Starting phenix.real_space_refine on Mon Jul 6 08:59:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4o_17421/07_2026/8p4o_17421.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4o_17421/07_2026/8p4o_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_17421/07_2026/8p4o_17421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4o_17421/07_2026/8p4o_17421.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4o_17421/07_2026/8p4o_17421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4o_17421/07_2026/8p4o_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-dev-6108/lib/python3.11/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, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 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: 7.91, per 1000 atoms: 0.23 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: 2.87 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.26 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: 7.42 Time building geometry restraints manager: 3.85 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: 1.100 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 32.240 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 are 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/Z covalent geometry : bond 0.00267 / 0.13 (34853) covalent geometry : angle 0.56959 / 0.28 (47178) hydrogen bonds : bond 0.17174 / 11.46 ( 2007) hydrogen bonds : angle 5.75517 / 4.13 ( 5799) Misc. bond : bond 0.89986 / 52.88 ( 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 : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 288 MET cc_start: 0.7846 (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: 0.2034 time to fit residues: 159.0298 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 : 1.455 ------------------------------------------------------------------------------- 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... 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 = 0.4044 r_free = 0.4044 target = 0.166500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.123887 restraints weight = 43371.337| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.19 r_work: 0.3331 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1029 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 : 0.559 8.339 47178 Z= 0.288 Chirality : 0.044 0.167 5771 Planarity : 0.004 0.055 6132 Dihedral : 8.472 178.309 5036 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.10 % Allowed : 7.87 % Favored : 91.03 % 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 are not related in a simple way. whole: 1.49 (0.12), residues: 4682 helix: 2.05 (0.11), residues: 2159 sheet: 0.95 (0.18), residues: 760 loop : -0.31 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 1 273 TYR 0.015 0.001 TYR E 360 PHE 0.020 0.001 PHE G 195 TRP 0.022 0.002 TRP 1 160 HIS 0.005 0.001 HIS 1 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (34853) covalent geometry : angle 0.55872 / 0.29 (47178) hydrogen bonds : bond 0.05261 / 3.55 ( 2007) hydrogen bonds : angle 4.34961 / 3.13 ( 5799) Misc. bond : bond 0.00695 / 0.40 ( 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 429 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 390 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7523 (t0) REVERT: A 307 MET cc_start: 0.6981 (mtp) cc_final: 0.6604 (mtm) REVERT: B 229 ASN cc_start: 0.7202 (OUTLIER) cc_final: 0.6294 (p0) REVERT: B 288 MET cc_start: 0.7860 (ptt) cc_final: 0.7130 (ptt) REVERT: B 291 ASP cc_start: 0.6231 (m-30) cc_final: 0.5899 (m-30) REVERT: C 111 MET cc_start: 0.8225 (mtt) cc_final: 0.7924 (mtt) REVERT: D 389 MET cc_start: 0.7944 (tpp) cc_final: 0.7663 (tpp) REVERT: E 272 LYS cc_start: 0.7950 (mppt) cc_final: 0.7704 (mttm) REVERT: P 88 GLU cc_start: 0.8692 (tm-30) cc_final: 0.7901 (tm-30) REVERT: S 3 ILE cc_start: 0.7989 (pt) cc_final: 0.7503 (pt) REVERT: U 58 ASP cc_start: 0.7925 (m-30) cc_final: 0.7658 (t0) REVERT: 1 21 ASP cc_start: 0.7688 (m-30) cc_final: 0.6894 (t0) REVERT: 1 368 TRP cc_start: 0.7681 (p90) cc_final: 0.7051 (p90) outliers start: 39 outliers final: 30 residues processed: 411 average time/residue: 0.2030 time to fit residues: 138.0440 Evaluate side-chains 390 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 358 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 190 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 348 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 389 optimal weight: 1.9990 chunk 338 optimal weight: 0.8980 chunk 162 optimal weight: 0.0020 chunk 156 optimal weight: 6.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.168117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.125693 restraints weight = 43064.312| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.14 r_work: 0.3356 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 34859 Z= 0.111 Angle : 0.502 7.492 47178 Z= 0.256 Chirality : 0.042 0.160 5771 Planarity : 0.003 0.054 6132 Dihedral : 8.292 176.666 5034 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.10 % Allowed : 10.37 % Favored : 88.53 % 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 are not related in a simple way. whole: 1.66 (0.12), residues: 4682 helix: 2.20 (0.11), residues: 2187 sheet: 0.96 (0.18), residues: 760 loop : -0.24 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 70 TYR 0.010 0.001 TYR G 199 PHE 0.016 0.001 PHE G 195 TRP 0.031 0.002 TRP 1 160 HIS 0.004 0.001 HIS 1 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (34853) covalent geometry : angle 0.50191 / 0.26 (47178) hydrogen bonds : bond 0.04345 / 2.93 ( 2007) hydrogen bonds : angle 4.01241 / 2.87 ( 5799) Misc. bond : bond 0.00078 / 0.05 ( 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 426 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 387 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7569 (t0) REVERT: A 520 MET cc_start: 0.8659 (mtt) cc_final: 0.8397 (mtm) REVERT: B 229 ASN cc_start: 0.7104 (OUTLIER) cc_final: 0.6228 (p0) REVERT: B 288 MET cc_start: 0.7737 (ptt) cc_final: 0.7097 (ptm) REVERT: B 291 ASP cc_start: 0.6191 (m-30) cc_final: 0.5829 (m-30) REVERT: C 111 MET cc_start: 0.8197 (mtt) cc_final: 0.7865 (mtt) REVERT: D 389 MET cc_start: 0.7825 (tpp) cc_final: 0.7546 (tpp) REVERT: D 495 ASP cc_start: 0.8225 (t70) cc_final: 0.7957 (t70) REVERT: E 367 GLU cc_start: 0.8067 (pp20) cc_final: 0.7734 (pp20) REVERT: F 321 LYS cc_start: 0.8141 (mptt) cc_final: 0.7923 (mmmm) REVERT: P 88 GLU cc_start: 0.8567 (tm-30) cc_final: 0.7720 (tm-30) REVERT: S 3 ILE cc_start: 0.7917 (pt) cc_final: 0.7438 (pt) REVERT: U 58 ASP cc_start: 0.7878 (m-30) cc_final: 0.7602 (t0) REVERT: U 88 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7518 (tm-30) REVERT: 1 21 ASP cc_start: 0.7704 (m-30) cc_final: 0.6925 (t0) REVERT: 1 200 GLN cc_start: 0.8353 (pp30) cc_final: 0.8143 (pp30) REVERT: 1 204 MET cc_start: 0.7503 (ttp) cc_final: 0.7004 (tpp) REVERT: 1 368 TRP cc_start: 0.7716 (p90) cc_final: 0.7076 (p90) outliers start: 39 outliers final: 27 residues processed: 411 average time/residue: 0.1936 time to fit residues: 132.5955 Evaluate side-chains 388 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 359 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 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 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 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 92 LEU Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 86 MET 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: 9.9990 chunk 332 optimal weight: 0.0060 chunk 308 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 271 optimal weight: 3.9990 chunk 202 optimal weight: 0.0770 chunk 122 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 overall best weight: 1.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 505 GLN P 45 ASN 1 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.166213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.123824 restraints weight = 43069.528| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.18 r_work: 0.3331 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34859 Z= 0.138 Angle : 0.514 7.267 47178 Z= 0.262 Chirality : 0.043 0.183 5771 Planarity : 0.003 0.053 6132 Dihedral : 8.169 169.908 5034 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.85 % Allowed : 12.09 % Favored : 86.06 % 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 are not related in a simple way. whole: 1.63 (0.12), residues: 4682 helix: 2.13 (0.11), residues: 2208 sheet: 1.05 (0.20), residues: 648 loop : -0.18 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 1 70 TYR 0.011 0.001 TYR C 476 PHE 0.016 0.001 PHE G 195 TRP 0.033 0.002 TRP 1 160 HIS 0.003 0.001 HIS 1 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (34853) covalent geometry : angle 0.51375 / 0.26 (47178) hydrogen bonds : bond 0.04794 / 3.23 ( 2007) hydrogen bonds : angle 3.91535 / 2.81 ( 5799) Misc. bond : bond 0.00046 / 0.03 ( 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 433 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 367 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7677 (mm-40) REVERT: A 520 MET cc_start: 0.8676 (mtt) cc_final: 0.8476 (mtm) REVERT: B 229 ASN cc_start: 0.7141 (OUTLIER) cc_final: 0.6166 (p0) REVERT: B 288 MET cc_start: 0.7891 (ptt) cc_final: 0.7267 (ptm) REVERT: B 291 ASP cc_start: 0.6364 (m-30) cc_final: 0.5988 (m-30) REVERT: C 69 MET cc_start: 0.8073 (mtt) cc_final: 0.7842 (mtt) REVERT: C 111 MET cc_start: 0.8191 (mtt) cc_final: 0.7906 (mtt) REVERT: D 288 MET cc_start: 0.7480 (mtt) cc_final: 0.7079 (mmt) REVERT: D 389 MET cc_start: 0.7906 (tpp) cc_final: 0.7634 (tpp) REVERT: E 367 GLU cc_start: 0.8028 (pp20) cc_final: 0.7755 (pp20) REVERT: F 321 LYS cc_start: 0.8278 (mptt) cc_final: 0.8026 (mmmm) REVERT: P 88 GLU cc_start: 0.8622 (tm-30) cc_final: 0.7764 (tm-30) REVERT: S 3 ILE cc_start: 0.8027 (pt) cc_final: 0.7503 (pt) REVERT: S 19 THR cc_start: 0.6906 (p) cc_final: 0.6652 (p) REVERT: U 58 ASP cc_start: 0.7874 (m-30) cc_final: 0.7625 (t0) REVERT: U 88 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7722 (tm-30) REVERT: 1 21 ASP cc_start: 0.7931 (m-30) cc_final: 0.7051 (t0) REVERT: 1 204 MET cc_start: 0.7546 (ttp) cc_final: 0.7055 (tpp) REVERT: 1 285 ASN cc_start: 0.7341 (m-40) cc_final: 0.7130 (m110) REVERT: 1 368 TRP cc_start: 0.7711 (p90) cc_final: 0.7037 (p90) outliers start: 66 outliers final: 51 residues processed: 416 average time/residue: 0.2077 time to fit residues: 143.8876 Evaluate side-chains 401 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 349 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 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 B residue 289 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 329 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 461 GLU 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 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 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 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 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: 0.4980 chunk 435 optimal weight: 40.0000 chunk 138 optimal weight: 20.0000 chunk 190 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 396 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 460 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 ASN 1 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.162445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119302 restraints weight = 43391.925| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.21 r_work: 0.3290 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 34859 Z= 0.222 Angle : 0.591 7.615 47178 Z= 0.302 Chirality : 0.046 0.182 5771 Planarity : 0.004 0.052 6132 Dihedral : 8.320 175.952 5034 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.61 % Allowed : 13.49 % Favored : 83.90 % 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 are not related in a simple way. whole: 1.26 (0.12), residues: 4682 helix: 1.77 (0.11), residues: 2208 sheet: 0.90 (0.20), residues: 646 loop : -0.30 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 37 TYR 0.019 0.002 TYR B 203 PHE 0.020 0.002 PHE G 195 TRP 0.035 0.003 TRP 1 160 HIS 0.004 0.001 HIS O 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.22 (34853) covalent geometry : angle 0.59133 / 0.30 (47178) hydrogen bonds : bond 0.06196 / 4.18 ( 2007) hydrogen bonds : angle 4.09140 / 2.93 ( 5799) Misc. bond : bond 0.00085 / 0.05 ( 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 468 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 375 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7780 (mtm) cc_final: 0.7517 (mtm) REVERT: A 307 MET cc_start: 0.7096 (mtp) cc_final: 0.6774 (mtm) REVERT: B 229 ASN cc_start: 0.7161 (OUTLIER) cc_final: 0.6161 (p0) REVERT: B 288 MET cc_start: 0.7885 (ptt) cc_final: 0.7316 (ptm) REVERT: B 291 ASP cc_start: 0.6519 (m-30) cc_final: 0.6114 (m-30) REVERT: B 309 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6686 (tp) REVERT: C 111 MET cc_start: 0.8269 (mtt) cc_final: 0.7984 (mtt) REVERT: C 286 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7524 (mmmm) REVERT: C 343 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.6897 (mt0) REVERT: D 203 TYR cc_start: 0.7575 (m-80) cc_final: 0.7326 (m-80) REVERT: D 273 VAL cc_start: 0.9088 (m) cc_final: 0.8861 (p) REVERT: D 288 MET cc_start: 0.7524 (mtt) cc_final: 0.7185 (mmt) REVERT: D 372 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7234 (mt) REVERT: E 292 ILE cc_start: 0.7991 (tt) cc_final: 0.7730 (mt) REVERT: F 321 LYS cc_start: 0.8333 (mptt) cc_final: 0.8074 (mmmm) REVERT: O 37 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7973 (mtt90) REVERT: P 88 GLU cc_start: 0.8753 (tm-30) cc_final: 0.7890 (tm-30) REVERT: R 36 THR cc_start: 0.7643 (t) cc_final: 0.7417 (m) REVERT: R 86 MET cc_start: 0.8343 (ptt) cc_final: 0.7842 (ptt) REVERT: S 19 THR cc_start: 0.6890 (p) cc_final: 0.6669 (p) REVERT: U 58 ASP cc_start: 0.7932 (m-30) cc_final: 0.7685 (t0) REVERT: U 88 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7858 (tm-30) REVERT: 1 21 ASP cc_start: 0.8219 (m-30) cc_final: 0.7140 (t0) REVERT: 1 204 MET cc_start: 0.7712 (ttp) cc_final: 0.7181 (tpp) REVERT: 1 368 TRP cc_start: 0.7764 (p90) cc_final: 0.7113 (p90) outliers start: 93 outliers final: 69 residues processed: 441 average time/residue: 0.1992 time to fit residues: 146.4824 Evaluate side-chains 432 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 359 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 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 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 289 LEU Chi-restraints excluded: chain B residue 309 LEU 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 273 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 174 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 372 LEU 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 266 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 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 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 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 28 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 26 VAL 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: 3.9990 chunk 11 optimal weight: 3.9990 chunk 454 optimal weight: 9.9990 chunk 445 optimal weight: 30.0000 chunk 300 optimal weight: 0.0370 chunk 182 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 335 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 259 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 GLN D 37 ASN G 343 GLN 1 15 HIS 1 196 GLN 1 285 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.165798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.122672 restraints weight = 43053.005| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.23 r_work: 0.3325 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34859 Z= 0.115 Angle : 0.505 8.325 47178 Z= 0.257 Chirality : 0.042 0.161 5771 Planarity : 0.003 0.052 6132 Dihedral : 8.150 177.412 5034 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.25 % Allowed : 14.31 % Favored : 83.45 % 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 are not related in a simple way. whole: 1.55 (0.12), residues: 4682 helix: 2.08 (0.11), residues: 2208 sheet: 0.93 (0.20), residues: 646 loop : -0.22 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 350 TYR 0.009 0.001 TYR C 478 PHE 0.015 0.001 PHE G 195 TRP 0.034 0.002 TRP 1 160 HIS 0.019 0.001 HIS 1 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (34853) covalent geometry : angle 0.50491 / 0.26 (47178) hydrogen bonds : bond 0.04513 / 3.04 ( 2007) hydrogen bonds : angle 3.86723 / 2.78 ( 5799) Misc. bond : bond 0.00041 / 0.02 ( 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 448 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 368 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7594 (mtm) cc_final: 0.7358 (mtm) REVERT: A 307 MET cc_start: 0.6747 (mtp) cc_final: 0.6395 (mtm) REVERT: B 229 ASN cc_start: 0.6971 (OUTLIER) cc_final: 0.5979 (p0) REVERT: B 288 MET cc_start: 0.7633 (ptt) cc_final: 0.7063 (ptm) REVERT: B 291 ASP cc_start: 0.6196 (m-30) cc_final: 0.5796 (m-30) REVERT: B 309 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6296 (tp) REVERT: B 366 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.6066 (mt0) REVERT: C 111 MET cc_start: 0.8254 (mtt) cc_final: 0.7946 (mtt) REVERT: C 286 LYS cc_start: 0.7652 (mmtt) cc_final: 0.7439 (mmmm) REVERT: C 307 MET cc_start: 0.6077 (tpt) cc_final: 0.5713 (mmm) REVERT: D 203 TYR cc_start: 0.7501 (m-80) cc_final: 0.7167 (m-80) REVERT: D 288 MET cc_start: 0.7337 (mtt) cc_final: 0.6996 (mmt) REVERT: D 389 MET cc_start: 0.7773 (tpp) cc_final: 0.7515 (tpp) REVERT: D 495 ASP cc_start: 0.8268 (t70) cc_final: 0.7853 (m-30) REVERT: E 288 MET cc_start: 0.7402 (mtp) cc_final: 0.6710 (mtt) REVERT: F 321 LYS cc_start: 0.8157 (mptt) cc_final: 0.7822 (mmmm) REVERT: O 37 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7692 (mtt90) REVERT: P 88 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7564 (tm-30) REVERT: S 19 THR cc_start: 0.6732 (p) cc_final: 0.6520 (p) REVERT: U 58 ASP cc_start: 0.7899 (m-30) cc_final: 0.7650 (t0) REVERT: U 88 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7504 (tm-30) REVERT: 1 21 ASP cc_start: 0.8161 (m-30) cc_final: 0.7108 (t0) REVERT: 1 25 ASP cc_start: 0.7765 (m-30) cc_final: 0.7415 (m-30) REVERT: 1 204 MET cc_start: 0.7486 (ttp) cc_final: 0.7008 (tpp) REVERT: 1 368 TRP cc_start: 0.7647 (p90) cc_final: 0.7005 (p90) outliers start: 80 outliers final: 55 residues processed: 431 average time/residue: 0.1870 time to fit residues: 134.1833 Evaluate side-chains 410 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 352 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 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 417 VAL 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 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 366 GLN 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 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 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 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 267 MET 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 360 TYR 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 27 LEU Chi-restraints excluded: chain U residue 84 LEU 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: 2.9990 chunk 269 optimal weight: 2.9990 chunk 402 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 358 optimal weight: 0.9980 chunk 390 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 286 optimal weight: 0.1980 chunk 310 optimal weight: 4.9990 chunk 454 optimal weight: 9.9990 chunk 214 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4046 r_free = 0.4046 target = 0.166891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123396 restraints weight = 43187.959| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.07 r_work: 0.3379 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 34859 Z= 0.109 Angle : 0.494 9.377 47178 Z= 0.251 Chirality : 0.042 0.182 5771 Planarity : 0.003 0.052 6132 Dihedral : 7.948 178.767 5034 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.11 % Allowed : 14.59 % Favored : 83.31 % 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 are not related in a simple way. whole: 1.70 (0.12), residues: 4682 helix: 2.24 (0.11), residues: 2208 sheet: 0.96 (0.20), residues: 646 loop : -0.16 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 350 TYR 0.009 0.001 TYR C 476 PHE 0.013 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/Z covalent geometry : bond 0.00241 / 0.11 (34853) covalent geometry : angle 0.49408 / 0.25 (47178) hydrogen bonds : bond 0.04144 / 2.79 ( 2007) hydrogen bonds : angle 3.73588 / 2.68 ( 5799) Misc. bond : bond 0.00027 / 0.02 ( 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 444 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 369 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7664 (mtm) cc_final: 0.7448 (mtm) REVERT: A 307 MET cc_start: 0.7009 (mtp) cc_final: 0.6678 (mtm) REVERT: B 226 LYS cc_start: 0.8027 (tttm) cc_final: 0.7779 (tttp) REVERT: B 229 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6132 (p0) REVERT: B 288 MET cc_start: 0.7899 (ptt) cc_final: 0.7330 (ptm) REVERT: B 291 ASP cc_start: 0.6456 (m-30) cc_final: 0.6065 (m-30) REVERT: B 309 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6751 (tp) REVERT: B 366 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6282 (mt0) REVERT: C 111 MET cc_start: 0.8142 (mtt) cc_final: 0.7893 (mtt) REVERT: C 307 MET cc_start: 0.6297 (tpt) cc_final: 0.5991 (mmm) REVERT: D 203 TYR cc_start: 0.7607 (m-80) cc_final: 0.7273 (m-80) REVERT: D 288 MET cc_start: 0.7457 (mtt) cc_final: 0.7104 (mmt) REVERT: D 389 MET cc_start: 0.7853 (tpp) cc_final: 0.7630 (tpp) REVERT: D 495 ASP cc_start: 0.8091 (t70) cc_final: 0.7857 (m-30) REVERT: G 102 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7382 (mt-10) REVERT: O 37 ARG cc_start: 0.8137 (mtt-85) cc_final: 0.7926 (mtt90) REVERT: P 88 GLU cc_start: 0.8661 (tm-30) cc_final: 0.7752 (tm-30) REVERT: S 19 THR cc_start: 0.7050 (p) cc_final: 0.6838 (p) REVERT: U 58 ASP cc_start: 0.7932 (m-30) cc_final: 0.7582 (t0) REVERT: U 88 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7643 (tm-30) REVERT: 1 21 ASP cc_start: 0.8111 (m-30) cc_final: 0.7053 (t0) REVERT: 1 25 ASP cc_start: 0.7798 (m-30) cc_final: 0.7515 (m-30) REVERT: 1 204 MET cc_start: 0.7652 (ttp) cc_final: 0.7210 (tpp) REVERT: 1 368 TRP cc_start: 0.7812 (p90) cc_final: 0.7138 (p90) outliers start: 75 outliers final: 64 residues processed: 427 average time/residue: 0.1959 time to fit residues: 139.0645 Evaluate side-chains 422 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 355 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 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 188 ASP 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 309 LEU 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 261 THR 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 523 ASP Chi-restraints excluded: chain E residue 213 VAL 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 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 G residue 521 VAL 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 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: 5.9990 chunk 159 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 459 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 371 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 505 GLN G 351 GLN 1 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119121 restraints weight = 43384.903| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.07 r_work: 0.3304 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 34859 Z= 0.243 Angle : 0.594 9.733 47178 Z= 0.303 Chirality : 0.047 0.183 5771 Planarity : 0.004 0.051 6132 Dihedral : 8.060 178.238 5034 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.64 % Allowed : 14.84 % Favored : 82.52 % 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 are not related in a simple way. whole: 1.26 (0.12), residues: 4682 helix: 1.79 (0.11), residues: 2208 sheet: 0.85 (0.20), residues: 646 loop : -0.30 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 404 TYR 0.020 0.002 TYR F 478 PHE 0.038 0.002 PHE F 281 TRP 0.021 0.002 TRP 1 160 HIS 0.004 0.001 HIS O 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.24 (34853) covalent geometry : angle 0.59404 / 0.30 (47178) hydrogen bonds : bond 0.06126 / 4.12 ( 2007) hydrogen bonds : angle 4.00164 / 2.87 ( 5799) Misc. bond : bond 0.00067 / 0.04 ( 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 463 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 369 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7794 (mtm) cc_final: 0.7425 (mtm) REVERT: A 307 MET cc_start: 0.7188 (mtp) cc_final: 0.6911 (mtm) REVERT: B 226 LYS cc_start: 0.8147 (tttm) cc_final: 0.7903 (tttp) REVERT: B 229 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6167 (p0) REVERT: B 288 MET cc_start: 0.7912 (ptt) cc_final: 0.7432 (ptm) REVERT: B 291 ASP cc_start: 0.6517 (m-30) cc_final: 0.6116 (m-30) REVERT: B 309 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6616 (tp) REVERT: B 366 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.6300 (mt0) REVERT: C 111 MET cc_start: 0.8242 (mtt) cc_final: 0.7954 (mtt) REVERT: C 247 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8358 (tp) REVERT: D 247 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8036 (tt) REVERT: D 288 MET cc_start: 0.7505 (mtt) cc_final: 0.7194 (mmt) REVERT: F 228 SER cc_start: 0.8494 (t) cc_final: 0.8017 (m) REVERT: F 321 LYS cc_start: 0.8517 (mptt) cc_final: 0.8156 (mmmm) REVERT: P 88 GLU cc_start: 0.8793 (tm-30) cc_final: 0.7923 (tm-30) REVERT: R 36 THR cc_start: 0.7616 (t) cc_final: 0.7411 (m) REVERT: R 86 MET cc_start: 0.8334 (ptt) cc_final: 0.7860 (ptt) REVERT: S 3 ILE cc_start: 0.8096 (pt) cc_final: 0.7602 (pt) REVERT: U 58 ASP cc_start: 0.7916 (m-30) cc_final: 0.7574 (t0) REVERT: U 88 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7838 (tm-30) REVERT: 1 21 ASP cc_start: 0.8129 (m-30) cc_final: 0.7006 (t0) REVERT: 1 25 ASP cc_start: 0.7815 (m-30) cc_final: 0.7555 (m-30) REVERT: 1 204 MET cc_start: 0.7694 (ttp) cc_final: 0.7231 (tpp) REVERT: 1 368 TRP cc_start: 0.7837 (p90) cc_final: 0.7185 (p90) outliers start: 94 outliers final: 79 residues processed: 445 average time/residue: 0.1929 time to fit residues: 142.5370 Evaluate side-chains 445 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 361 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 417 VAL 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 74 VAL Chi-restraints excluded: chain B residue 188 ASP 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 309 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 376 VAL 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 247 LEU Chi-restraints excluded: chain C residue 261 THR 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 174 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 247 LEU 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 523 ASP Chi-restraints excluded: chain E residue 169 VAL 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 267 MET 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 G residue 521 VAL 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 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 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 U residue 86 MET Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 295 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 269 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 450 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 285 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.165109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122574 restraints weight = 42976.210| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.04 r_work: 0.3326 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1900 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= 0.130 Angle : 0.518 10.172 47178 Z= 0.264 Chirality : 0.043 0.168 5771 Planarity : 0.003 0.052 6132 Dihedral : 7.923 175.468 5034 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.28 % Allowed : 15.43 % Favored : 82.29 % 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 are not related in a simple way. whole: 1.49 (0.12), residues: 4682 helix: 2.04 (0.11), residues: 2208 sheet: 0.85 (0.20), residues: 646 loop : -0.23 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 37 TYR 0.015 0.001 TYR F 478 PHE 0.022 0.001 PHE F 281 TRP 0.027 0.002 TRP 1 160 HIS 0.003 0.000 HIS 1 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (34853) covalent geometry : angle 0.51776 / 0.26 (47178) hydrogen bonds : bond 0.04657 / 3.13 ( 2007) hydrogen bonds : angle 3.83753 / 2.75 ( 5799) Misc. bond : bond 0.00040 / 0.03 ( 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 448 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 367 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7801 (mtm) cc_final: 0.7502 (mtm) REVERT: A 307 MET cc_start: 0.7092 (mtp) cc_final: 0.6848 (mtm) REVERT: B 226 LYS cc_start: 0.8121 (tttm) cc_final: 0.7874 (tttp) REVERT: B 288 MET cc_start: 0.7853 (ptt) cc_final: 0.7403 (ptm) REVERT: B 291 ASP cc_start: 0.6454 (m-30) cc_final: 0.6062 (m-30) REVERT: B 309 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6706 (tp) REVERT: B 366 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6274 (mt0) REVERT: C 111 MET cc_start: 0.8165 (mtt) cc_final: 0.7918 (mtt) REVERT: C 307 MET cc_start: 0.6436 (tpt) cc_final: 0.6094 (mmm) REVERT: D 247 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7784 (tt) REVERT: D 288 MET cc_start: 0.7425 (mtt) cc_final: 0.7180 (mmt) REVERT: D 389 MET cc_start: 0.7877 (tpp) cc_final: 0.7594 (tpp) REVERT: D 495 ASP cc_start: 0.8141 (t70) cc_final: 0.7865 (t70) REVERT: F 130 GLU cc_start: 0.8297 (tp30) cc_final: 0.8038 (mm-30) REVERT: F 228 SER cc_start: 0.8465 (t) cc_final: 0.7980 (m) REVERT: F 321 LYS cc_start: 0.8472 (mptt) cc_final: 0.8111 (mmmm) REVERT: P 88 GLU cc_start: 0.8688 (tm-30) cc_final: 0.7777 (tm-30) REVERT: R 36 THR cc_start: 0.7539 (t) cc_final: 0.7334 (m) REVERT: S 3 ILE cc_start: 0.7995 (pt) cc_final: 0.7589 (pt) REVERT: U 58 ASP cc_start: 0.7892 (m-30) cc_final: 0.7549 (t0) REVERT: U 88 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7678 (tm-30) REVERT: 1 21 ASP cc_start: 0.8118 (m-30) cc_final: 0.6980 (t0) REVERT: 1 25 ASP cc_start: 0.7751 (m-30) cc_final: 0.7485 (m-30) REVERT: 1 204 MET cc_start: 0.7648 (ttp) cc_final: 0.7196 (tpp) REVERT: 1 368 TRP cc_start: 0.7813 (p90) cc_final: 0.7138 (p90) outliers start: 81 outliers final: 73 residues processed: 433 average time/residue: 0.2004 time to fit residues: 144.5982 Evaluate side-chains 436 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 360 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 417 VAL 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 188 ASP 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 309 LEU 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 261 THR 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 247 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 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 521 VAL 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 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 S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 85 ILE 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 U residue 86 MET 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: 0.9990 chunk 315 optimal weight: 3.9990 chunk 432 optimal weight: 30.0000 chunk 444 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 364 optimal weight: 0.0970 chunk 351 optimal weight: 0.9980 chunk 393 optimal weight: 3.9990 chunk 443 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 434 optimal weight: 20.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.166291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122552 restraints weight = 43164.175| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.12 r_work: 0.3366 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1916 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= 0.114 Angle : 0.502 10.577 47178 Z= 0.255 Chirality : 0.042 0.163 5771 Planarity : 0.003 0.052 6132 Dihedral : 7.712 168.866 5034 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.28 % Allowed : 15.63 % Favored : 82.10 % 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 are not related in a simple way. whole: 1.66 (0.12), residues: 4682 helix: 2.21 (0.11), residues: 2208 sheet: 0.89 (0.20), residues: 646 loop : -0.17 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 37 TYR 0.014 0.001 TYR F 478 PHE 0.020 0.001 PHE F 281 TRP 0.030 0.002 TRP 1 160 HIS 0.003 0.000 HIS 1 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (34853) covalent geometry : angle 0.50232 / 0.26 (47178) hydrogen bonds : bond 0.04227 / 2.84 ( 2007) hydrogen bonds : angle 3.73370 / 2.68 ( 5799) Misc. bond : bond 0.00028 / 0.02 ( 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 448 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 367 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7638 (mtm) cc_final: 0.7421 (mtm) REVERT: A 307 MET cc_start: 0.7075 (mtp) cc_final: 0.6822 (mtm) REVERT: B 226 LYS cc_start: 0.7979 (tttm) cc_final: 0.7670 (tttp) REVERT: B 288 MET cc_start: 0.7876 (ptt) cc_final: 0.7416 (ptm) REVERT: B 291 ASP cc_start: 0.6460 (m-30) cc_final: 0.6072 (m-30) REVERT: B 309 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6669 (tp) REVERT: B 325 ILE cc_start: 0.8728 (mt) cc_final: 0.8332 (mt) REVERT: B 366 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6295 (mt0) REVERT: C 111 MET cc_start: 0.8153 (mtt) cc_final: 0.7924 (mtt) REVERT: C 307 MET cc_start: 0.6593 (tpt) cc_final: 0.6313 (mmm) REVERT: D 247 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7791 (tt) REVERT: D 288 MET cc_start: 0.7439 (mtt) cc_final: 0.7123 (mmt) REVERT: D 389 MET cc_start: 0.7876 (tpp) cc_final: 0.7654 (tpp) REVERT: D 495 ASP cc_start: 0.8145 (t70) cc_final: 0.7906 (m-30) REVERT: F 228 SER cc_start: 0.8454 (t) cc_final: 0.7967 (m) REVERT: P 88 GLU cc_start: 0.8719 (tm-30) cc_final: 0.7811 (tm-30) REVERT: S 3 ILE cc_start: 0.7991 (pt) cc_final: 0.7586 (pt) REVERT: U 58 ASP cc_start: 0.7927 (m-30) cc_final: 0.7590 (t0) REVERT: U 88 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7720 (tm-30) REVERT: 1 21 ASP cc_start: 0.8155 (m-30) cc_final: 0.6981 (t0) REVERT: 1 25 ASP cc_start: 0.7747 (m-30) cc_final: 0.7470 (m-30) REVERT: 1 204 MET cc_start: 0.7665 (ttp) cc_final: 0.7230 (tpp) REVERT: 1 368 TRP cc_start: 0.7844 (p90) cc_final: 0.7146 (p90) outliers start: 81 outliers final: 72 residues processed: 432 average time/residue: 0.1947 time to fit residues: 139.5107 Evaluate side-chains 428 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 353 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 417 VAL 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 188 ASP 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 309 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 376 VAL 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 261 THR 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 247 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 169 VAL 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 29 VAL Chi-restraints excluded: chain G residue 74 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 360 TYR Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 521 VAL 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 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 S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 85 ILE 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 59 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 134 optimal weight: 8.9990 chunk 209 optimal weight: 0.9990 chunk 372 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 chunk 377 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 285 optimal weight: 0.5980 chunk 404 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 239 optimal weight: 9.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4048 r_free = 0.4048 target = 0.167144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123750 restraints weight = 42847.268| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.10 r_work: 0.3360 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34859 Z= 0.105 Angle : 0.499 10.252 47178 Z= 0.253 Chirality : 0.042 0.171 5771 Planarity : 0.003 0.051 6132 Dihedral : 7.580 161.988 5034 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.97 % Allowed : 16.08 % Favored : 81.96 % 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 are not related in a simple way. whole: 1.76 (0.12), residues: 4682 helix: 2.30 (0.11), residues: 2208 sheet: 0.94 (0.20), residues: 646 loop : -0.13 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 37 TYR 0.013 0.001 TYR F 478 PHE 0.012 0.001 PHE G 195 TRP 0.029 0.002 TRP 1 160 HIS 0.003 0.000 HIS 1 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (34853) covalent geometry : angle 0.49936 / 0.25 (47178) hydrogen bonds : bond 0.03960 / 2.66 ( 2007) hydrogen bonds : angle 3.66885 / 2.63 ( 5799) Misc. bond : bond 0.00040 / 0.02 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9687.49 seconds wall clock time: 165 minutes 58.68 seconds (9958.68 seconds total)