Starting phenix.real_space_refine on Sun Jun 29 09:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4o_17421/06_2025/8p4o_17421.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4o_17421/06_2025/8p4o_17421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p4o_17421/06_2025/8p4o_17421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4o_17421/06_2025/8p4o_17421.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4o_17421/06_2025/8p4o_17421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4o_17421/06_2025/8p4o_17421.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'GLU:plan': 9, 'ARG: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: {'TYR:plan': 1, 'GLU:plan': 9, 'ARG: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: {'TYR:plan': 1, 'GLU:plan': 9, 'ARG: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: {'TYR:plan': 1, 'GLU:plan': 9, 'ARG: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: {'TYR:plan': 1, 'GLU:plan': 9, 'ARG: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: {'TYR:plan': 1, 'GLU:plan': 9, 'ARG: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: {'TYR:plan': 1, 'GLU:plan': 9, 'ARG: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, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 20.35, per 1000 atoms: 0.59 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: 9.75 Conformation dependent library (CDL) restraints added in 4.8 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: 5.16 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: 15.93 Time building geometry restraints manager: 11.31 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 525 or resid 1600 th \ rough 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 525 or resid 1600 th \ rough 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 525 or resid 1600 th \ rough 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 525 or resid 1600 th \ rough 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 525 or resid 1600 th \ rough 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 525 or resid 1600 th \ rough 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: 0.710 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: 0.030 Extract box with map and model: 1.450 Check model and map are aligned: 0.220 Set scattering table: 0.300 Process input model: 82.860 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.901 34859 Z= 1.188 Angle : 0.570 11.354 47178 Z= 0.283 Chirality : 0.041 0.151 5771 Planarity : 0.003 0.077 6132 Dihedral : 14.860 179.003 12908 Min Nonbonded Distance : 1.349 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.06 % Allowed : 0.22 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (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 TRP 0.017 0.002 TRP 1 62 HIS 0.004 0.001 HIS 1 15 PHE 0.015 0.001 PHE B 44 TYR 0.019 0.001 TYR E 203 ARG 0.005 0.000 ARG G 362 Details of bonding type rmsd hydrogen bonds : bond 0.17174 ( 2007) hydrogen bonds : angle 5.75517 ( 5799) covalent geometry : bond 0.00267 (34853) covalent geometry : angle 0.56959 (47178) Misc. bond : bond 0.89986 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 468 time to evaluate : 3.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 288 MET cc_start: 0.7847 (ptt) cc_final: 0.7340 (ptt) REVERT: C 111 MET cc_start: 0.7548 (mtt) cc_final: 0.7317 (mtt) REVERT: D 291 ASP cc_start: 0.7093 (m-30) cc_final: 0.6793 (m-30) REVERT: D 389 MET cc_start: 0.7072 (tpp) cc_final: 0.6687 (tpp) REVERT: E 272 LYS cc_start: 0.7778 (mppt) cc_final: 0.7569 (mttm) REVERT: P 88 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7753 (tm-30) REVERT: S 3 ILE cc_start: 0.8015 (pt) cc_final: 0.7654 (pt) REVERT: S 68 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7454 (p0) REVERT: U 28 THR cc_start: 0.7200 (p) cc_final: 0.6501 (t) REVERT: U 58 ASP cc_start: 0.7606 (m-30) cc_final: 0.7394 (t0) REVERT: 1 21 ASP cc_start: 0.7246 (m-30) cc_final: 0.6967 (t0) REVERT: 1 368 TRP cc_start: 0.8061 (p90) cc_final: 0.7514 (p90) outliers start: 2 outliers final: 0 residues processed: 469 average time/residue: 0.4361 time to fit residues: 338.7717 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 : 3.964 ------------------------------------------------------------------------------- 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 391 optimal weight: 4.9990 chunk 351 optimal weight: 0.9990 chunk 195 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 363 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 270 optimal weight: 2.9990 chunk 421 optimal weight: 0.0970 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN B 37 ASN F 37 ASN ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN P 45 ASN S 68 ASN 1 143 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.168220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126306 restraints weight = 42958.711| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.07 r_work: 0.3375 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34859 Z= 0.130 Angle : 0.530 7.575 47178 Z= 0.274 Chirality : 0.043 0.174 5771 Planarity : 0.003 0.056 6132 Dihedral : 8.310 172.167 5036 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.96 % Allowed : 7.11 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.12), residues: 4682 helix: 2.20 (0.11), residues: 2159 sheet: 0.97 (0.19), residues: 690 loop : -0.18 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 1 160 HIS 0.006 0.001 HIS 1 365 PHE 0.017 0.001 PHE G 195 TYR 0.013 0.001 TYR E 360 ARG 0.007 0.000 ARG 1 273 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 2007) hydrogen bonds : angle 4.34582 ( 5799) covalent geometry : bond 0.00271 (34853) covalent geometry : angle 0.52956 (47178) Misc. bond : bond 0.00288 ( 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 419 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 385 time to evaluate : 4.017 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7532 (t0) REVERT: B 229 ASN cc_start: 0.7180 (OUTLIER) cc_final: 0.6282 (p0) REVERT: B 288 MET cc_start: 0.7756 (ptt) cc_final: 0.6988 (ptt) REVERT: B 291 ASP cc_start: 0.6174 (m-30) cc_final: 0.5843 (m-30) REVERT: C 111 MET cc_start: 0.8171 (mtt) cc_final: 0.7863 (mtt) REVERT: D 389 MET cc_start: 0.7862 (tpp) cc_final: 0.7589 (tpp) REVERT: E 272 LYS cc_start: 0.7902 (mppt) cc_final: 0.7692 (mttm) REVERT: P 88 GLU cc_start: 0.8665 (tm-30) cc_final: 0.7884 (tm-30) REVERT: S 3 ILE cc_start: 0.7948 (pt) cc_final: 0.7465 (pt) REVERT: U 58 ASP cc_start: 0.7892 (m-30) cc_final: 0.7622 (t0) REVERT: 1 21 ASP cc_start: 0.7703 (m-30) cc_final: 0.6897 (t0) REVERT: 1 368 TRP cc_start: 0.7662 (p90) cc_final: 0.7052 (p90) outliers start: 34 outliers final: 25 residues processed: 404 average time/residue: 0.5125 time to fit residues: 347.5933 Evaluate side-chains 384 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 357 time to evaluate : 3.725 ------------------------------------------------------------------------------- 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 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 Q residue 11 ILE Chi-restraints excluded: chain Q residue 87 SER 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 103 optimal weight: 0.4980 chunk 432 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 355 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 398 optimal weight: 10.0000 chunk 407 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 266 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 505 GLN E 82 ASN F 453 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.165169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.123368 restraints weight = 43080.599| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.37 r_work: 0.3302 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34859 Z= 0.164 Angle : 0.545 6.760 47178 Z= 0.280 Chirality : 0.044 0.177 5771 Planarity : 0.003 0.053 6132 Dihedral : 8.205 159.313 5034 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.49 % Allowed : 10.03 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.12), residues: 4682 helix: 2.00 (0.11), residues: 2208 sheet: 0.90 (0.19), residues: 690 loop : -0.19 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP 1 160 HIS 0.004 0.001 HIS 1 365 PHE 0.020 0.001 PHE G 195 TYR 0.012 0.001 TYR C 476 ARG 0.004 0.000 ARG 1 70 Details of bonding type rmsd hydrogen bonds : bond 0.05398 ( 2007) hydrogen bonds : angle 4.09252 ( 5799) covalent geometry : bond 0.00394 (34853) covalent geometry : angle 0.54510 (47178) Misc. bond : bond 0.00091 ( 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 430 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 377 time to evaluate : 3.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7587 (t0) REVERT: A 307 MET cc_start: 0.6896 (mtp) cc_final: 0.6567 (mtm) REVERT: B 229 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6203 (p0) REVERT: B 288 MET cc_start: 0.7838 (ptt) cc_final: 0.7141 (ptt) REVERT: B 291 ASP cc_start: 0.6248 (m-30) cc_final: 0.5885 (m-30) REVERT: B 380 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7193 (mttp) REVERT: C 111 MET cc_start: 0.8226 (mtt) cc_final: 0.7921 (mtt) REVERT: D 389 MET cc_start: 0.7972 (tpp) cc_final: 0.7652 (tpp) REVERT: F 321 LYS cc_start: 0.8180 (mptt) cc_final: 0.7963 (mmmm) REVERT: P 88 GLU cc_start: 0.8661 (tm-30) cc_final: 0.7832 (tm-30) REVERT: R 86 MET cc_start: 0.8333 (ptt) cc_final: 0.7931 (ptt) REVERT: S 3 ILE cc_start: 0.7981 (pt) cc_final: 0.7492 (pt) REVERT: S 19 THR cc_start: 0.6669 (p) cc_final: 0.6396 (p) REVERT: U 58 ASP cc_start: 0.7885 (m-30) cc_final: 0.7616 (t0) REVERT: U 88 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7724 (tm-30) REVERT: 1 21 ASP cc_start: 0.7941 (m-30) cc_final: 0.7112 (t0) REVERT: 1 204 MET cc_start: 0.7554 (ttp) cc_final: 0.7065 (tpp) REVERT: 1 368 TRP cc_start: 0.7754 (p90) cc_final: 0.7073 (p90) outliers start: 53 outliers final: 35 residues processed: 411 average time/residue: 0.4754 time to fit residues: 326.0399 Evaluate side-chains 393 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 355 time to evaluate : 4.841 ------------------------------------------------------------------------------- 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 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 380 LYS 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 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 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 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 R residue 90 ASP Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 84 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 175 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 445 optimal weight: 20.0000 chunk 378 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 313 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 295 optimal weight: 20.0000 chunk 231 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN D 37 ASN P 45 ASN 1 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.163777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121592 restraints weight = 43217.073| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.39 r_work: 0.3264 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34859 Z= 0.180 Angle : 0.556 8.752 47178 Z= 0.285 Chirality : 0.045 0.183 5771 Planarity : 0.003 0.053 6132 Dihedral : 8.140 160.598 5034 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.25 % Allowed : 12.62 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.12), residues: 4682 helix: 1.88 (0.11), residues: 2208 sheet: 0.93 (0.20), residues: 646 loop : -0.26 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP 1 160 HIS 0.003 0.001 HIS O 7 PHE 0.019 0.001 PHE D 195 TYR 0.013 0.001 TYR E 199 ARG 0.006 0.000 ARG S 9 Details of bonding type rmsd hydrogen bonds : bond 0.05571 ( 2007) hydrogen bonds : angle 4.04155 ( 5799) covalent geometry : bond 0.00442 (34853) covalent geometry : angle 0.55619 (47178) Misc. bond : bond 0.00059 ( 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 451 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 371 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.6870 (mtp) cc_final: 0.6560 (mtm) REVERT: B 229 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.6165 (p0) REVERT: B 288 MET cc_start: 0.7846 (ptt) cc_final: 0.7241 (ptm) REVERT: B 291 ASP cc_start: 0.6310 (m-30) cc_final: 0.5913 (m-30) REVERT: C 111 MET cc_start: 0.8241 (mtt) cc_final: 0.7931 (mtt) REVERT: D 203 TYR cc_start: 0.7457 (m-80) cc_final: 0.7199 (m-80) REVERT: D 288 MET cc_start: 0.7439 (mtt) cc_final: 0.7071 (mmt) REVERT: E 292 ILE cc_start: 0.7825 (tt) cc_final: 0.7576 (mt) REVERT: F 321 LYS cc_start: 0.8243 (mptt) cc_final: 0.7966 (mmmm) REVERT: O 37 ARG cc_start: 0.8122 (mtt-85) cc_final: 0.7759 (mtt90) REVERT: P 88 GLU cc_start: 0.8619 (tm-30) cc_final: 0.7718 (tm-30) REVERT: R 86 MET cc_start: 0.8263 (ptt) cc_final: 0.7858 (ptt) REVERT: S 19 THR cc_start: 0.6746 (p) cc_final: 0.6482 (p) REVERT: T 37 ARG cc_start: 0.7906 (mtt-85) cc_final: 0.7696 (mtt90) REVERT: U 58 ASP cc_start: 0.7869 (m-30) cc_final: 0.7611 (t0) REVERT: U 88 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7664 (tm-30) REVERT: 1 21 ASP cc_start: 0.8136 (m-30) cc_final: 0.7111 (t0) REVERT: 1 204 MET cc_start: 0.7643 (ttp) cc_final: 0.7088 (tpp) REVERT: 1 368 TRP cc_start: 0.7777 (p90) cc_final: 0.7149 (p90) outliers start: 80 outliers final: 62 residues processed: 427 average time/residue: 0.4774 time to fit residues: 339.8115 Evaluate side-chains 424 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 361 time to evaluate : 4.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 289 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 213 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 387 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 417 VAL 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 266 THR Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 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 87 SER Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 86 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 299 optimal weight: 4.9990 chunk 337 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 chunk 443 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 319 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 446 optimal weight: 6.9990 chunk 368 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 HIS 1 196 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 = 0.4032 r_free = 0.4032 target = 0.165594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123280 restraints weight = 43184.556| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.19 r_work: 0.3321 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34859 Z= 0.126 Angle : 0.506 7.734 47178 Z= 0.258 Chirality : 0.043 0.164 5771 Planarity : 0.003 0.051 6132 Dihedral : 8.004 160.445 5034 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.94 % Allowed : 14.05 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.12), residues: 4682 helix: 2.08 (0.11), residues: 2208 sheet: 0.95 (0.20), residues: 646 loop : -0.23 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP 1 160 HIS 0.003 0.001 HIS 1 365 PHE 0.015 0.001 PHE G 195 TYR 0.010 0.001 TYR C 476 ARG 0.004 0.000 ARG S 9 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 2007) hydrogen bonds : angle 3.88125 ( 5799) covalent geometry : bond 0.00292 (34853) covalent geometry : angle 0.50619 (47178) Misc. bond : bond 0.00029 ( 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 440 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 371 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7826 (mtm) cc_final: 0.7622 (mtm) REVERT: A 290 GLN cc_start: 0.7993 (tp-100) cc_final: 0.7662 (mm-40) REVERT: A 307 MET cc_start: 0.7112 (mtp) cc_final: 0.6797 (mtm) REVERT: B 229 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.6199 (p0) REVERT: B 288 MET cc_start: 0.7858 (ptt) cc_final: 0.7276 (ptm) REVERT: B 291 ASP cc_start: 0.6392 (m-30) cc_final: 0.6007 (m-30) REVERT: C 111 MET cc_start: 0.8194 (mtt) cc_final: 0.7929 (mtt) REVERT: C 286 LYS cc_start: 0.7693 (mmtt) cc_final: 0.7459 (mmmm) REVERT: C 307 MET cc_start: 0.6166 (tpt) cc_final: 0.5671 (tpt) REVERT: C 343 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.6804 (mt0) REVERT: D 288 MET cc_start: 0.7473 (mtt) cc_final: 0.7146 (mmt) REVERT: D 389 MET cc_start: 0.7892 (tpp) cc_final: 0.7630 (tpp) REVERT: E 292 ILE cc_start: 0.7883 (tt) cc_final: 0.7666 (mt) REVERT: F 321 LYS cc_start: 0.8283 (mptt) cc_final: 0.8011 (mmmm) REVERT: O 37 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7882 (mtt90) REVERT: P 88 GLU cc_start: 0.8625 (tm-30) cc_final: 0.7714 (tm-30) REVERT: R 86 MET cc_start: 0.8383 (ptt) cc_final: 0.8027 (ptt) REVERT: S 19 THR cc_start: 0.6714 (p) cc_final: 0.6488 (p) REVERT: U 58 ASP cc_start: 0.7910 (m-30) cc_final: 0.7656 (t0) REVERT: U 88 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7687 (tm-30) REVERT: 1 21 ASP cc_start: 0.8160 (m-30) cc_final: 0.7142 (t0) REVERT: 1 204 MET cc_start: 0.7666 (ttp) cc_final: 0.7135 (tpp) REVERT: 1 368 TRP cc_start: 0.7760 (p90) cc_final: 0.7133 (p90) outliers start: 69 outliers final: 53 residues processed: 425 average time/residue: 0.4505 time to fit residues: 317.5035 Evaluate side-chains 407 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 352 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 289 LEU 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 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 417 VAL Chi-restraints excluded: chain D residue 420 ILE 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 238 GLU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain 1 residue 15 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 254 optimal weight: 0.9980 chunk 371 optimal weight: 0.0050 chunk 458 optimal weight: 8.9990 chunk 436 optimal weight: 6.9990 chunk 253 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 416 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 343 optimal weight: 0.9990 chunk 413 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN C 82 ASN C 505 GLN G 343 GLN P 45 ASN 1 285 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.167345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125359 restraints weight = 42918.637| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.19 r_work: 0.3352 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34859 Z= 0.104 Angle : 0.488 8.495 47178 Z= 0.248 Chirality : 0.042 0.186 5771 Planarity : 0.003 0.050 6132 Dihedral : 7.875 160.436 5034 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.19 % Allowed : 14.42 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.12), residues: 4682 helix: 2.26 (0.11), residues: 2208 sheet: 0.95 (0.20), residues: 646 loop : -0.14 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 1 160 HIS 0.022 0.001 HIS 1 15 PHE 0.034 0.001 PHE F 281 TYR 0.009 0.001 TYR F 478 ARG 0.009 0.000 ARG T 37 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 2007) hydrogen bonds : angle 3.73862 ( 5799) covalent geometry : bond 0.00225 (34853) covalent geometry : angle 0.48828 (47178) Misc. bond : bond 0.00013 ( 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: 78 poor density : 370 time to evaluate : 4.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.7105 (mtp) cc_final: 0.6754 (mtm) REVERT: B 229 ASN cc_start: 0.7096 (OUTLIER) cc_final: 0.6115 (p0) REVERT: B 288 MET cc_start: 0.7813 (ptt) cc_final: 0.7225 (ptm) REVERT: B 291 ASP cc_start: 0.6352 (m-30) cc_final: 0.5943 (m-30) REVERT: B 366 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.6267 (mt0) REVERT: B 380 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7195 (mttp) REVERT: C 111 MET cc_start: 0.8135 (mtt) cc_final: 0.7889 (mtt) REVERT: C 286 LYS cc_start: 0.7673 (mmtt) cc_final: 0.7468 (mmmm) REVERT: C 307 MET cc_start: 0.6200 (tpt) cc_final: 0.5840 (mmm) REVERT: D 288 MET cc_start: 0.7431 (mtt) cc_final: 0.7100 (mmt) REVERT: D 389 MET cc_start: 0.7843 (tpp) cc_final: 0.7622 (tpp) REVERT: D 495 ASP cc_start: 0.8072 (t70) cc_final: 0.7845 (m-30) REVERT: E 292 ILE cc_start: 0.7866 (tt) cc_final: 0.7652 (mt) REVERT: G 102 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7320 (mt-10) REVERT: O 37 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7892 (mtt90) REVERT: P 88 GLU cc_start: 0.8632 (tm-30) cc_final: 0.7725 (tm-30) REVERT: R 86 MET cc_start: 0.8372 (ptt) cc_final: 0.8032 (ptt) REVERT: S 19 THR cc_start: 0.6996 (p) cc_final: 0.6783 (p) REVERT: U 58 ASP cc_start: 0.7920 (m-30) cc_final: 0.7669 (t0) REVERT: U 88 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7678 (tm-30) REVERT: 1 21 ASP cc_start: 0.8050 (m-30) cc_final: 0.7012 (t0) REVERT: 1 25 ASP cc_start: 0.7744 (m-30) cc_final: 0.7401 (m-30) REVERT: 1 31 ILE cc_start: 0.7349 (mm) cc_final: 0.6895 (tp) REVERT: 1 204 MET cc_start: 0.7584 (ttp) cc_final: 0.7085 (tpp) REVERT: 1 368 TRP cc_start: 0.7724 (p90) cc_final: 0.7083 (p90) outliers start: 78 outliers final: 55 residues processed: 433 average time/residue: 0.7777 time to fit residues: 569.1751 Evaluate side-chains 408 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 350 time to evaluate : 6.340 ------------------------------------------------------------------------------- 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 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain 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 P residue 3 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain 1 residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 415 optimal weight: 0.9980 chunk 460 optimal weight: 8.9990 chunk 342 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 345 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 505 GLN 1 15 HIS 1 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.165997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123301 restraints weight = 43095.415| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.10 r_work: 0.3334 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1724 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= 0.126 Angle : 0.502 8.980 47178 Z= 0.255 Chirality : 0.043 0.165 5771 Planarity : 0.003 0.050 6132 Dihedral : 7.859 163.142 5034 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.42 % Allowed : 14.47 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.12), residues: 4682 helix: 2.21 (0.11), residues: 2208 sheet: 0.96 (0.20), residues: 646 loop : -0.13 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 1 160 HIS 0.003 0.000 HIS 1 365 PHE 0.023 0.001 PHE F 281 TYR 0.010 0.001 TYR C 476 ARG 0.006 0.000 ARG T 37 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 2007) hydrogen bonds : angle 3.73862 ( 5799) covalent geometry : bond 0.00294 (34853) covalent geometry : angle 0.50184 (47178) Misc. bond : bond 0.00022 ( 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 440 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 354 time to evaluate : 3.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7898 (mtp) cc_final: 0.7389 (mtm) REVERT: A 307 MET cc_start: 0.7132 (mtp) cc_final: 0.6791 (mtm) REVERT: B 69 MET cc_start: 0.7867 (ptp) cc_final: 0.7548 (ptp) REVERT: B 226 LYS cc_start: 0.8012 (tttm) cc_final: 0.7764 (tttp) REVERT: B 229 ASN cc_start: 0.7139 (OUTLIER) cc_final: 0.6139 (p0) REVERT: B 288 MET cc_start: 0.7870 (ptt) cc_final: 0.7361 (ptm) REVERT: B 291 ASP cc_start: 0.6381 (m-30) cc_final: 0.5980 (m-30) REVERT: B 366 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6269 (mt0) REVERT: C 111 MET cc_start: 0.8140 (mtt) cc_final: 0.7898 (mtt) REVERT: C 307 MET cc_start: 0.6306 (tpt) cc_final: 0.5992 (mmm) REVERT: D 203 TYR cc_start: 0.7616 (m-80) cc_final: 0.7270 (m-80) REVERT: D 389 MET cc_start: 0.7848 (tpp) cc_final: 0.7624 (tpp) REVERT: D 495 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7765 (t70) REVERT: E 292 ILE cc_start: 0.7897 (tt) cc_final: 0.7652 (mt) REVERT: O 37 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7884 (mtt90) REVERT: P 88 GLU cc_start: 0.8640 (tm-30) cc_final: 0.7735 (tm-30) REVERT: R 86 MET cc_start: 0.8345 (ptt) cc_final: 0.8055 (ptt) REVERT: S 3 ILE cc_start: 0.7966 (pt) cc_final: 0.7595 (pt) REVERT: S 19 THR cc_start: 0.7048 (p) cc_final: 0.6835 (p) REVERT: U 58 ASP cc_start: 0.7907 (m-30) cc_final: 0.7555 (t0) REVERT: U 88 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7608 (tm-30) REVERT: 1 21 ASP cc_start: 0.8106 (m-30) cc_final: 0.7055 (t0) REVERT: 1 25 ASP cc_start: 0.7783 (m-30) cc_final: 0.7497 (m-30) REVERT: 1 31 ILE cc_start: 0.7406 (mm) cc_final: 0.6953 (tp) REVERT: 1 204 MET cc_start: 0.7660 (ttp) cc_final: 0.7180 (tpp) REVERT: 1 368 TRP cc_start: 0.7792 (p90) cc_final: 0.7120 (p90) outliers start: 86 outliers final: 73 residues processed: 422 average time/residue: 0.4591 time to fit residues: 323.1743 Evaluate side-chains 428 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 352 time to evaluate : 4.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 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 183 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 183 LEU 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 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 417 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 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 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 R residue 19 THR Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 354 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 405 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN G 351 GLN P 7 HIS 1 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.162009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118567 restraints weight = 43367.988| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.16 r_work: 0.3289 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 34859 Z= 0.237 Angle : 0.599 8.838 47178 Z= 0.306 Chirality : 0.047 0.193 5771 Planarity : 0.004 0.051 6132 Dihedral : 8.096 168.927 5034 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.78 % Allowed : 14.87 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.12), residues: 4682 helix: 1.78 (0.11), residues: 2208 sheet: 0.80 (0.20), residues: 646 loop : -0.28 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 1 160 HIS 0.004 0.001 HIS O 7 PHE 0.019 0.002 PHE G 195 TYR 0.018 0.002 TYR E 199 ARG 0.005 0.000 ARG T 37 Details of bonding type rmsd hydrogen bonds : bond 0.06253 ( 2007) hydrogen bonds : angle 4.01500 ( 5799) covalent geometry : bond 0.00592 (34853) covalent geometry : angle 0.59873 (47178) Misc. bond : bond 0.00059 ( 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 468 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 369 time to evaluate : 4.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: A 288 MET cc_start: 0.8059 (mtp) cc_final: 0.7579 (mtm) REVERT: A 307 MET cc_start: 0.6894 (mtp) cc_final: 0.6639 (mtm) REVERT: B 69 MET cc_start: 0.8050 (ptp) cc_final: 0.7711 (ptp) REVERT: B 226 LYS cc_start: 0.8136 (tttm) cc_final: 0.7899 (tttp) REVERT: B 288 MET cc_start: 0.7926 (ptt) cc_final: 0.7520 (ptm) REVERT: B 291 ASP cc_start: 0.6509 (m-30) cc_final: 0.6103 (m-30) REVERT: B 366 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6295 (mt0) REVERT: B 380 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7274 (mttp) REVERT: C 111 MET cc_start: 0.8211 (mtt) cc_final: 0.7920 (mtt) REVERT: C 247 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8369 (tp) REVERT: C 307 MET cc_start: 0.6345 (tpt) cc_final: 0.6005 (mmm) REVERT: D 495 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: E 292 ILE cc_start: 0.7991 (tt) cc_final: 0.7734 (mt) REVERT: F 228 SER cc_start: 0.8508 (t) cc_final: 0.8030 (m) REVERT: F 321 LYS cc_start: 0.8489 (mptt) cc_final: 0.8140 (mmmm) REVERT: P 88 GLU cc_start: 0.8806 (tm-30) cc_final: 0.7929 (tm-30) REVERT: R 36 THR cc_start: 0.7629 (t) cc_final: 0.7390 (m) REVERT: S 3 ILE cc_start: 0.8139 (pt) cc_final: 0.7649 (pt) REVERT: U 58 ASP cc_start: 0.7900 (m-30) cc_final: 0.7570 (t0) REVERT: U 88 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7847 (tm-30) REVERT: 1 21 ASP cc_start: 0.8130 (m-30) cc_final: 0.7001 (t0) REVERT: 1 25 ASP cc_start: 0.7810 (m-30) cc_final: 0.7551 (m-30) REVERT: 1 57 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6694 (mm) REVERT: 1 368 TRP cc_start: 0.7835 (p90) cc_final: 0.7158 (p90) outliers start: 99 outliers final: 80 residues processed: 447 average time/residue: 0.4434 time to fit residues: 329.5402 Evaluate side-chains 449 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 363 time to evaluate : 3.693 ------------------------------------------------------------------------------- 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 255 GLU 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 213 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 380 LYS 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 136 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 MET 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 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 495 ASP 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 266 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 360 TYR Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 514 MET Chi-restraints excluded: chain 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 R residue 19 THR Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 57 ILE Chi-restraints excluded: chain 1 residue 218 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 246 optimal weight: 0.0370 chunk 248 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 375 optimal weight: 10.0000 chunk 444 optimal weight: 0.0270 chunk 354 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN C 505 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 = 0.4050 r_free = 0.4050 target = 0.167424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124098 restraints weight = 43148.123| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.10 r_work: 0.3386 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 34859 Z= 0.101 Angle : 0.496 9.795 47178 Z= 0.254 Chirality : 0.042 0.176 5771 Planarity : 0.003 0.051 6132 Dihedral : 7.852 167.671 5034 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.69 % Allowed : 16.19 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.12), residues: 4682 helix: 2.23 (0.11), residues: 2208 sheet: 0.84 (0.20), residues: 646 loop : -0.14 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP 1 160 HIS 0.003 0.000 HIS 1 365 PHE 0.012 0.001 PHE B 195 TYR 0.009 0.001 TYR F 478 ARG 0.007 0.000 ARG O 37 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 2007) hydrogen bonds : angle 3.72728 ( 5799) covalent geometry : bond 0.00209 (34853) covalent geometry : angle 0.49601 (47178) Misc. bond : bond 0.00017 ( 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 422 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 362 time to evaluate : 4.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7947 (mtp) cc_final: 0.7447 (mtm) REVERT: A 307 MET cc_start: 0.7085 (mtp) cc_final: 0.6777 (mtm) REVERT: B 226 LYS cc_start: 0.8024 (tttm) cc_final: 0.7779 (tttp) REVERT: B 288 MET cc_start: 0.7931 (ptt) cc_final: 0.7427 (ptm) REVERT: B 291 ASP cc_start: 0.6446 (m-30) cc_final: 0.6057 (m-30) REVERT: B 366 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6330 (mt0) REVERT: C 111 MET cc_start: 0.8113 (mtt) cc_final: 0.7887 (mtt) REVERT: C 307 MET cc_start: 0.6584 (tpt) cc_final: 0.6309 (mmm) REVERT: D 203 TYR cc_start: 0.7618 (m-80) cc_final: 0.7083 (m-80) REVERT: D 389 MET cc_start: 0.7882 (tpp) cc_final: 0.7640 (tpp) REVERT: P 88 GLU cc_start: 0.8677 (tm-30) cc_final: 0.7764 (tm-30) REVERT: Q 15 LYS cc_start: 0.6745 (mmtp) cc_final: 0.6425 (mmtt) REVERT: S 3 ILE cc_start: 0.7909 (pt) cc_final: 0.7531 (pt) REVERT: U 58 ASP cc_start: 0.7927 (m-30) cc_final: 0.7587 (t0) REVERT: U 88 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7712 (tm-30) REVERT: 1 21 ASP cc_start: 0.8124 (m-30) cc_final: 0.7023 (t0) REVERT: 1 25 ASP cc_start: 0.7775 (m-30) cc_final: 0.7501 (m-30) REVERT: 1 204 MET cc_start: 0.7678 (ttp) cc_final: 0.7188 (tpp) REVERT: 1 368 TRP cc_start: 0.7856 (p90) cc_final: 0.7173 (p90) outliers start: 60 outliers final: 46 residues processed: 409 average time/residue: 0.4597 time to fit residues: 312.8409 Evaluate side-chains 393 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 346 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 MET 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 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 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 213 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 29 VAL 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 P residue 25 ILE Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 218 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 312 optimal weight: 2.9990 chunk 243 optimal weight: 0.0270 chunk 413 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 171 optimal weight: 0.0040 chunk 41 optimal weight: 6.9990 chunk 293 optimal weight: 0.0000 chunk 60 optimal weight: 7.9990 chunk 246 optimal weight: 4.9990 chunk 315 optimal weight: 4.9990 overall best weight: 1.0058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.166860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124165 restraints weight = 42893.166| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.10 r_work: 0.3338 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34859 Z= 0.108 Angle : 0.496 10.206 47178 Z= 0.252 Chirality : 0.042 0.163 5771 Planarity : 0.003 0.050 6132 Dihedral : 7.776 170.636 5034 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.43 % Allowed : 16.72 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.12), residues: 4682 helix: 2.30 (0.11), residues: 2208 sheet: 0.85 (0.20), residues: 646 loop : -0.10 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 1 160 HIS 0.003 0.000 HIS 1 365 PHE 0.013 0.001 PHE G 195 TYR 0.009 0.001 TYR C 476 ARG 0.006 0.000 ARG O 37 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 2007) hydrogen bonds : angle 3.67021 ( 5799) covalent geometry : bond 0.00242 (34853) covalent geometry : angle 0.49621 (47178) Misc. bond : bond 0.00016 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9364 Ramachandran restraints generated. 4682 Oldfield, 0 Emsley, 4682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 356 time to evaluate : 4.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7865 (mtp) cc_final: 0.7350 (mtm) REVERT: A 307 MET cc_start: 0.6929 (mtp) cc_final: 0.6601 (mtm) REVERT: B 226 LYS cc_start: 0.7857 (tttm) cc_final: 0.7607 (tttp) REVERT: B 288 MET cc_start: 0.7702 (ptt) cc_final: 0.7298 (ptm) REVERT: B 291 ASP cc_start: 0.6200 (m-30) cc_final: 0.5800 (m-30) REVERT: B 325 ILE cc_start: 0.8613 (mt) cc_final: 0.8209 (mt) REVERT: B 366 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6105 (mt0) REVERT: C 111 MET cc_start: 0.8189 (mtt) cc_final: 0.7939 (mtt) REVERT: C 307 MET cc_start: 0.6483 (tpt) cc_final: 0.6282 (mmm) REVERT: D 389 MET cc_start: 0.7768 (tpp) cc_final: 0.7566 (tpp) REVERT: F 228 SER cc_start: 0.8387 (t) cc_final: 0.7874 (m) REVERT: P 88 GLU cc_start: 0.8552 (tm-30) cc_final: 0.7603 (tm-30) REVERT: Q 15 LYS cc_start: 0.6545 (mmtp) cc_final: 0.6230 (mmtt) REVERT: S 3 ILE cc_start: 0.7805 (pt) cc_final: 0.7430 (pt) REVERT: U 58 ASP cc_start: 0.7885 (m-30) cc_final: 0.7537 (t0) REVERT: U 88 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7590 (tm-30) REVERT: 1 21 ASP cc_start: 0.8110 (m-30) cc_final: 0.6950 (t0) REVERT: 1 25 ASP cc_start: 0.7733 (m-30) cc_final: 0.7465 (m-30) REVERT: 1 204 MET cc_start: 0.7549 (ttp) cc_final: 0.7086 (tpp) REVERT: 1 368 TRP cc_start: 0.7730 (p90) cc_final: 0.7039 (p90) outliers start: 51 outliers final: 47 residues processed: 399 average time/residue: 0.4770 time to fit residues: 316.5252 Evaluate side-chains 398 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 350 time to evaluate : 3.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 517 THR 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 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 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 213 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 29 VAL 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 P residue 25 ILE Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 218 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 295 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 223 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 197 optimal weight: 0.6980 chunk 237 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 422 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 348 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 = 0.4042 r_free = 0.4042 target = 0.166729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123163 restraints weight = 42983.843| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.11 r_work: 0.3343 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34859 Z= 0.112 Angle : 0.497 10.253 47178 Z= 0.253 Chirality : 0.042 0.180 5771 Planarity : 0.003 0.051 6132 Dihedral : 7.751 171.198 5034 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.63 % Allowed : 16.89 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.12), residues: 4682 helix: 2.31 (0.11), residues: 2208 sheet: 0.88 (0.20), residues: 646 loop : -0.11 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 1 160 HIS 0.003 0.000 HIS 1 365 PHE 0.013 0.001 PHE G 195 TYR 0.009 0.001 TYR C 476 ARG 0.006 0.000 ARG O 37 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 2007) hydrogen bonds : angle 3.65305 ( 5799) covalent geometry : bond 0.00255 (34853) covalent geometry : angle 0.49707 (47178) Misc. bond : bond 0.00020 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22508.20 seconds wall clock time: 397 minutes 58.51 seconds (23878.51 seconds total)