 28 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA S 32 " --> pdb=" O GLY S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing helix chain 'T' and resid 28 through 32 removed outlier: 4.264A pdb=" N ALA T 31 " --> pdb=" O THR T 28 " (cutoff:3.500A) Processing helix chain '1' and resid 15 through 35 Processing helix chain '1' and resid 64 through 77 removed outlier: 4.358A pdb=" N ILE 1 68 " --> pdb=" O ASP 1 64 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE 1 76 " --> pdb=" O THR 1 72 " (cutoff:3.500A) Processing helix chain '1' and resid 111 through 115 Processing helix chain '1' and resid 136 through 156 Processing helix chain '1' and resid 195 through 207 removed outlier: 3.831A pdb=" N GLU 1 201 " --> pdb=" O LYS 1 197 " (cutoff:3.500A) Processing helix chain '1' and resid 235 through 239 removed outlier: 3.568A pdb=" N ASP 1 239 " --> pdb=" O PRO 1 236 " (cutoff:3.500A) Processing helix chain '1' and resid 246 through 252 removed outlier: 3.578A pdb=" N TYR 1 252 " --> pdb=" O ILE 1 248 " (cutoff:3.500A) Processing helix chain '1' and resid 270 through 289 removed outlier: 3.655A pdb=" N SER 1 274 " --> pdb=" O LYS 1 270 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA 1 276 " --> pdb=" O ASP 1 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA 1 289 " --> pdb=" O ASN 1 285 " (cutoff:3.500A) Processing helix chain '1' and resid 322 through 334 Processing helix chain '1' and resid 339 through 346 Processing helix chain '1' and resid 351 through 356 removed outlier: 4.350A pdb=" N THR 1 355 " --> pdb=" O ILE 1 351 " (cutoff:3.500A) Processing helix chain '1' and resid 366 through 370 removed outlier: 3.787A pdb=" N LYS 1 370 " --> pdb=" O PRO 1 367 " (cutoff:3.500A) Processing helix chain '1' and resid 373 through 382 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 4.961A pdb=" N THR A 517 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL B 39 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N CYS A 519 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 7.779A pdb=" N ASN A 37 " --> pdb=" O GLU G 518 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET G 520 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A 39 " --> pdb=" O MET G 520 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR G 522 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 179 removed outlier: 3.698A pdb=" N VAL A 174 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 186 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195 removed outlier: 3.715A pdb=" N ARG A 322 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 193 through 195 removed outlier: 3.715A pdb=" N ARG A 322 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.102A pdb=" N ASN C 37 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS B 519 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.346A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 376 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.602A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 325 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.602A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AB4, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB5, first strand: chain 'C' and resid 4 through 8 removed outlier: 5.235A pdb=" N THR C 517 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL D 39 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N CYS C 519 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 174 through 179 removed outlier: 6.272A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU C 178 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 195 removed outlier: 4.248A pdb=" N MET C 193 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 332 " --> pdb=" O MET C 193 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 193 through 195 removed outlier: 4.248A pdb=" N MET C 193 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 332 " --> pdb=" O MET C 193 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU C 247 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC1, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 8 removed outlier: 7.388A pdb=" N VAL E 39 " --> pdb=" O GLU D 518 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N MET D 520 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 173 through 179 removed outlier: 6.298A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL D 376 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 193 through 195 Processing sheet with id=AC5, first strand: chain 'D' and resid 273 through 276 Processing sheet with id=AC6, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AC7, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AC8, first strand: chain 'E' and resid 4 through 8 removed outlier: 4.993A pdb=" N THR E 517 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL F 39 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS E 519 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 174 through 179 removed outlier: 3.709A pdb=" N VAL E 174 " --> pdb=" O GLY E 375 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 193 through 195 removed outlier: 3.754A pdb=" N MET E 193 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 193 through 195 removed outlier: 3.754A pdb=" N MET E 193 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU E 247 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD4, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AD5, first strand: chain 'F' and resid 4 through 8 removed outlier: 4.989A pdb=" N THR F 517 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL G 39 " --> pdb=" O THR F 517 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS F 519 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 174 through 179 removed outlier: 6.320A pdb=" N VAL F 174 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE F 379 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU F 178 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 193 through 195 removed outlier: 3.634A pdb=" N MET F 193 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG F 322 " --> pdb=" O ILE F 333 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 273 through 277 removed outlier: 6.261A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ILE F 301 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU F 222 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 273 through 277 removed outlier: 6.261A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE2, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AE3, first strand: chain 'G' and resid 174 through 179 removed outlier: 6.317A pdb=" N VAL G 174 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE G 379 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR G 176 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL G 381 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU G 178 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 193 through 195 removed outlier: 3.553A pdb=" N MET G 193 " --> pdb=" O ILE G 332 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG G 322 " --> pdb=" O ILE G 333 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 213 through 216 removed outlier: 8.449A pdb=" N ILE G 301 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU G 222 " --> pdb=" O ILE G 301 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AE7, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AE8, first strand: chain 'O' and resid 3 through 5 removed outlier: 6.576A pdb=" N ILE U 66 " --> pdb=" O LEU U 92 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE U 94 " --> pdb=" O ILE U 64 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE U 64 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE U 11 " --> pdb=" O LEU U 41 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N VAL U 43 " --> pdb=" O ARG U 9 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG U 9 " --> pdb=" O VAL U 43 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG U 14 " --> pdb=" O GLU U 82 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N GLU U 82 " --> pdb=" O ARG U 14 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 74 through 78 removed outlier: 8.435A pdb=" N GLU O 82 " --> pdb=" O ARG O 14 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ARG O 14 " --> pdb=" O GLU O 82 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE O 11 " --> pdb=" O LEU O 41 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE O 64 " --> pdb=" O VAL O 95 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 47 through 48 Processing sheet with id=AF2, first strand: chain 'P' and resid 74 through 78 removed outlier: 8.859A pdb=" N GLU P 82 " --> pdb=" O ARG P 14 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG P 14 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG P 9 " --> pdb=" O VAL P 43 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL P 43 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE P 11 " --> pdb=" O LEU P 41 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE P 64 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE P 94 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE P 66 " --> pdb=" O LEU P 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 47 through 48 Processing sheet with id=AF4, first strand: chain 'Q' and resid 74 through 78 removed outlier: 8.528A pdb=" N GLU Q 82 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG Q 14 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ARG Q 9 " --> pdb=" O VAL Q 43 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL Q 43 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE Q 11 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE Q 64 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE Q 94 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE Q 66 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 47 through 48 Processing sheet with id=AF6, first strand: chain 'R' and resid 74 through 78 removed outlier: 8.489A pdb=" N GLU R 82 " --> pdb=" O ARG R 14 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ARG R 14 " --> pdb=" O GLU R 82 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ARG R 9 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL R 43 " --> pdb=" O ARG R 9 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE R 11 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE R 64 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE R 94 " --> pdb=" O ILE R 64 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE R 66 " --> pdb=" O LEU R 92 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 47 through 48 Processing sheet with id=AF8, first strand: chain 'S' and resid 74 through 78 removed outlier: 3.501A pdb=" N ILE S 78 " --> pdb=" O GLU S 81 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU S 82 " --> pdb=" O ARG S 14 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ARG S 14 " --> pdb=" O GLU S 82 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ARG S 9 " --> pdb=" O VAL S 43 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL S 43 " --> pdb=" O ARG S 9 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE S 11 " --> pdb=" O LEU S 41 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE S 64 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE S 94 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE S 66 " --> pdb=" O LEU S 92 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 47 through 48 removed outlier: 3.522A pdb=" N ARG S 47 " --> pdb=" O LYS S 55 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 74 through 78 removed outlier: 8.455A pdb=" N GLU T 82 " --> pdb=" O ARG T 14 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG T 14 " --> pdb=" O GLU T 82 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG T 9 " --> pdb=" O VAL T 43 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL T 43 " --> pdb=" O ARG T 9 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE T 11 " --> pdb=" O LEU T 41 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE T 64 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA T 93 " --> pdb=" O ILE T 66 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 47 through 48 Processing sheet with id=AG3, first strand: chain 'U' and resid 47 through 48 Processing sheet with id=AG4, first strand: chain '1' and resid 5 through 11 removed outlier: 5.696A pdb=" N ASP 1 164 " --> pdb=" O GLN 1 189 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA 1 183 " --> pdb=" O THR 1 170 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN 1 172 " --> pdb=" O ILE 1 181 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE 1 181 " --> pdb=" O GLN 1 172 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASP 1 174 " --> pdb=" O VAL 1 179 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL 1 179 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N LYS 1 222 " --> pdb=" O GLY 1 180 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP 1 182 " --> pdb=" O LYS 1 222 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N PHE 1 224 " --> pdb=" O ASP 1 182 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL 1 184 " --> pdb=" O PHE 1 224 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '1' and resid 91 through 97 removed outlier: 6.565A pdb=" N VAL 1 51 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA 1 95 " --> pdb=" O VAL 1 51 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL 1 53 " --> pdb=" O ALA 1 95 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY 1 97 " --> pdb=" O VAL 1 53 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY 1 55 " --> pdb=" O GLY 1 97 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '1' and resid 121 through 124 removed outlier: 3.501A pdb=" N ALA 1 127 " --> pdb=" O CYS 1 295 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain '1' and resid 121 through 124 2045 hydrogen bonds defined for protein. 5799 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: 6.75 Time building geometry restraints manager: 2.95 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: 11905 1.34 - 1.46: 3137 1.46 - 1.57: 19495 1.57 - 1.69: 21 1.69 - 1.81: 295 Bond restraints: 34853 Sorted by residual: bond pdb=" F2 BEF D1602 " pdb="BE BEF D1602 " ideal model delta sigma weight residual 1.476 1.539 -0.063 2.00e-02 2.50e+03 9.79e+00 bond pdb=" F2 BEF A1602 " pdb="BE BEF A1602 " ideal model delta sigma weight residual 1.476 1.538 -0.062 2.00e-02 2.50e+03 9.61e+00 bond pdb=" F2 BEF F1602 " pdb="BE BEF F1602 " ideal model delta sigma weight residual 1.476 1.538 -0.062 2.00e-02 2.50e+03 9.50e+00 bond pdb=" F2 BEF E1602 " pdb="BE BEF E1602 " ideal model delta sigma weight residual 1.476 1.537 -0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" F2 BEF G1602 " pdb="BE BEF G1602 " ideal model delta sigma weight residual 1.476 1.537 -0.061 2.00e-02 2.50e+03 9.40e+00 ... (remaining 34848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 46739 2.27 - 4.54: 338 4.54 - 6.81: 77 6.81 - 9.08: 3 9.08 - 11.35: 21 Bond angle restraints: 47178 Sorted by residual: angle pdb=" N ILE C 305 " pdb=" CA ILE C 305 " pdb=" C ILE C 305 " ideal model delta sigma weight residual 111.91 107.72 4.19 8.90e-01 1.26e+00 2.22e+01 angle pdb=" F1 BEF C1602 " pdb="BE BEF C1602 " pdb=" F3 BEF C1602 " ideal model delta sigma weight residual 120.12 108.77 11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" F2 BEF D1602 " pdb="BE BEF D1602 " pdb=" F3 BEF D1602 " ideal model delta sigma weight residual 119.96 108.68 11.28 3.00e+00 1.11e-01 1.41e+01 angle pdb=" F1 BEF E1602 " pdb="BE BEF E1602 " pdb=" F3 BEF E1602 " ideal model delta sigma weight residual 120.12 108.85 11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" F2 BEF B1602 " pdb="BE BEF B1602 " pdb=" F3 BEF B1602 " ideal model delta sigma weight residual 119.96 108.72 11.24 3.00e+00 1.11e-01 1.40e+01 ... (remaining 47173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 21024 35.80 - 71.60: 348 71.60 - 107.40: 41 107.40 - 143.20: 4 143.20 - 179.00: 7 Dihedral angle restraints: 21424 sinusoidal: 8150 harmonic: 13274 Sorted by residual: dihedral pdb=" O1B ADP C1600 " pdb=" O3A ADP C1600 " pdb=" PB ADP C1600 " pdb=" PA ADP C1600 " ideal model delta sinusoidal sigma weight residual -60.00 119.00 -179.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP G1600 " pdb=" O3A ADP G1600 " pdb=" PB ADP G1600 " pdb=" PA ADP G1600 " ideal model delta sinusoidal sigma weight residual -60.00 107.98 -167.98 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O1B ADP B1600 " pdb=" O3A ADP B1600 " pdb=" PB ADP B1600 " pdb=" PA ADP B1600 " ideal model delta sinusoidal sigma weight residual -60.00 105.68 -165.68 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 21421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3697 0.030 - 0.060: 1225 0.060 - 0.091: 510 0.091 - 0.121: 318 0.121 - 0.151: 21 Chirality restraints: 5771 Sorted by residual: chirality pdb=" CA GLU F 102 " pdb=" N GLU F 102 " pdb=" C GLU F 102 " pdb=" CB GLU F 102 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE S 85 " pdb=" N ILE S 85 " pdb=" C ILE S 85 " pdb=" CB ILE S 85 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ASP 1 346 " pdb=" N ASP 1 346 " pdb=" C ASP 1 346 " pdb=" CB ASP 1 346 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 5768 not shown) Planarity restraints: 6132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 201 " -0.051 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO D 202 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 202 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 202 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET 1 135 " -0.033 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO 1 136 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO 1 136 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO 1 136 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 98 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C ALA F 98 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA F 98 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE F 99 " 0.011 2.00e-02 2.50e+03 ... (remaining 6129 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.11: 32 2.11 - 2.87: 12010 2.87 - 3.62: 55511 3.62 - 4.38: 90652 4.38 - 5.14: 166950 Nonbonded interactions: 325155 Sorted by model distance: nonbonded pdb=" O3B ADP G1600 " pdb=" F3 BEF G1602 " model vdw 1.349 2.990 nonbonded pdb=" O3B ADP G1600 " pdb="BE BEF G1602 " model vdw 1.400 2.420 nonbonded pdb="MG MG D1601 " pdb=" O HOH D1701 " model vdw 1.974 2.170 nonbonded pdb="MG MG F1601 " pdb=" O HOH F1701 " model vdw 1.977 2.170 nonbonded pdb=" OD1 ASP D 87 " pdb="MG MG D1601 " model vdw 1.981 2.170 ... (remaining 325150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 338 or (resid 339 through 341 and (name N or nam \ e CA or name C or name O or name CB )) or resid 342 through 1603)) selection = (chain 'B' and (resid 2 through 338 or (resid 339 through 341 and (name N or nam \ e CA or name C or name O or name CB )) or resid 342 through 1603)) selection = chain 'C' selection = (chain 'D' and (resid 2 through 338 or (resid 339 through 341 and (name N or nam \ e CA or name C or name O or name CB )) or resid 342 through 1603)) selection = (chain 'E' and (resid 2 through 338 or (resid 339 through 341 and (name N or nam \ e CA or name C or name O or name CB )) or resid 342 through 1603)) selection = (chain 'F' and (resid 2 through 338 or (resid 339 through 341 and (name N or nam \ e CA or name C or name O or name CB )) or resid 342 through 1603)) selection = (chain 'G' and (resid 2 through 338 or (resid 339 through 341 and (name N or nam \ e CA or name C or name O or name CB )) or resid 342 through 1603)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 1.190 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 28.640 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.012 0.901 34859 Z= 1.188 Angle : 0.570 11.354 47178 Z= 0.283 Chirality : 0.041 0.151 5771 Planarity : 0.003 0.077 6132 Dihedral : 14.860 179.003 12908 Min Nonbonded Distance : 1.349 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.06 % Allowed : 0.22 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.12), residues: 4682 helix: 2.04 (0.11), residues: 2138 sheet: 1.30 (0.20), residues: 701 loop : -0.24 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 362 TYR 0.019 0.001 TYR E 203 PHE 0.015 0.001 PHE B 44 TRP 0.017 0.002 TRP 1 62 HIS 0.004 0.001 HIS 1 15 Details of bonding type rmsd covalent geometry : bond 0.00267 (34853) covalent geometry : angle 0.56959 (47178) hydrogen bonds : bond 0.17174 ( 2007) hydrogen bonds : angle 5.75517 ( 5799) Misc. bond : bond 0.89986 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 468 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 288 MET cc_start: 0.7847 (ptt) cc_final: 0.7340 (ptt) REVERT: C 111 MET cc_start: 0.7548 (mtt) cc_final: 0.7317 (mtt) REVERT: D 291 ASP cc_start: 0.7093 (m-30) cc_final: 0.6793 (m-30) REVERT: D 389 MET cc_start: 0.7072 (tpp) cc_final: 0.6687 (tpp) REVERT: E 272 LYS cc_start: 0.7778 (mppt) cc_final: 0.7569 (mttm) REVERT: P 88 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7753 (tm-30) REVERT: S 3 ILE cc_start: 0.8015 (pt) cc_final: 0.7654 (pt) REVERT: S 68 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7454 (p0) REVERT: U 28 THR cc_start: 0.7200 (p) cc_final: 0.6501 (t) REVERT: U 58 ASP cc_start: 0.7606 (m-30) cc_final: 0.7394 (t0) REVERT: 1 21 ASP cc_start: 0.7246 (m-30) cc_final: 0.6967 (t0) REVERT: 1 368 TRP cc_start: 0.8061 (p90) cc_final: 0.7514 (p90) outliers start: 2 outliers final: 0 residues processed: 469 average time/residue: 0.1705 time to fit residues: 133.3923 Evaluate side-chains 363 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 362 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 68 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 9.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN B 37 ASN F 37 ASN F 453 GLN G 37 ASN P 7 HIS P 45 ASN S 68 ASN 1 143 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.166451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123987 restraints weight = 43321.581| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.21 r_work: 0.3324 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 34859 Z= 0.154 Angle : 0.556 8.108 47178 Z= 0.287 Chirality : 0.044 0.169 5771 Planarity : 0.004 0.055 6132 Dihedral : 8.317 167.851 5036 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.07 % Allowed : 7.76 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.12), residues: 4682 helix: 2.06 (0.11), residues: 2159 sheet: 0.92 (0.19), residues: 690 loop : -0.21 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 1 273 TYR 0.014 0.001 TYR E 360 PHE 0.018 0.001 PHE G 195 TRP 0.025 0.002 TRP 1 160 HIS 0.005 0.001 HIS 1 365 Details of bonding type rmsd covalent geometry : bond 0.00357 (34853) covalent geometry : angle 0.55607 (47178) hydrogen bonds : bond 0.05314 ( 2007) hydrogen bonds : angle 4.35168 ( 5799) Misc. bond : bond 0.00251 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 388 time to evaluate : 1.443 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7529 (t0) REVERT: A 307 MET cc_start: 0.6962 (mtp) cc_final: 0.6584 (mtm) REVERT: B 229 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6289 (p0) REVERT: B 288 MET cc_start: 0.7858 (ptt) cc_final: 0.7124 (ptt) REVERT: B 291 ASP cc_start: 0.6220 (m-30) cc_final: 0.5878 (m-30) REVERT: C 111 MET cc_start: 0.8237 (mtt) cc_final: 0.7943 (mtt) REVERT: D 389 MET cc_start: 0.7965 (tpp) cc_final: 0.7685 (tpp) REVERT: E 272 LYS cc_start: 0.7952 (mppt) cc_final: 0.7708 (mttm) REVERT: P 88 GLU cc_start: 0.8697 (tm-30) cc_final: 0.7898 (tm-30) REVERT: S 3 ILE cc_start: 0.7984 (pt) cc_final: 0.7503 (pt) REVERT: U 58 ASP cc_start: 0.7906 (m-30) cc_final: 0.7635 (t0) REVERT: 1 21 ASP cc_start: 0.7717 (m-30) cc_final: 0.6903 (t0) REVERT: 1 368 TRP cc_start: 0.7676 (p90) cc_final: 0.7078 (p90) outliers start: 38 outliers final: 29 residues processed: 409 average time/residue: 0.1844 time to fit residues: 124.8237 Evaluate side-chains 387 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 356 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain E residue 203 TYR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 13 LYS Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain 1 residue 135 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 225 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 348 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 389 optimal weight: 0.7980 chunk 338 optimal weight: 0.9990 chunk 162 optimal weight: 0.0170 chunk 156 optimal weight: 6.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 ASN 1 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.167200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124810 restraints weight = 43038.594| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.18 r_work: 0.3341 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34859 Z= 0.120 Angle : 0.509 7.708 47178 Z= 0.261 Chirality : 0.042 0.161 5771 Planarity : 0.003 0.054 6132 Dihedral : 8.163 158.852 5034 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.18 % Allowed : 10.48 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.12), residues: 4682 helix: 2.13 (0.11), residues: 2208 sheet: 0.92 (0.19), residues: 690 loop : -0.15 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 273 TYR 0.010 0.001 TYR F 478 PHE 0.017 0.001 PHE G 195 TRP 0.030 0.002 TRP 1 160 HIS 0.004 0.001 HIS 1 365 Details of bonding type rmsd covalent geometry : bond 0.00272 (34853) covalent geometry : angle 0.50947 (47178) hydrogen bonds : bond 0.04612 ( 2007) hydrogen bonds : angle 4.02859 ( 5799) Misc. bond : bond 0.00059 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 382 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7565 (t0) REVERT: A 520 MET cc_start: 0.8648 (mtt) cc_final: 0.8422 (mtm) REVERT: B 229 ASN cc_start: 0.7114 (OUTLIER) cc_final: 0.6230 (p0) REVERT: B 288 MET cc_start: 0.7823 (ptt) cc_final: 0.7172 (ptm) REVERT: B 291 ASP cc_start: 0.6316 (m-30) cc_final: 0.5963 (m-30) REVERT: C 111 MET cc_start: 0.8180 (mtt) cc_final: 0.7888 (mtt) REVERT: D 389 MET cc_start: 0.7936 (tpp) cc_final: 0.7619 (tpp) REVERT: D 495 ASP cc_start: 0.8147 (t70) cc_final: 0.7899 (t70) REVERT: E 367 GLU cc_start: 0.8183 (pp20) cc_final: 0.7865 (pp20) REVERT: F 321 LYS cc_start: 0.8225 (mptt) cc_final: 0.8017 (mmmm) REVERT: P 88 GLU cc_start: 0.8670 (tm-30) cc_final: 0.7845 (tm-30) REVERT: S 3 ILE cc_start: 0.8019 (pt) cc_final: 0.7519 (pt) REVERT: U 58 ASP cc_start: 0.7905 (m-30) cc_final: 0.7636 (t0) REVERT: U 88 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7697 (tm-30) REVERT: 1 21 ASP cc_start: 0.7914 (m-30) cc_final: 0.7085 (t0) REVERT: 1 204 MET cc_start: 0.7525 (ttp) cc_final: 0.7025 (tpp) REVERT: 1 368 TRP cc_start: 0.7722 (p90) cc_final: 0.7088 (p90) outliers start: 42 outliers final: 30 residues processed: 409 average time/residue: 0.1820 time to fit residues: 123.2743 Evaluate side-chains 386 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 354 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 27 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 96 optimal weight: 3.9990 chunk 426 optimal weight: 10.0000 chunk 332 optimal weight: 0.0370 chunk 308 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 271 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 177 optimal weight: 0.5980 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 45 ASN 1 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.167508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.125422 restraints weight = 42979.531| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.20 r_work: 0.3347 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34859 Z= 0.112 Angle : 0.495 7.609 47178 Z= 0.252 Chirality : 0.042 0.176 5771 Planarity : 0.003 0.054 6132 Dihedral : 8.033 158.533 5034 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.71 % Allowed : 11.83 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.12), residues: 4682 helix: 2.23 (0.11), residues: 2208 sheet: 1.06 (0.20), residues: 648 loop : -0.15 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 9 TYR 0.009 0.001 TYR F 478 PHE 0.014 0.001 PHE G 195 TRP 0.035 0.002 TRP 1 160 HIS 0.004 0.000 HIS 1 365 Details of bonding type rmsd covalent geometry : bond 0.00251 (34853) covalent geometry : angle 0.49451 (47178) hydrogen bonds : bond 0.04277 ( 2007) hydrogen bonds : angle 3.85955 ( 5799) Misc. bond : bond 0.00024 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 373 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7548 (t0) REVERT: A 290 GLN cc_start: 0.7885 (tp-100) cc_final: 0.7591 (mm-40) REVERT: B 229 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6182 (p0) REVERT: B 288 MET cc_start: 0.7866 (ptt) cc_final: 0.7250 (ptm) REVERT: B 291 ASP cc_start: 0.6338 (m-30) cc_final: 0.5959 (m-30) REVERT: C 111 MET cc_start: 0.8184 (mtt) cc_final: 0.7890 (mtt) REVERT: D 273 VAL cc_start: 0.8982 (m) cc_final: 0.8763 (p) REVERT: D 288 MET cc_start: 0.7483 (mtt) cc_final: 0.7082 (mmt) REVERT: D 389 MET cc_start: 0.7919 (tpp) cc_final: 0.7654 (tpp) REVERT: D 495 ASP cc_start: 0.8165 (t70) cc_final: 0.7901 (t70) REVERT: E 288 MET cc_start: 0.7685 (mtp) cc_final: 0.7154 (mtt) REVERT: E 367 GLU cc_start: 0.8018 (pp20) cc_final: 0.7753 (pp20) REVERT: F 321 LYS cc_start: 0.8279 (mptt) cc_final: 0.8031 (mmmm) REVERT: P 88 GLU cc_start: 0.8612 (tm-30) cc_final: 0.7741 (tm-30) REVERT: S 3 ILE cc_start: 0.8034 (pt) cc_final: 0.7514 (pt) REVERT: S 19 THR cc_start: 0.6886 (p) cc_final: 0.6633 (p) REVERT: U 58 ASP cc_start: 0.7885 (m-30) cc_final: 0.7636 (t0) REVERT: U 88 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7709 (tm-30) REVERT: 1 21 ASP cc_start: 0.7919 (m-30) cc_final: 0.7008 (t0) REVERT: 1 25 ASP cc_start: 0.7618 (m-30) cc_final: 0.7267 (m-30) REVERT: 1 31 ILE cc_start: 0.7291 (mm) cc_final: 0.6862 (tp) REVERT: 1 204 MET cc_start: 0.7544 (ttp) cc_final: 0.7057 (tpp) REVERT: 1 285 ASN cc_start: 0.7440 (m-40) cc_final: 0.6896 (m110) REVERT: 1 368 TRP cc_start: 0.7679 (p90) cc_final: 0.7004 (p90) outliers start: 61 outliers final: 48 residues processed: 416 average time/residue: 0.1797 time to fit residues: 124.1111 Evaluate side-chains 401 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 351 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 86 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 326 optimal weight: 2.9990 chunk 435 optimal weight: 40.0000 chunk 138 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 chunk 396 optimal weight: 0.0570 chunk 137 optimal weight: 9.9990 chunk 236 optimal weight: 0.9980 chunk 460 optimal weight: 7.9990 chunk 290 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 overall best weight: 2.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 505 GLN 1 15 HIS 1 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.165040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121735 restraints weight = 43209.639| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.21 r_work: 0.3308 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 34859 Z= 0.152 Angle : 0.525 6.792 47178 Z= 0.268 Chirality : 0.044 0.166 5771 Planarity : 0.003 0.052 6132 Dihedral : 7.983 159.239 5034 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.30 % Allowed : 13.21 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.12), residues: 4682 helix: 2.09 (0.11), residues: 2208 sheet: 1.00 (0.20), residues: 648 loop : -0.18 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 37 TYR 0.011 0.001 TYR C 476 PHE 0.017 0.001 PHE G 195 TRP 0.036 0.003 TRP 1 160 HIS 0.003 0.001 HIS 1 365 Details of bonding type rmsd covalent geometry : bond 0.00367 (34853) covalent geometry : angle 0.52493 (47178) hydrogen bonds : bond 0.05090 ( 2007) hydrogen bonds : angle 3.88435 ( 5799) Misc. bond : bond 0.00036 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 368 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 GLN cc_start: 0.7985 (tp-100) cc_final: 0.7656 (mm-40) REVERT: B 229 ASN cc_start: 0.7113 (OUTLIER) cc_final: 0.6138 (p0) REVERT: B 288 MET cc_start: 0.7856 (ptt) cc_final: 0.7307 (ptm) REVERT: B 291 ASP cc_start: 0.6373 (m-30) cc_final: 0.5986 (m-30) REVERT: C 111 MET cc_start: 0.8211 (mtt) cc_final: 0.7918 (mtt) REVERT: C 286 LYS cc_start: 0.7682 (mmtt) cc_final: 0.7461 (mmmm) REVERT: C 343 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.6767 (mt0) REVERT: D 203 TYR cc_start: 0.7474 (m-80) cc_final: 0.7242 (m-80) REVERT: D 273 VAL cc_start: 0.9045 (m) cc_final: 0.8825 (p) REVERT: D 288 MET cc_start: 0.7456 (mtt) cc_final: 0.7090 (mmt) REVERT: D 389 MET cc_start: 0.7894 (tpp) cc_final: 0.7636 (tpp) REVERT: E 288 MET cc_start: 0.7670 (mtp) cc_final: 0.7009 (mtt) REVERT: E 292 ILE cc_start: 0.7923 (tt) cc_final: 0.7682 (mt) REVERT: F 321 LYS cc_start: 0.8309 (mptt) cc_final: 0.8037 (mmmm) REVERT: O 37 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7852 (mtt90) REVERT: P 88 GLU cc_start: 0.8632 (tm-30) cc_final: 0.7742 (tm-30) REVERT: R 86 MET cc_start: 0.8287 (ptt) cc_final: 0.7843 (ptt) REVERT: S 19 THR cc_start: 0.6978 (p) cc_final: 0.6747 (p) REVERT: U 58 ASP cc_start: 0.7887 (m-30) cc_final: 0.7645 (t0) REVERT: U 88 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7666 (tm-30) REVERT: 1 21 ASP cc_start: 0.8177 (m-30) cc_final: 0.7126 (t0) REVERT: 1 25 ASP cc_start: 0.7653 (m-30) cc_final: 0.7317 (m-30) REVERT: 1 204 MET cc_start: 0.7620 (ttp) cc_final: 0.7177 (tpp) REVERT: 1 285 ASN cc_start: 0.7329 (m-40) cc_final: 0.7123 (m110) REVERT: 1 368 TRP cc_start: 0.7719 (p90) cc_final: 0.7087 (p90) outliers start: 82 outliers final: 60 residues processed: 428 average time/residue: 0.1833 time to fit residues: 129.5978 Evaluate side-chains 418 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 356 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 514 MET Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain 1 residue 15 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 377 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 454 optimal weight: 9.9990 chunk 445 optimal weight: 20.0000 chunk 300 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 335 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 259 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN D 37 ASN G 343 GLN G 351 GLN 1 15 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.166266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.123046 restraints weight = 43032.451| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.23 r_work: 0.3320 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34859 Z= 0.117 Angle : 0.496 6.646 47178 Z= 0.253 Chirality : 0.042 0.160 5771 Planarity : 0.003 0.051 6132 Dihedral : 7.906 157.870 5034 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.36 % Allowed : 13.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.12), residues: 4682 helix: 2.21 (0.11), residues: 2208 sheet: 0.99 (0.20), residues: 646 loop : -0.14 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 37 TYR 0.009 0.001 TYR C 478 PHE 0.014 0.001 PHE G 195 TRP 0.033 0.002 TRP 1 160 HIS 0.020 0.001 HIS 1 15 Details of bonding type rmsd covalent geometry : bond 0.00266 (34853) covalent geometry : angle 0.49556 (47178) hydrogen bonds : bond 0.04442 ( 2007) hydrogen bonds : angle 3.79378 ( 5799) Misc. bond : bond 0.00018 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 363 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 GLN cc_start: 0.7956 (tp-100) cc_final: 0.7607 (mm-40) REVERT: B 229 ASN cc_start: 0.7120 (OUTLIER) cc_final: 0.6127 (p0) REVERT: B 288 MET cc_start: 0.7783 (ptt) cc_final: 0.7273 (ptm) REVERT: B 291 ASP cc_start: 0.6360 (m-30) cc_final: 0.5985 (m-30) REVERT: B 366 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6398 (mt0) REVERT: C 69 MET cc_start: 0.8202 (mtt) cc_final: 0.7957 (mtt) REVERT: C 111 MET cc_start: 0.8191 (mtt) cc_final: 0.7921 (mtt) REVERT: C 286 LYS cc_start: 0.7672 (mmtt) cc_final: 0.7467 (mmmm) REVERT: D 288 MET cc_start: 0.7435 (mtt) cc_final: 0.7116 (mmt) REVERT: D 389 MET cc_start: 0.7861 (tpp) cc_final: 0.7627 (tpp) REVERT: D 495 ASP cc_start: 0.8120 (t70) cc_final: 0.7870 (m-30) REVERT: E 288 MET cc_start: 0.7655 (mtp) cc_final: 0.6996 (mtt) REVERT: E 292 ILE cc_start: 0.7871 (tt) cc_final: 0.7643 (mt) REVERT: F 321 LYS cc_start: 0.8316 (mptt) cc_final: 0.8014 (mmmm) REVERT: O 37 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7874 (mtt90) REVERT: P 88 GLU cc_start: 0.8651 (tm-30) cc_final: 0.7756 (tm-30) REVERT: R 86 MET cc_start: 0.8273 (ptt) cc_final: 0.7760 (ptt) REVERT: S 19 THR cc_start: 0.7037 (p) cc_final: 0.6809 (p) REVERT: U 58 ASP cc_start: 0.7885 (m-30) cc_final: 0.7644 (t0) REVERT: U 88 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7660 (tm-30) REVERT: 1 21 ASP cc_start: 0.8140 (m-30) cc_final: 0.7109 (t0) REVERT: 1 25 ASP cc_start: 0.7734 (m-30) cc_final: 0.7403 (m-30) REVERT: 1 31 ILE cc_start: 0.7350 (mm) cc_final: 0.6896 (tp) REVERT: 1 204 MET cc_start: 0.7613 (ttp) cc_final: 0.7193 (tpp) REVERT: 1 368 TRP cc_start: 0.7712 (p90) cc_final: 0.7074 (p90) outliers start: 84 outliers final: 65 residues processed: 427 average time/residue: 0.2079 time to fit residues: 147.1525 Evaluate side-chains 415 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 348 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 360 TYR Chi-restraints excluded: chain G residue 514 MET Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain 1 residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 91 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 402 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 358 optimal weight: 0.4980 chunk 390 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 310 optimal weight: 0.9990 chunk 454 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 351 GLN 1 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.166206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.123332 restraints weight = 43209.504| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.11 r_work: 0.3334 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34859 Z= 0.123 Angle : 0.502 9.292 47178 Z= 0.255 Chirality : 0.043 0.186 5771 Planarity : 0.003 0.051 6132 Dihedral : 7.869 158.382 5034 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.39 % Allowed : 14.25 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.12), residues: 4682 helix: 2.21 (0.11), residues: 2208 sheet: 0.96 (0.20), residues: 648 loop : -0.13 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 37 TYR 0.010 0.001 TYR C 476 PHE 0.032 0.001 PHE F 281 TRP 0.024 0.002 TRP 1 160 HIS 0.003 0.000 HIS 1 365 Details of bonding type rmsd covalent geometry : bond 0.00287 (34853) covalent geometry : angle 0.50227 (47178) hydrogen bonds : bond 0.04470 ( 2007) hydrogen bonds : angle 3.77153 ( 5799) Misc. bond : bond 0.00014 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 356 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 229 ASN cc_start: 0.7014 (OUTLIER) cc_final: 0.6025 (p0) REVERT: B 288 MET cc_start: 0.7646 (ptt) cc_final: 0.7224 (ptm) REVERT: B 291 ASP cc_start: 0.6166 (m-30) cc_final: 0.5786 (m-30) REVERT: B 366 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6061 (mt0) REVERT: C 69 MET cc_start: 0.7997 (mtt) cc_final: 0.7778 (mtt) REVERT: C 111 MET cc_start: 0.8235 (mtt) cc_final: 0.7919 (mtt) REVERT: C 307 MET cc_start: 0.6032 (tpt) cc_final: 0.5651 (mmm) REVERT: D 203 TYR cc_start: 0.7430 (m-80) cc_final: 0.7176 (m-80) REVERT: D 288 MET cc_start: 0.7337 (mtt) cc_final: 0.7011 (mmt) REVERT: D 389 MET cc_start: 0.7760 (tpp) cc_final: 0.7547 (tpp) REVERT: D 495 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7888 (t70) REVERT: E 288 MET cc_start: 0.7461 (mtp) cc_final: 0.6783 (mtt) REVERT: E 292 ILE cc_start: 0.7581 (tt) cc_final: 0.7366 (mt) REVERT: O 37 ARG cc_start: 0.8028 (mtt-85) cc_final: 0.7741 (mtt90) REVERT: P 88 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7576 (tm-30) REVERT: R 86 MET cc_start: 0.8150 (ptt) cc_final: 0.7686 (ptt) REVERT: S 19 THR cc_start: 0.6917 (p) cc_final: 0.6705 (p) REVERT: U 58 ASP cc_start: 0.7888 (m-30) cc_final: 0.7519 (t0) REVERT: U 88 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7554 (tm-30) REVERT: 1 21 ASP cc_start: 0.8127 (m-30) cc_final: 0.7055 (t0) REVERT: 1 25 ASP cc_start: 0.7735 (m-30) cc_final: 0.7367 (m-30) REVERT: 1 31 ILE cc_start: 0.7353 (mm) cc_final: 0.6900 (tp) REVERT: 1 204 MET cc_start: 0.7499 (ttp) cc_final: 0.7063 (tpp) REVERT: 1 285 ASN cc_start: 0.7416 (m-40) cc_final: 0.6947 (m110) REVERT: 1 368 TRP cc_start: 0.7624 (p90) cc_final: 0.6991 (p90) outliers start: 85 outliers final: 71 residues processed: 422 average time/residue: 0.2195 time to fit residues: 153.3892 Evaluate side-chains 421 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 347 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 360 TYR Chi-restraints excluded: chain G residue 514 MET Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain 1 residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 428 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 459 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 371 optimal weight: 0.4980 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.161908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118462 restraints weight = 43374.633| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.12 r_work: 0.3298 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 34859 Z= 0.232 Angle : 0.602 9.821 47178 Z= 0.307 Chirality : 0.047 0.189 5771 Planarity : 0.004 0.051 6132 Dihedral : 8.123 165.095 5034 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.47 % Allowed : 14.56 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.12), residues: 4682 helix: 1.75 (0.11), residues: 2208 sheet: 0.82 (0.20), residues: 646 loop : -0.29 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 345 TYR 0.019 0.002 TYR E 199 PHE 0.023 0.002 PHE F 281 TRP 0.023 0.002 TRP 1 160 HIS 0.004 0.001 HIS O 7 Details of bonding type rmsd covalent geometry : bond 0.00577 (34853) covalent geometry : angle 0.60209 (47178) hydrogen bonds : bond 0.06364 ( 2007) hydrogen bonds : angle 4.06376 ( 5799) Misc. bond : bond 0.00047 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 368 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.6969 (mtp) cc_final: 0.6711 (mtm) REVERT: B 226 LYS cc_start: 0.8138 (tttm) cc_final: 0.7896 (tttp) REVERT: B 229 ASN cc_start: 0.7113 (OUTLIER) cc_final: 0.6063 (p0) REVERT: B 288 MET cc_start: 0.8006 (ptt) cc_final: 0.7618 (ptm) REVERT: B 291 ASP cc_start: 0.6510 (m-30) cc_final: 0.6131 (m-30) REVERT: B 366 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6290 (mt0) REVERT: B 520 MET cc_start: 0.8985 (mtp) cc_final: 0.8780 (mtm) REVERT: C 111 MET cc_start: 0.8222 (mtt) cc_final: 0.7917 (mtt) REVERT: C 114 MET cc_start: 0.7784 (mmt) cc_final: 0.7546 (mmm) REVERT: C 307 MET cc_start: 0.6351 (tpt) cc_final: 0.6022 (mmm) REVERT: D 495 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: E 292 ILE cc_start: 0.7968 (tt) cc_final: 0.7724 (mt) REVERT: F 321 LYS cc_start: 0.8488 (mptt) cc_final: 0.8116 (mmmm) REVERT: P 88 GLU cc_start: 0.8794 (tm-30) cc_final: 0.7931 (tm-30) REVERT: R 36 THR cc_start: 0.7631 (t) cc_final: 0.7417 (m) REVERT: S 3 ILE cc_start: 0.8056 (pt) cc_final: 0.7647 (pt) REVERT: S 19 THR cc_start: 0.7254 (p) cc_final: 0.7054 (p) REVERT: U 58 ASP cc_start: 0.7916 (m-30) cc_final: 0.7572 (t0) REVERT: U 88 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7828 (tm-30) REVERT: 1 21 ASP cc_start: 0.8093 (m-30) cc_final: 0.6971 (t0) REVERT: 1 25 ASP cc_start: 0.7812 (m-30) cc_final: 0.7552 (m-30) REVERT: 1 204 MET cc_start: 0.7737 (ttp) cc_final: 0.7303 (tpp) REVERT: 1 368 TRP cc_start: 0.7787 (p90) cc_final: 0.7128 (p90) outliers start: 88 outliers final: 73 residues processed: 438 average time/residue: 0.1987 time to fit residues: 143.7143 Evaluate side-chains 433 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 357 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 360 TYR Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 514 MET Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain 1 residue 44 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 269 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 450 optimal weight: 4.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN G 229 ASN G 351 GLN 1 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.165511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.122444 restraints weight = 42926.063| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.19 r_work: 0.3352 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34859 Z= 0.117 Angle : 0.511 10.418 47178 Z= 0.261 Chirality : 0.042 0.164 5771 Planarity : 0.003 0.051 6132 Dihedral : 7.928 163.923 5034 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.91 % Allowed : 15.43 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.12), residues: 4682 helix: 2.08 (0.11), residues: 2208 sheet: 0.85 (0.20), residues: 646 loop : -0.20 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 37 TYR 0.010 0.001 TYR F 478 PHE 0.014 0.001 PHE G 195 TRP 0.027 0.002 TRP 1 160 HIS 0.003 0.000 HIS 1 365 Details of bonding type rmsd covalent geometry : bond 0.00263 (34853) covalent geometry : angle 0.51099 (47178) hydrogen bonds : bond 0.04491 ( 2007) hydrogen bonds : angle 3.82390 ( 5799) Misc. bond : bond 0.00014 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 357 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.6976 (mtp) cc_final: 0.6702 (mtm) REVERT: B 226 LYS cc_start: 0.8144 (tttm) cc_final: 0.7895 (tttp) REVERT: B 288 MET cc_start: 0.7859 (ptt) cc_final: 0.7471 (ptm) REVERT: B 291 ASP cc_start: 0.6477 (m-30) cc_final: 0.6113 (m-30) REVERT: B 366 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6293 (mt0) REVERT: C 111 MET cc_start: 0.8140 (mtt) cc_final: 0.7885 (mtt) REVERT: C 114 MET cc_start: 0.7706 (mmt) cc_final: 0.7440 (mmm) REVERT: C 286 LYS cc_start: 0.7716 (mmtt) cc_final: 0.7485 (mmmm) REVERT: C 307 MET cc_start: 0.6275 (tpt) cc_final: 0.5943 (mmm) REVERT: D 203 TYR cc_start: 0.7557 (m-80) cc_final: 0.7286 (m-80) REVERT: D 288 MET cc_start: 0.7396 (mtt) cc_final: 0.7170 (mmt) REVERT: D 389 MET cc_start: 0.7934 (tpp) cc_final: 0.7664 (tpp) REVERT: D 495 ASP cc_start: 0.8174 (t70) cc_final: 0.7934 (m-30) REVERT: G 69 MET cc_start: 0.8106 (mtm) cc_final: 0.7870 (mtm) REVERT: P 88 GLU cc_start: 0.8719 (tm-30) cc_final: 0.7828 (tm-30) REVERT: S 3 ILE cc_start: 0.7973 (pt) cc_final: 0.7577 (pt) REVERT: S 19 THR cc_start: 0.7256 (p) cc_final: 0.7027 (p) REVERT: U 58 ASP cc_start: 0.7917 (m-30) cc_final: 0.7574 (t0) REVERT: U 88 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7705 (tm-30) REVERT: 1 21 ASP cc_start: 0.8175 (m-30) cc_final: 0.7098 (t0) REVERT: 1 25 ASP cc_start: 0.7772 (m-30) cc_final: 0.7492 (m-30) REVERT: 1 204 MET cc_start: 0.7701 (ttp) cc_final: 0.7245 (tpp) REVERT: 1 368 TRP cc_start: 0.7813 (p90) cc_final: 0.7139 (p90) outliers start: 68 outliers final: 62 residues processed: 411 average time/residue: 0.1803 time to fit residues: 122.9325 Evaluate side-chains 413 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 350 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 360 TYR Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain 1 residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 357 optimal weight: 0.6980 chunk 315 optimal weight: 0.7980 chunk 432 optimal weight: 8.9990 chunk 444 optimal weight: 7.9990 chunk 67 optimal weight: 0.0870 chunk 364 optimal weight: 0.6980 chunk 351 optimal weight: 0.9990 chunk 393 optimal weight: 3.9990 chunk 443 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 434 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 505 GLN 1 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.168111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.125245 restraints weight = 43071.386| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.07 r_work: 0.3367 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34859 Z= 0.097 Angle : 0.487 10.789 47178 Z= 0.247 Chirality : 0.042 0.174 5771 Planarity : 0.003 0.051 6132 Dihedral : 7.733 164.672 5034 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.80 % Allowed : 15.49 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.12), residues: 4682 helix: 2.35 (0.11), residues: 2208 sheet: 0.92 (0.20), residues: 646 loop : -0.09 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 37 TYR 0.008 0.001 TYR F 478 PHE 0.014 0.001 PHE G 281 TRP 0.032 0.002 TRP 1 160 HIS 0.003 0.000 HIS 1 365 Details of bonding type rmsd covalent geometry : bond 0.00208 (34853) covalent geometry : angle 0.48661 (47178) hydrogen bonds : bond 0.03655 ( 2007) hydrogen bonds : angle 3.64520 ( 5799) Misc. bond : bond 0.00016 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 362 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.7024 (mtp) cc_final: 0.6716 (mtm) REVERT: B 226 LYS cc_start: 0.8028 (tttm) cc_final: 0.7771 (tttp) REVERT: B 288 MET cc_start: 0.7817 (ptt) cc_final: 0.7445 (ptm) REVERT: B 291 ASP cc_start: 0.6315 (m-30) cc_final: 0.5946 (m-30) REVERT: B 325 ILE cc_start: 0.8692 (mt) cc_final: 0.8282 (mt) REVERT: B 366 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6258 (mt0) REVERT: C 111 MET cc_start: 0.8108 (mtt) cc_final: 0.7891 (mtt) REVERT: C 286 LYS cc_start: 0.7712 (mmtt) cc_final: 0.7490 (mmmm) REVERT: D 203 TYR cc_start: 0.7576 (m-80) cc_final: 0.7304 (m-80) REVERT: D 288 MET cc_start: 0.7438 (mtt) cc_final: 0.7125 (mmt) REVERT: D 389 MET cc_start: 0.7794 (tpp) cc_final: 0.7589 (tpp) REVERT: D 495 ASP cc_start: 0.8101 (t70) cc_final: 0.7853 (m-30) REVERT: F 215 LEU cc_start: 0.8043 (mt) cc_final: 0.7709 (mt) REVERT: F 228 SER cc_start: 0.8417 (t) cc_final: 0.7933 (m) REVERT: P 88 GLU cc_start: 0.8639 (tm-30) cc_final: 0.7708 (tm-30) REVERT: Q 15 LYS cc_start: 0.6678 (mmtp) cc_final: 0.6359 (mmtt) REVERT: S 3 ILE cc_start: 0.7804 (pt) cc_final: 0.7465 (pt) REVERT: U 58 ASP cc_start: 0.7897 (m-30) cc_final: 0.7561 (t0) REVERT: U 88 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7697 (tm-30) REVERT: 1 21 ASP cc_start: 0.8151 (m-30) cc_final: 0.7079 (t0) REVERT: 1 25 ASP cc_start: 0.7763 (m-30) cc_final: 0.7504 (m-30) REVERT: 1 31 ILE cc_start: 0.7390 (mm) cc_final: 0.6925 (tp) REVERT: 1 57 ILE cc_start: 0.6783 (OUTLIER) cc_final: 0.6551 (mm) REVERT: 1 204 MET cc_start: 0.7620 (ttp) cc_final: 0.7228 (tpp) REVERT: 1 368 TRP cc_start: 0.7804 (p90) cc_final: 0.7102 (p90) outliers start: 64 outliers final: 57 residues processed: 410 average time/residue: 0.1876 time to fit residues: 127.1454 Evaluate side-chains 408 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 349 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 360 TYR Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 57 ILE Chi-restraints excluded: chain 1 residue 218 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 134 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 372 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 377 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 404 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 239 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.166790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124130 restraints weight = 42827.560| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.17 r_work: 0.3349 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34859 Z= 0.115 Angle : 0.498 10.770 47178 Z= 0.253 Chirality : 0.042 0.167 5771 Planarity : 0.003 0.051 6132 Dihedral : 7.734 167.852 5034 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.85 % Allowed : 15.74 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.12), residues: 4682 helix: 2.33 (0.11), residues: 2208 sheet: 0.92 (0.20), residues: 646 loop : -0.09 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 37 TYR 0.010 0.001 TYR C 476 PHE 0.013 0.001 PHE G 195 TRP 0.028 0.002 TRP 1 160 HIS 0.003 0.000 HIS 1 365 Details of bonding type rmsd covalent geometry : bond 0.00263 (34853) covalent geometry : angle 0.49850 (47178) hydrogen bonds : bond 0.04167 ( 2007) hydrogen bonds : angle 3.65648 ( 5799) Misc. bond : bond 0.00012 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8880.72 seconds wall clock time: 152 minutes 2.22 seconds (9122.22 seconds total)