Starting phenix.real_space_refine on Sat Jun 6 16:21:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7v_42012/06_2026/8u7v_42012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7v_42012/06_2026/8u7v_42012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7v_42012/06_2026/8u7v_42012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7v_42012/06_2026/8u7v_42012.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7v_42012/06_2026/8u7v_42012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7v_42012/06_2026/8u7v_42012.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.081 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: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 184 5.16 5 C 18456 2.51 5 N 5040 2.21 5 O 5904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29680 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "B" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "C" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "D" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "E" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "F" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "G" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "H" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna2p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 6.41, per 1000 atoms: 0.22 Number of scatterers: 29680 At special positions: 0 Unit cell: (172.84, 172.84, 142.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 96 15.00 O 5904 8.00 N 5040 7.00 C 18456 6.00 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=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6784 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 40 sheets defined 42.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 20 through 26 removed outlier: 4.262A pdb=" N SER A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.725A pdb=" N ALA A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.816A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 4.349A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.929A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.146A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 452 through 470 Proline residue: A 458 - end of helix removed outlier: 3.531A pdb=" N ILE A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'B' and resid 20 through 26 removed outlier: 4.257A pdb=" N SER B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.724A pdb=" N ALA B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.814A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.351A pdb=" N TYR B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.927A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.145A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 452 through 470 Proline residue: B 458 - end of helix removed outlier: 3.551A pdb=" N ILE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'C' and resid 20 through 26 removed outlier: 4.256A pdb=" N SER C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 84 removed outlier: 3.719A pdb=" N ALA C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 254 through 267 removed outlier: 4.350A pdb=" N TYR C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.925A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.150A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 452 through 470 Proline residue: C 458 - end of helix removed outlier: 3.534A pdb=" N ILE C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 486 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'D' and resid 20 through 26 removed outlier: 4.262A pdb=" N SER D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 84 removed outlier: 3.742A pdb=" N ALA D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.813A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.926A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.124A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 452 through 470 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'E' and resid 20 through 26 removed outlier: 4.262A pdb=" N SER E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 84 removed outlier: 3.742A pdb=" N ALA E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 223 through 233 removed outlier: 3.813A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 267 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 3.926A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 355 removed outlier: 4.124A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 452 through 470 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'F' and resid 20 through 26 removed outlier: 4.262A pdb=" N SER F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 84 removed outlier: 3.725A pdb=" N ALA F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 223 through 233 removed outlier: 3.816A pdb=" N LEU F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 267 removed outlier: 4.349A pdb=" N TYR F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.928A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.145A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 452 through 470 Proline residue: F 458 - end of helix removed outlier: 3.526A pdb=" N ILE F 464 " --> pdb=" O LEU F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'G' and resid 20 through 26 removed outlier: 4.258A pdb=" N SER G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 84 removed outlier: 3.724A pdb=" N ALA G 81 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 174 through 178 Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 223 through 233 removed outlier: 3.813A pdb=" N LEU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 267 removed outlier: 4.351A pdb=" N TYR G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 3.927A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 355 removed outlier: 4.145A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 452 through 470 Proline residue: G 458 - end of helix removed outlier: 3.600A pdb=" N ILE G 464 " --> pdb=" O LEU G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 486 Processing helix chain 'G' and resid 494 through 499 Processing helix chain 'H' and resid 20 through 26 removed outlier: 4.256A pdb=" N SER H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 84 removed outlier: 3.721A pdb=" N ALA H 81 " --> pdb=" O ASP H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 174 through 178 Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 254 through 267 removed outlier: 4.350A pdb=" N TYR H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.925A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 355 removed outlier: 4.150A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'H' and resid 452 through 470 Proline residue: H 458 - end of helix removed outlier: 3.534A pdb=" N ILE H 464 " --> pdb=" O LEU H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 486 Processing helix chain 'H' and resid 494 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.600A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.607A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 320 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.525A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 157 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.191A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 211 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.595A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.556A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY B 89 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA B 249 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 320 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 322 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.650A pdb=" N ILE B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 188 through 189 removed outlier: 6.209A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE B 211 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 18 through 19 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.592A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.557A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLY C 89 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA C 249 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 320 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C 322 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.673A pdb=" N ILE C 157 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.697A pdb=" N ALA C 188 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 212 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU C 209 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE C 221 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 18 through 19 Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.597A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.611A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY D 320 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG D 322 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.669A pdb=" N ILE D 157 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.204A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE D 211 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 18 through 19 Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.597A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.507A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY E 89 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA E 249 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY E 320 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG E 322 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.669A pdb=" N ILE E 157 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.204A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 211 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AC9, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.600A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.607A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY F 89 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA F 249 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY F 320 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG F 322 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.525A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F 157 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.191A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE F 211 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AD5, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.553A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY G 320 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG G 322 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.650A pdb=" N ILE G 157 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.209A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE G 211 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AE1, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.592A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.557A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY H 89 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA H 249 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG H 322 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.674A pdb=" N ILE H 157 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 188 through 189 removed outlier: 3.699A pdb=" N ALA H 188 " --> pdb=" O PRO H 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 212 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU H 209 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE H 221 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE H 211 " --> pdb=" O VAL H 219 " (cutoff:3.500A) 1046 hydrogen bonds defined for protein. 2841 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: 5.70 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4848 1.29 - 1.42: 7216 1.42 - 1.55: 17679 1.55 - 1.68: 161 1.68 - 1.81: 312 Bond restraints: 30216 Sorted by residual: bond pdb=" C2 IMP F 603 " pdb=" N3 IMP F 603 " ideal model delta sigma weight residual 1.301 1.461 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" C2 IMP D 603 " pdb=" N3 IMP D 603 " ideal model delta sigma weight residual 1.301 1.461 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C2 IMP H 603 " pdb=" N3 IMP H 603 " ideal model delta sigma weight residual 1.301 1.461 -0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" C2 IMP B 603 " pdb=" N3 IMP B 603 " ideal model delta sigma weight residual 1.301 1.460 -0.159 2.00e-02 2.50e+03 6.36e+01 bond pdb=" C2 IMP G 603 " pdb=" N3 IMP G 603 " ideal model delta sigma weight residual 1.301 1.460 -0.159 2.00e-02 2.50e+03 6.36e+01 ... (remaining 30211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 40532 4.43 - 8.85: 465 8.85 - 13.28: 104 13.28 - 17.70: 11 17.70 - 22.13: 8 Bond angle restraints: 41120 Sorted by residual: angle pdb=" PA ATP A 604 " pdb=" O3A ATP A 604 " pdb=" PB ATP A 604 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 angle pdb=" PA ATP F 604 " pdb=" O3A ATP F 604 " pdb=" PB ATP F 604 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 angle pdb=" PA ATP D 604 " pdb=" O3A ATP D 604 " pdb=" PB ATP D 604 " ideal model delta sigma weight residual 136.83 124.03 12.80 1.00e+00 1.00e+00 1.64e+02 angle pdb=" PA ATP E 604 " pdb=" O3A ATP E 604 " pdb=" PB ATP E 604 " ideal model delta sigma weight residual 136.83 124.05 12.78 1.00e+00 1.00e+00 1.63e+02 angle pdb=" PA ATP B 604 " pdb=" O3A ATP B 604 " pdb=" PB ATP B 604 " ideal model delta sigma weight residual 136.83 124.09 12.74 1.00e+00 1.00e+00 1.62e+02 ... (remaining 41115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 17644 35.18 - 70.37: 719 70.37 - 105.55: 99 105.55 - 140.74: 10 140.74 - 175.92: 48 Dihedral angle restraints: 18520 sinusoidal: 7896 harmonic: 10624 Sorted by residual: dihedral pdb=" O5' GTP B 601 " pdb=" O3A GTP B 601 " pdb=" PA GTP B 601 " pdb=" PB GTP B 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.20 175.92 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP G 601 " pdb=" O3A GTP G 601 " pdb=" PA GTP G 601 " pdb=" PB GTP G 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.27 175.85 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP D 601 " pdb=" O3A GTP D 601 " pdb=" PA GTP D 601 " pdb=" PB GTP D 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.51 175.61 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 18517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.245: 4672 0.245 - 0.489: 88 0.489 - 0.734: 0 0.734 - 0.978: 0 0.978 - 1.223: 16 Chirality restraints: 4776 Sorted by residual: chirality pdb=" C2' IMP B 603 " pdb=" C1' IMP B 603 " pdb=" C3' IMP B 603 " pdb=" O2' IMP B 603 " both_signs ideal model delta sigma weight residual False -2.77 -1.55 -1.22 2.00e-01 2.50e+01 3.74e+01 chirality pdb=" C2' IMP G 603 " pdb=" C1' IMP G 603 " pdb=" C3' IMP G 603 " pdb=" O2' IMP G 603 " both_signs ideal model delta sigma weight residual False -2.77 -1.55 -1.22 2.00e-01 2.50e+01 3.73e+01 chirality pdb=" C2' IMP F 603 " pdb=" C1' IMP F 603 " pdb=" C3' IMP F 603 " pdb=" O2' IMP F 603 " both_signs ideal model delta sigma weight residual False -2.77 -1.55 -1.22 2.00e-01 2.50e+01 3.73e+01 ... (remaining 4773 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 180 " 0.079 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO H 181 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO H 181 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 181 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR E 180 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C THR E 180 " 0.052 2.00e-02 2.50e+03 pdb=" O THR E 180 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO E 181 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 180 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C THR G 180 " -0.051 2.00e-02 2.50e+03 pdb=" O THR G 180 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO G 181 " 0.017 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 775 2.68 - 3.24: 30073 3.24 - 3.79: 44310 3.79 - 4.35: 62667 4.35 - 4.90: 105070 Nonbonded interactions: 242895 Sorted by model distance: nonbonded pdb=" O VAL E 73 " pdb=" OG1 THR E 74 " model vdw 2.127 3.040 nonbonded pdb=" O VAL H 73 " pdb=" OG1 THR H 74 " model vdw 2.128 3.040 nonbonded pdb=" O VAL C 73 " pdb=" OG1 THR C 74 " model vdw 2.128 3.040 nonbonded pdb=" O VAL D 73 " pdb=" OG1 THR D 74 " model vdw 2.130 3.040 nonbonded pdb=" O VAL G 73 " pdb=" OG1 THR G 74 " model vdw 2.133 3.040 ... (remaining 242890 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.360 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.007 0.160 30216 Z= 0.375 Angle : 1.241 22.127 41120 Z= 0.601 Chirality : 0.095 1.223 4776 Planarity : 0.005 0.108 5056 Dihedral : 21.227 175.921 11736 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.27 % Favored : 96.52 % Rotamer: Outliers : 0.85 % Allowed : 11.98 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.13), residues: 3704 helix: -0.08 (0.14), residues: 1376 sheet: -0.61 (0.32), residues: 216 loop : -0.98 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 105 TYR 0.013 0.001 TYR D 509 PHE 0.013 0.001 PHE B 456 HIS 0.003 0.001 HIS H 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.37 (30216) covalent geometry : angle 1.24098 / 0.60 (41120) hydrogen bonds : bond 0.14453 / 9.53 ( 1046) hydrogen bonds : angle 6.05735 / 4.23 ( 2841) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 349 time to evaluate : 0.881 Fit side-chains REVERT: A 327 CYS cc_start: 0.8340 (p) cc_final: 0.7988 (p) REVERT: B 327 CYS cc_start: 0.8319 (p) cc_final: 0.7987 (p) REVERT: C 327 CYS cc_start: 0.8287 (p) cc_final: 0.7961 (p) REVERT: D 327 CYS cc_start: 0.8307 (p) cc_final: 0.7969 (p) REVERT: E 327 CYS cc_start: 0.8300 (p) cc_final: 0.7970 (p) REVERT: F 327 CYS cc_start: 0.8341 (p) cc_final: 0.7993 (p) REVERT: G 327 CYS cc_start: 0.8316 (p) cc_final: 0.7988 (p) REVERT: H 327 CYS cc_start: 0.8256 (p) cc_final: 0.7954 (p) outliers start: 26 outliers final: 11 residues processed: 373 average time/residue: 0.1611 time to fit residues: 102.5529 Evaluate side-chains 317 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 306 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain H residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 33 ASN D 33 ASN E 33 ASN F 33 ASN G 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.179199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.152944 restraints weight = 38649.895| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.41 r_work: 0.3896 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30216 Z= 0.136 Angle : 0.670 7.502 41120 Z= 0.328 Chirality : 0.046 0.166 4776 Planarity : 0.005 0.054 5056 Dihedral : 19.464 155.136 5142 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.48 % Favored : 96.30 % Rotamer: Outliers : 1.53 % Allowed : 11.43 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3704 helix: 0.20 (0.14), residues: 1376 sheet: -0.27 (0.27), residues: 328 loop : -0.57 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 412 TYR 0.007 0.001 TYR G 509 PHE 0.009 0.001 PHE F 456 HIS 0.002 0.000 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (30216) covalent geometry : angle 0.66982 / 0.33 (41120) hydrogen bonds : bond 0.03742 / 2.59 ( 1046) hydrogen bonds : angle 4.69746 / 3.33 ( 2841) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 336 time to evaluate : 1.143 Fit side-chains REVERT: A 48 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: A 260 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8398 (tp) REVERT: A 512 LEU cc_start: 0.5945 (tt) cc_final: 0.5703 (tp) REVERT: B 48 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: B 144 ILE cc_start: 0.7868 (mm) cc_final: 0.7544 (mm) REVERT: B 512 LEU cc_start: 0.5994 (tt) cc_final: 0.5748 (tp) REVERT: C 260 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8394 (tp) REVERT: C 512 LEU cc_start: 0.6000 (tt) cc_final: 0.5733 (tp) REVERT: D 144 ILE cc_start: 0.7847 (mm) cc_final: 0.7528 (mm) REVERT: D 512 LEU cc_start: 0.6011 (tt) cc_final: 0.5761 (tp) REVERT: E 144 ILE cc_start: 0.7830 (mm) cc_final: 0.7509 (mm) REVERT: E 512 LEU cc_start: 0.5995 (tt) cc_final: 0.5739 (tp) REVERT: F 48 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: F 260 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8389 (tp) REVERT: F 512 LEU cc_start: 0.5943 (tt) cc_final: 0.5685 (tp) REVERT: G 48 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: G 144 ILE cc_start: 0.7845 (mm) cc_final: 0.7512 (mm) REVERT: G 512 LEU cc_start: 0.5979 (tt) cc_final: 0.5743 (tp) REVERT: H 512 LEU cc_start: 0.5986 (tt) cc_final: 0.5731 (tp) outliers start: 47 outliers final: 34 residues processed: 383 average time/residue: 0.1501 time to fit residues: 102.0507 Evaluate side-chains 339 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 298 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 48 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 119 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 360 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 163 optimal weight: 0.2980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN H 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.172570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146288 restraints weight = 38496.691| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.43 r_work: 0.3800 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 30216 Z= 0.241 Angle : 0.742 7.569 41120 Z= 0.367 Chirality : 0.050 0.185 4776 Planarity : 0.005 0.046 5056 Dihedral : 18.578 157.902 5142 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.10 % Favored : 94.68 % Rotamer: Outliers : 3.16 % Allowed : 14.45 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3704 helix: -0.16 (0.14), residues: 1376 sheet: -0.05 (0.34), residues: 216 loop : -0.66 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 203 TYR 0.012 0.002 TYR G 282 PHE 0.019 0.002 PHE B 139 HIS 0.005 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.24 (30216) covalent geometry : angle 0.74209 / 0.37 (41120) hydrogen bonds : bond 0.04710 / 3.22 ( 1046) hydrogen bonds : angle 4.86843 / 3.43 ( 2841) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 325 time to evaluate : 1.061 Fit side-chains REVERT: A 135 MET cc_start: 0.8470 (tmm) cc_final: 0.8038 (tmm) REVERT: A 144 ILE cc_start: 0.8441 (mm) cc_final: 0.8075 (mt) REVERT: A 448 GLN cc_start: 0.8289 (mm110) cc_final: 0.7994 (tt0) REVERT: A 483 MET cc_start: 0.8865 (tmm) cc_final: 0.8480 (tmm) REVERT: B 135 MET cc_start: 0.8389 (tmm) cc_final: 0.7960 (tmm) REVERT: B 500 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5545 (mt-10) REVERT: C 117 ASP cc_start: 0.8220 (m-30) cc_final: 0.8002 (p0) REVERT: C 135 MET cc_start: 0.8403 (tmm) cc_final: 0.7954 (tmm) REVERT: C 184 GLU cc_start: 0.7497 (tm-30) cc_final: 0.6829 (mt-10) REVERT: C 500 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.5885 (mt-10) REVERT: D 135 MET cc_start: 0.8402 (tmm) cc_final: 0.7958 (tmm) REVERT: D 483 MET cc_start: 0.8832 (tmm) cc_final: 0.8427 (tmm) REVERT: D 500 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.5918 (mt-10) REVERT: E 117 ASP cc_start: 0.8222 (m-30) cc_final: 0.8014 (p0) REVERT: E 135 MET cc_start: 0.8455 (tmm) cc_final: 0.8011 (tmm) REVERT: E 483 MET cc_start: 0.8848 (tmm) cc_final: 0.8438 (tmm) REVERT: E 500 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.5905 (mt-10) REVERT: F 135 MET cc_start: 0.8402 (tmm) cc_final: 0.7973 (tmm) REVERT: F 144 ILE cc_start: 0.8439 (mm) cc_final: 0.8084 (mt) REVERT: F 448 GLN cc_start: 0.8249 (mm110) cc_final: 0.7985 (tt0) REVERT: F 483 MET cc_start: 0.8858 (tmm) cc_final: 0.8467 (tmm) REVERT: G 117 ASP cc_start: 0.8210 (m-30) cc_final: 0.7993 (p0) REVERT: G 135 MET cc_start: 0.8457 (tmm) cc_final: 0.8030 (tmm) REVERT: G 500 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5539 (mt-10) REVERT: H 135 MET cc_start: 0.8395 (tmm) cc_final: 0.7955 (tmm) REVERT: H 144 ILE cc_start: 0.8383 (mm) cc_final: 0.8142 (mm) REVERT: H 184 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6824 (mt-10) REVERT: H 500 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.5914 (mt-10) outliers start: 97 outliers final: 54 residues processed: 404 average time/residue: 0.1665 time to fit residues: 115.8268 Evaluate side-chains 353 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 293 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 370 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN H 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.160964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132523 restraints weight = 38059.868| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.57 r_work: 0.3635 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30216 Z= 0.153 Angle : 0.616 6.315 41120 Z= 0.305 Chirality : 0.046 0.166 4776 Planarity : 0.004 0.043 5056 Dihedral : 17.740 154.206 5128 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.13 % Favored : 96.65 % Rotamer: Outliers : 3.74 % Allowed : 14.91 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3704 helix: 0.21 (0.14), residues: 1368 sheet: -0.09 (0.33), residues: 216 loop : -0.53 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 203 TYR 0.009 0.001 TYR C 348 PHE 0.011 0.002 PHE B 139 HIS 0.001 0.000 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.15 (30216) covalent geometry : angle 0.61589 / 0.31 (41120) hydrogen bonds : bond 0.03603 / 2.48 ( 1046) hydrogen bonds : angle 4.52241 / 3.20 ( 2841) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 331 time to evaluate : 1.039 Fit side-chains REVERT: A 33 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.9086 (m-40) REVERT: A 135 MET cc_start: 0.8441 (tmm) cc_final: 0.7956 (tmm) REVERT: A 448 GLN cc_start: 0.8216 (mm110) cc_final: 0.7908 (tt0) REVERT: A 500 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5750 (mt-10) REVERT: B 135 MET cc_start: 0.8480 (tmm) cc_final: 0.7995 (tmm) REVERT: B 500 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5589 (mt-10) REVERT: C 135 MET cc_start: 0.8264 (tmm) cc_final: 0.7845 (tmm) REVERT: C 260 LEU cc_start: 0.8782 (tt) cc_final: 0.8499 (tp) REVERT: C 500 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.5726 (mt-10) REVERT: D 33 ASN cc_start: 0.9303 (OUTLIER) cc_final: 0.9098 (m-40) REVERT: D 135 MET cc_start: 0.8395 (tmm) cc_final: 0.7937 (tmm) REVERT: D 500 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.5708 (mt-10) REVERT: E 33 ASN cc_start: 0.9288 (OUTLIER) cc_final: 0.9083 (m-40) REVERT: E 135 MET cc_start: 0.8392 (tmm) cc_final: 0.7929 (tmm) REVERT: E 500 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.5716 (mt-10) REVERT: F 33 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.9085 (m-40) REVERT: F 135 MET cc_start: 0.8444 (tmm) cc_final: 0.7956 (tmm) REVERT: F 448 GLN cc_start: 0.8232 (mm110) cc_final: 0.7919 (tt0) REVERT: F 500 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.5749 (mt-10) REVERT: G 135 MET cc_start: 0.8475 (tmm) cc_final: 0.7990 (tmm) REVERT: G 500 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5591 (mt-10) REVERT: H 135 MET cc_start: 0.8453 (tmm) cc_final: 0.7928 (tmm) REVERT: H 184 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6739 (mt-10) REVERT: H 500 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.5731 (mt-10) outliers start: 115 outliers final: 69 residues processed: 417 average time/residue: 0.1586 time to fit residues: 114.3727 Evaluate side-chains 393 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 312 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 201 optimal weight: 0.0020 chunk 230 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 297 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 262 optimal weight: 0.6980 chunk 331 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN C 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.163882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135543 restraints weight = 38032.948| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.57 r_work: 0.3678 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 30216 Z= 0.110 Angle : 0.577 6.362 41120 Z= 0.280 Chirality : 0.044 0.157 4776 Planarity : 0.004 0.044 5056 Dihedral : 17.092 154.202 5128 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.48 % Favored : 96.30 % Rotamer: Outliers : 3.16 % Allowed : 16.63 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3704 helix: 0.49 (0.15), residues: 1368 sheet: -0.29 (0.29), residues: 280 loop : -0.33 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 412 TYR 0.008 0.001 TYR H 348 PHE 0.009 0.001 PHE A 456 HIS 0.002 0.000 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (30216) covalent geometry : angle 0.57682 / 0.28 (41120) hydrogen bonds : bond 0.03123 / 2.15 ( 1046) hydrogen bonds : angle 4.27152 / 3.03 ( 2841) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 359 time to evaluate : 1.190 Fit side-chains REVERT: A 204 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.7913 (p) REVERT: A 500 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.5861 (mt-10) REVERT: B 204 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.7904 (p) REVERT: B 500 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5769 (mt-10) REVERT: C 82 MET cc_start: 0.8788 (tpt) cc_final: 0.8502 (tpt) REVERT: C 204 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.7902 (p) REVERT: C 500 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5652 (mt-10) REVERT: D 204 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.7885 (p) REVERT: D 500 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.5728 (mt-10) REVERT: E 204 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.7900 (p) REVERT: E 500 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5688 (mt-10) REVERT: F 204 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.7924 (p) REVERT: F 500 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.5796 (mt-10) REVERT: G 204 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.7910 (p) REVERT: G 500 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.5781 (mt-10) REVERT: H 82 MET cc_start: 0.8784 (tpt) cc_final: 0.8536 (tpt) REVERT: H 204 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.7909 (p) REVERT: H 500 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5659 (mt-10) outliers start: 97 outliers final: 54 residues processed: 436 average time/residue: 0.1749 time to fit residues: 128.2020 Evaluate side-chains 368 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 298 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 84 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 336 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 274 optimal weight: 8.9990 chunk 341 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 188 optimal weight: 0.1980 chunk 83 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN C 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.162377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131879 restraints weight = 39548.024| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.67 r_work: 0.3603 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30216 Z= 0.159 Angle : 0.612 6.701 41120 Z= 0.300 Chirality : 0.046 0.163 4776 Planarity : 0.004 0.042 5056 Dihedral : 17.104 155.065 5128 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.97 % Favored : 95.82 % Rotamer: Outliers : 3.81 % Allowed : 15.40 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3704 helix: 0.39 (0.14), residues: 1376 sheet: -0.48 (0.29), residues: 280 loop : -0.39 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 203 TYR 0.012 0.001 TYR C 509 PHE 0.011 0.002 PHE H 35 HIS 0.002 0.001 HIS E 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 (30216) covalent geometry : angle 0.61153 / 0.30 (41120) hydrogen bonds : bond 0.03560 / 2.45 ( 1046) hydrogen bonds : angle 4.35671 / 3.09 ( 2841) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 301 time to evaluate : 1.239 Fit side-chains REVERT: A 82 MET cc_start: 0.8907 (tpt) cc_final: 0.8414 (tpt) REVERT: A 204 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7918 (p) REVERT: A 500 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.5823 (mt-10) REVERT: B 82 MET cc_start: 0.8917 (tpt) cc_final: 0.8589 (tpt) REVERT: B 204 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.7902 (p) REVERT: B 500 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.5780 (mt-10) REVERT: C 82 MET cc_start: 0.8845 (tpt) cc_final: 0.8267 (tpt) REVERT: C 500 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.5897 (mt-10) REVERT: D 204 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.7899 (p) REVERT: D 500 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.5731 (mt-10) REVERT: E 204 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.7917 (p) REVERT: E 500 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5739 (mt-10) REVERT: F 82 MET cc_start: 0.8908 (tpt) cc_final: 0.8412 (tpt) REVERT: F 204 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.7926 (p) REVERT: F 500 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.5823 (mt-10) REVERT: G 82 MET cc_start: 0.8906 (tpt) cc_final: 0.8498 (tpt) REVERT: G 204 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.7910 (p) REVERT: G 483 MET cc_start: 0.8921 (tmm) cc_final: 0.8675 (tmm) REVERT: G 500 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.5790 (mt-10) REVERT: H 82 MET cc_start: 0.8845 (tpt) cc_final: 0.8271 (tpt) REVERT: H 500 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.5907 (mt-10) outliers start: 117 outliers final: 78 residues processed: 407 average time/residue: 0.1812 time to fit residues: 124.3514 Evaluate side-chains 377 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 285 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 154 optimal weight: 0.7980 chunk 273 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 354 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 345 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 298 optimal weight: 9.9990 chunk 338 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 372 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 21 GLN B 33 ASN C 21 GLN C 33 ASN D 21 GLN E 21 GLN F 21 GLN G 21 GLN G 33 ASN H 21 GLN H 33 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.163106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134998 restraints weight = 37988.232| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.55 r_work: 0.3657 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 30216 Z= 0.111 Angle : 0.566 6.385 41120 Z= 0.275 Chirality : 0.043 0.158 4776 Planarity : 0.004 0.042 5056 Dihedral : 16.673 155.227 5128 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.65 % Favored : 97.14 % Rotamer: Outliers : 2.51 % Allowed : 16.57 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3704 helix: 0.60 (0.14), residues: 1376 sheet: -0.66 (0.26), residues: 320 loop : -0.29 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 224 TYR 0.012 0.001 TYR C 509 PHE 0.009 0.001 PHE F 456 HIS 0.002 0.000 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (30216) covalent geometry : angle 0.56567 / 0.28 (41120) hydrogen bonds : bond 0.03033 / 2.10 ( 1046) hydrogen bonds : angle 4.20851 / 2.99 ( 2841) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 320 time to evaluate : 1.214 Fit side-chains REVERT: A 500 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.5823 (mt-10) REVERT: B 94 ASN cc_start: 0.9422 (t0) cc_final: 0.9154 (t0) REVERT: B 204 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.7905 (p) REVERT: B 500 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.5847 (mt-10) REVERT: C 483 MET cc_start: 0.9008 (tmm) cc_final: 0.8751 (tmm) REVERT: C 500 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.5689 (mt-10) REVERT: D 204 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.7888 (p) REVERT: D 500 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.5824 (mt-10) REVERT: E 94 ASN cc_start: 0.9414 (t0) cc_final: 0.9143 (t0) REVERT: E 204 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.7916 (p) REVERT: E 500 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.5834 (mt-10) REVERT: F 500 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5827 (mt-10) REVERT: G 94 ASN cc_start: 0.9416 (t0) cc_final: 0.9145 (t0) REVERT: G 204 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.7904 (p) REVERT: G 500 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.5869 (mt-10) REVERT: H 483 MET cc_start: 0.9006 (tmm) cc_final: 0.8785 (tmm) REVERT: H 500 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5701 (mt-10) outliers start: 77 outliers final: 54 residues processed: 385 average time/residue: 0.1840 time to fit residues: 117.8839 Evaluate side-chains 361 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 295 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 303 optimal weight: 0.6980 chunk 363 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 344 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 366 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 33 ASN C 33 ASN C 112 GLN D 33 ASN E 33 ASN E 112 GLN F 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.162623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.133971 restraints weight = 38064.601| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.59 r_work: 0.3645 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30216 Z= 0.120 Angle : 0.569 8.056 41120 Z= 0.276 Chirality : 0.044 0.157 4776 Planarity : 0.004 0.041 5056 Dihedral : 16.521 155.952 5128 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.91 % Favored : 95.87 % Rotamer: Outliers : 3.06 % Allowed : 16.34 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3704 helix: 0.63 (0.14), residues: 1376 sheet: -0.59 (0.26), residues: 320 loop : -0.26 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 224 TYR 0.012 0.001 TYR H 509 PHE 0.010 0.001 PHE D 35 HIS 0.001 0.000 HIS D 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (30216) covalent geometry : angle 0.56934 / 0.28 (41120) hydrogen bonds : bond 0.03114 / 2.15 ( 1046) hydrogen bonds : angle 4.16808 / 2.96 ( 2841) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 296 time to evaluate : 1.150 Fit side-chains REVERT: A 204 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.7882 (p) REVERT: A 500 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.5875 (mt-10) REVERT: B 94 ASN cc_start: 0.9440 (t0) cc_final: 0.9149 (t0) REVERT: B 204 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.7895 (p) REVERT: B 500 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.5934 (mt-10) REVERT: C 94 ASN cc_start: 0.9435 (t0) cc_final: 0.9137 (t0) REVERT: C 483 MET cc_start: 0.9022 (tmm) cc_final: 0.8788 (tmm) REVERT: C 500 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5750 (mt-10) REVERT: D 204 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.7867 (p) REVERT: D 500 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.5755 (mt-10) REVERT: E 94 ASN cc_start: 0.9439 (t0) cc_final: 0.9166 (t0) REVERT: E 204 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.7895 (p) REVERT: E 500 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.5764 (mt-10) REVERT: F 204 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.7882 (p) REVERT: F 500 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.5870 (mt-10) REVERT: G 94 ASN cc_start: 0.9434 (t0) cc_final: 0.9161 (t0) REVERT: G 204 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.7885 (p) REVERT: G 500 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.5935 (mt-10) REVERT: H 500 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5753 (mt-10) outliers start: 94 outliers final: 65 residues processed: 372 average time/residue: 0.1685 time to fit residues: 107.2481 Evaluate side-chains 360 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 281 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 72 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 280 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 241 optimal weight: 0.0670 chunk 177 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 292 optimal weight: 3.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 33 ASN C 33 ASN D 33 ASN E 33 ASN F 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135257 restraints weight = 37970.263| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.59 r_work: 0.3661 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30216 Z= 0.110 Angle : 0.563 8.434 41120 Z= 0.273 Chirality : 0.044 0.159 4776 Planarity : 0.004 0.040 5056 Dihedral : 16.252 156.330 5128 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.73 % Favored : 97.06 % Rotamer: Outliers : 2.86 % Allowed : 17.06 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3704 helix: 0.72 (0.14), residues: 1384 sheet: -0.52 (0.26), residues: 320 loop : -0.20 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 322 TYR 0.014 0.001 TYR A 509 PHE 0.009 0.001 PHE F 456 HIS 0.002 0.000 HIS E 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (30216) covalent geometry : angle 0.56340 / 0.27 (41120) hydrogen bonds : bond 0.02936 / 2.03 ( 1046) hydrogen bonds : angle 4.11200 / 2.92 ( 2841) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 309 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.9410 (t0) cc_final: 0.9114 (t0) REVERT: A 204 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.7870 (p) REVERT: A 483 MET cc_start: 0.9027 (tmm) cc_final: 0.8811 (tmm) REVERT: A 500 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.5852 (mt-10) REVERT: B 94 ASN cc_start: 0.9423 (t0) cc_final: 0.9165 (t0) REVERT: B 204 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.7850 (p) REVERT: B 500 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.5879 (mt-10) REVERT: C 94 ASN cc_start: 0.9421 (t0) cc_final: 0.9153 (t0) REVERT: C 483 MET cc_start: 0.9017 (tmm) cc_final: 0.8760 (tmm) REVERT: C 500 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5831 (mt-10) REVERT: D 94 ASN cc_start: 0.9412 (t0) cc_final: 0.9118 (t0) REVERT: D 204 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.7838 (p) REVERT: D 483 MET cc_start: 0.9032 (tmm) cc_final: 0.8824 (tmm) REVERT: D 500 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5932 (mt-10) REVERT: E 94 ASN cc_start: 0.9425 (t0) cc_final: 0.9164 (t0) REVERT: E 204 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.7857 (p) REVERT: E 483 MET cc_start: 0.9034 (tmm) cc_final: 0.8821 (tmm) REVERT: E 500 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.5932 (mt-10) REVERT: F 94 ASN cc_start: 0.9407 (t0) cc_final: 0.9109 (t0) REVERT: F 204 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7862 (p) REVERT: F 483 MET cc_start: 0.9038 (tmm) cc_final: 0.8828 (tmm) REVERT: F 500 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.5858 (mt-10) REVERT: G 94 ASN cc_start: 0.9421 (t0) cc_final: 0.9158 (t0) REVERT: G 204 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.7839 (p) REVERT: G 500 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.5876 (mt-10) REVERT: H 94 ASN cc_start: 0.9424 (t0) cc_final: 0.9155 (t0) REVERT: H 500 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.5836 (mt-10) outliers start: 88 outliers final: 70 residues processed: 384 average time/residue: 0.1702 time to fit residues: 111.6903 Evaluate side-chains 377 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 293 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 58 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 287 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 278 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 368 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 21 GLN B 33 ASN D 33 ASN E 33 ASN F 33 ASN G 33 ASN H 33 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.161447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132844 restraints weight = 37949.232| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.59 r_work: 0.3637 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30216 Z= 0.137 Angle : 0.587 8.610 41120 Z= 0.286 Chirality : 0.045 0.171 4776 Planarity : 0.004 0.045 5056 Dihedral : 16.329 157.413 5128 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.27 % Favored : 95.52 % Rotamer: Outliers : 2.96 % Allowed : 17.81 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3704 helix: 0.65 (0.14), residues: 1384 sheet: -0.61 (0.26), residues: 320 loop : -0.30 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 322 TYR 0.013 0.001 TYR B 509 PHE 0.013 0.001 PHE H 35 HIS 0.002 0.000 HIS B 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (30216) covalent geometry : angle 0.58728 / 0.29 (41120) hydrogen bonds : bond 0.03232 / 2.24 ( 1046) hydrogen bonds : angle 4.18061 / 2.97 ( 2841) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 293 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7891 (p) REVERT: A 500 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.5891 (mt-10) REVERT: B 94 ASN cc_start: 0.9435 (t0) cc_final: 0.9153 (t0) REVERT: B 204 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.7849 (p) REVERT: B 500 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.5921 (mt-10) REVERT: C 94 ASN cc_start: 0.9448 (t0) cc_final: 0.9167 (t0) REVERT: C 500 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.5855 (mt-10) REVERT: D 204 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.7848 (p) REVERT: D 500 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.5927 (mt-10) REVERT: E 94 ASN cc_start: 0.9434 (t0) cc_final: 0.9163 (t0) REVERT: E 204 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.7858 (p) REVERT: E 500 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.5955 (mt-10) REVERT: F 204 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7890 (p) REVERT: F 500 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.5904 (mt-10) REVERT: G 94 ASN cc_start: 0.9427 (t0) cc_final: 0.9145 (t0) REVERT: G 204 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.7849 (p) REVERT: G 500 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.5923 (mt-10) REVERT: H 94 ASN cc_start: 0.9430 (t0) cc_final: 0.9159 (t0) REVERT: H 500 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5852 (mt-10) outliers start: 91 outliers final: 70 residues processed: 374 average time/residue: 0.1675 time to fit residues: 107.7188 Evaluate side-chains 367 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 283 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 0.0060 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 160 optimal weight: 0.5980 chunk 339 optimal weight: 0.9990 chunk 282 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 353 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 448 GLN B 33 ASN C 33 ASN D 33 ASN E 33 ASN F 33 ASN F 448 GLN G 33 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.163417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134810 restraints weight = 38184.197| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.60 r_work: 0.3661 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30216 Z= 0.108 Angle : 0.565 8.649 41120 Z= 0.274 Chirality : 0.043 0.191 4776 Planarity : 0.004 0.044 5056 Dihedral : 16.125 158.110 5128 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.92 % Favored : 96.87 % Rotamer: Outliers : 2.67 % Allowed : 18.49 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3704 helix: 0.78 (0.14), residues: 1392 sheet: -0.49 (0.26), residues: 320 loop : -0.21 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 224 TYR 0.015 0.001 TYR A 509 PHE 0.009 0.001 PHE A 456 HIS 0.001 0.000 HIS D 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (30216) covalent geometry : angle 0.56505 / 0.27 (41120) hydrogen bonds : bond 0.02949 / 2.04 ( 1046) hydrogen bonds : angle 4.10985 / 2.93 ( 2841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7411.17 seconds wall clock time: 127 minutes 53.96 seconds (7673.96 seconds total)