Starting phenix.real_space_refine on Sat Feb 7 08:42:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6l_44265/02_2026/9b6l_44265.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6l_44265/02_2026/9b6l_44265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b6l_44265/02_2026/9b6l_44265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6l_44265/02_2026/9b6l_44265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b6l_44265/02_2026/9b6l_44265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6l_44265/02_2026/9b6l_44265.map" } resolution = 2.33 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= 0.096 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 Mg 10 5.21 5 S 170 5.16 5 C 20150 2.51 5 N 5260 2.21 5 O 5720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31310 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3130 Classifications: {'peptide': 399} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3130 Classifications: {'peptide': 399} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3130 Classifications: {'peptide': 399} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3130 Classifications: {'peptide': 399} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3130 Classifications: {'peptide': 399} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3130 Classifications: {'peptide': 399} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3130 Classifications: {'peptide': 399} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3130 Classifications: {'peptide': 399} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3130 Classifications: {'peptide': 399} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3130 Classifications: {'peptide': 399} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.16, per 1000 atoms: 0.23 Number of scatterers: 31310 At special positions: 0 Unit cell: (169.05, 162.75, 108.15, 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 170 16.00 Mg 10 11.99 O 5720 8.00 N 5260 7.00 C 20150 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: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 20 sheets defined 46.6% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 7 through 13 removed outlier: 3.520A pdb=" N LEU A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 19 Processing helix chain 'A' and resid 47 through 60 Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.798A pdb=" N ILE A 109 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 174 through 188 Processing helix chain 'A' and resid 206 through 226 Processing helix chain 'A' and resid 239 through 252 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 407 through 416 Processing helix chain 'A' and resid 434 through 452 Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'B' and resid 47 through 60 Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.776A pdb=" N ILE B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 174 through 188 Processing helix chain 'B' and resid 206 through 226 Processing helix chain 'B' and resid 239 through 252 Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 293 through 298 Processing helix chain 'B' and resid 306 through 318 Processing helix chain 'B' and resid 404 through 406 No H-bonds generated for 'chain 'B' and resid 404 through 406' Processing helix chain 'B' and resid 407 through 416 Processing helix chain 'B' and resid 434 through 452 Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'C' and resid 8 through 12 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 105 through 114 removed outlier: 3.802A pdb=" N ILE C 109 " --> pdb=" O ASN C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 174 through 188 Processing helix chain 'C' and resid 206 through 226 Processing helix chain 'C' and resid 239 through 252 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'C' and resid 306 through 318 Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 407 through 416 Processing helix chain 'C' and resid 434 through 452 Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'D' and resid 8 through 12 Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 47 through 60 Processing helix chain 'D' and resid 71 through 77 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.813A pdb=" N ILE D 109 " --> pdb=" O ASN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 174 through 188 Processing helix chain 'D' and resid 206 through 226 Processing helix chain 'D' and resid 239 through 252 Processing helix chain 'D' and resid 270 through 281 Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 306 through 318 Processing helix chain 'D' and resid 404 through 406 No H-bonds generated for 'chain 'D' and resid 404 through 406' Processing helix chain 'D' and resid 407 through 416 Processing helix chain 'D' and resid 434 through 452 Processing helix chain 'D' and resid 454 through 459 Processing helix chain 'E' and resid 8 through 13 Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 71 through 77 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 105 through 114 removed outlier: 3.773A pdb=" N ILE E 109 " --> pdb=" O ASN E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 174 through 188 Processing helix chain 'E' and resid 206 through 226 Processing helix chain 'E' and resid 239 through 252 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 293 through 298 Processing helix chain 'E' and resid 306 through 318 Processing helix chain 'E' and resid 404 through 406 No H-bonds generated for 'chain 'E' and resid 404 through 406' Processing helix chain 'E' and resid 407 through 416 Processing helix chain 'E' and resid 434 through 452 Processing helix chain 'E' and resid 454 through 459 Processing helix chain 'F' and resid 8 through 13 Processing helix chain 'F' and resid 14 through 19 Processing helix chain 'F' and resid 47 through 60 Processing helix chain 'F' and resid 71 through 77 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 105 through 114 removed outlier: 3.788A pdb=" N ILE F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 134 through 139 Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 174 through 188 Processing helix chain 'F' and resid 206 through 226 Processing helix chain 'F' and resid 239 through 252 Processing helix chain 'F' and resid 270 through 281 Processing helix chain 'F' and resid 293 through 298 Processing helix chain 'F' and resid 306 through 318 Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 407 through 416 Processing helix chain 'F' and resid 434 through 452 Processing helix chain 'F' and resid 454 through 459 Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 14 through 19 Processing helix chain 'G' and resid 47 through 60 Processing helix chain 'G' and resid 71 through 77 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 105 through 114 removed outlier: 3.767A pdb=" N ILE G 109 " --> pdb=" O ASN G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 120 Processing helix chain 'G' and resid 134 through 140 removed outlier: 4.141A pdb=" N GLN G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 174 through 188 Processing helix chain 'G' and resid 206 through 226 Processing helix chain 'G' and resid 239 through 252 Processing helix chain 'G' and resid 270 through 281 Processing helix chain 'G' and resid 293 through 298 Processing helix chain 'G' and resid 306 through 318 Processing helix chain 'G' and resid 404 through 406 No H-bonds generated for 'chain 'G' and resid 404 through 406' Processing helix chain 'G' and resid 407 through 416 Processing helix chain 'G' and resid 434 through 452 Processing helix chain 'G' and resid 454 through 459 Processing helix chain 'H' and resid 8 through 13 removed outlier: 3.501A pdb=" N THR H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU H 13 " --> pdb=" O LEU H 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 8 through 13' Processing helix chain 'H' and resid 14 through 19 Processing helix chain 'H' and resid 47 through 60 Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 105 through 114 removed outlier: 3.764A pdb=" N ILE H 109 " --> pdb=" O ASN H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 120 Processing helix chain 'H' and resid 134 through 140 removed outlier: 4.140A pdb=" N GLN H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 156 Processing helix chain 'H' and resid 174 through 188 Processing helix chain 'H' and resid 206 through 226 Processing helix chain 'H' and resid 239 through 252 Processing helix chain 'H' and resid 270 through 281 Processing helix chain 'H' and resid 293 through 298 Processing helix chain 'H' and resid 306 through 318 Processing helix chain 'H' and resid 404 through 406 No H-bonds generated for 'chain 'H' and resid 404 through 406' Processing helix chain 'H' and resid 407 through 416 Processing helix chain 'H' and resid 434 through 452 Processing helix chain 'H' and resid 454 through 459 Processing helix chain 'I' and resid 8 through 13 removed outlier: 3.557A pdb=" N LEU I 13 " --> pdb=" O LEU I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 19 Processing helix chain 'I' and resid 47 through 60 Processing helix chain 'I' and resid 71 through 77 Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 105 through 114 removed outlier: 3.785A pdb=" N ILE I 109 " --> pdb=" O ASN I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 120 Processing helix chain 'I' and resid 134 through 139 Processing helix chain 'I' and resid 147 through 156 Processing helix chain 'I' and resid 174 through 188 Processing helix chain 'I' and resid 206 through 226 Processing helix chain 'I' and resid 239 through 252 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 293 through 298 Processing helix chain 'I' and resid 306 through 318 Processing helix chain 'I' and resid 404 through 406 No H-bonds generated for 'chain 'I' and resid 404 through 406' Processing helix chain 'I' and resid 407 through 416 Processing helix chain 'I' and resid 434 through 452 Processing helix chain 'I' and resid 454 through 459 Processing helix chain 'J' and resid 8 through 13 removed outlier: 3.521A pdb=" N LEU J 13 " --> pdb=" O LEU J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 19 Processing helix chain 'J' and resid 47 through 60 Processing helix chain 'J' and resid 71 through 77 Processing helix chain 'J' and resid 98 through 100 No H-bonds generated for 'chain 'J' and resid 98 through 100' Processing helix chain 'J' and resid 105 through 114 removed outlier: 3.798A pdb=" N ILE J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 120 Processing helix chain 'J' and resid 134 through 139 Processing helix chain 'J' and resid 147 through 156 Processing helix chain 'J' and resid 174 through 188 Processing helix chain 'J' and resid 206 through 226 Processing helix chain 'J' and resid 239 through 252 Processing helix chain 'J' and resid 270 through 281 Processing helix chain 'J' and resid 293 through 298 Processing helix chain 'J' and resid 306 through 318 Processing helix chain 'J' and resid 404 through 406 No H-bonds generated for 'chain 'J' and resid 404 through 406' Processing helix chain 'J' and resid 407 through 416 Processing helix chain 'J' and resid 434 through 452 Processing helix chain 'J' and resid 454 through 459 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 85 removed outlier: 5.757A pdb=" N VAL A 81 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA A 94 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 83 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP A 130 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS A 39 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU A 128 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE A 41 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU A 126 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N GLY A 304 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 126 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 166 removed outlier: 6.536A pdb=" N LEU A 163 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N KCX A 194 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 165 " --> pdb=" O KCX A 194 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 193 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASN A 234 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS A 231 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 263 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N PHE A 233 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASP A 265 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TYR A 260 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N HIS A 287 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 262 " --> pdb=" O HIS A 287 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HIS A 289 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE A 264 " --> pdb=" O HIS A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 85 removed outlier: 5.644A pdb=" N VAL B 81 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 83 " --> pdb=" O TRP B 92 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR B 33 " --> pdb=" O TRP B 132 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TRP B 132 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 35 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP B 130 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL B 37 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU B 128 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS B 39 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 126 " --> pdb=" O HIS B 39 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE B 41 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLY B 304 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B 126 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 162 through 166 removed outlier: 6.548A pdb=" N LEU B 163 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N KCX B 194 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR B 165 " --> pdb=" O KCX B 194 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 193 " --> pdb=" O SER B 232 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ASN B 234 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N HIS B 231 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B 263 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE B 233 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ASP B 265 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N TYR B 260 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N HIS B 287 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE B 262 " --> pdb=" O HIS B 287 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS B 289 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE B 264 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE B 162 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N MET B 424 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLY B 164 " --> pdb=" O MET B 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 85 removed outlier: 5.687A pdb=" N VAL C 81 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA C 94 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 83 " --> pdb=" O TRP C 92 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 35 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL C 131 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C 37 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLY C 304 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU C 126 " --> pdb=" O GLY C 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 166 removed outlier: 6.414A pdb=" N LEU C 163 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N KCX C 194 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR C 165 " --> pdb=" O KCX C 194 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 193 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASN C 234 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N HIS C 231 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU C 263 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE C 233 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ASP C 265 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR C 260 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N HIS C 287 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE C 262 " --> pdb=" O HIS C 287 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N HIS C 289 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE C 264 " --> pdb=" O HIS C 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 85 removed outlier: 5.684A pdb=" N VAL D 81 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA D 94 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 83 " --> pdb=" O TRP D 92 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU D 35 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL D 131 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL D 37 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLY D 304 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU D 126 " --> pdb=" O GLY D 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 162 through 166 removed outlier: 6.411A pdb=" N LEU D 163 " --> pdb=" O PHE D 192 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N KCX D 194 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR D 165 " --> pdb=" O KCX D 194 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL D 193 " --> pdb=" O SER D 232 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ASN D 234 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS D 231 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU D 263 " --> pdb=" O HIS D 231 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE D 233 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ASP D 265 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N TYR D 260 " --> pdb=" O PHE D 285 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N HIS D 287 " --> pdb=" O TYR D 260 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE D 262 " --> pdb=" O HIS D 287 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N HIS D 289 " --> pdb=" O PHE D 262 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE D 264 " --> pdb=" O HIS D 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 80 through 85 removed outlier: 5.644A pdb=" N VAL E 81 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA E 94 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN E 83 " --> pdb=" O TRP E 92 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR E 33 " --> pdb=" O TRP E 132 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP E 132 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU E 35 " --> pdb=" O ASP E 130 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP E 130 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL E 37 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU E 128 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N HIS E 39 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 126 " --> pdb=" O HIS E 39 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE E 41 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLY E 304 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU E 126 " --> pdb=" O GLY E 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 162 through 166 removed outlier: 6.549A pdb=" N LEU E 163 " --> pdb=" O PHE E 192 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N KCX E 194 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR E 165 " --> pdb=" O KCX E 194 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL E 193 " --> pdb=" O SER E 232 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ASN E 234 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS E 231 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU E 263 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE E 233 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ASP E 265 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N TYR E 260 " --> pdb=" O PHE E 285 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N HIS E 287 " --> pdb=" O TYR E 260 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE E 262 " --> pdb=" O HIS E 287 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N HIS E 289 " --> pdb=" O PHE E 262 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE E 264 " --> pdb=" O HIS E 289 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE E 162 " --> pdb=" O THR E 422 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N MET E 424 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLY E 164 " --> pdb=" O MET E 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 80 through 85 removed outlier: 5.667A pdb=" N VAL F 81 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA F 94 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN F 83 " --> pdb=" O TRP F 92 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR F 33 " --> pdb=" O TRP F 132 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TRP F 132 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU F 35 " --> pdb=" O ASP F 130 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP F 130 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL F 37 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU F 128 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS F 39 " --> pdb=" O LEU F 126 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 126 " --> pdb=" O HIS F 39 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE F 41 " --> pdb=" O SER F 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 162 through 166 removed outlier: 6.535A pdb=" N LEU F 163 " --> pdb=" O PHE F 192 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N KCX F 194 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR F 165 " --> pdb=" O KCX F 194 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL F 193 " --> pdb=" O SER F 232 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ASN F 234 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS F 231 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU F 263 " --> pdb=" O HIS F 231 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE F 233 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ASP F 265 " --> pdb=" O PHE F 233 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N TYR F 260 " --> pdb=" O PHE F 285 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N HIS F 287 " --> pdb=" O TYR F 260 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE F 262 " --> pdb=" O HIS F 287 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N HIS F 289 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE F 264 " --> pdb=" O HIS F 289 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE F 162 " --> pdb=" O THR F 422 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N MET F 424 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLY F 164 " --> pdb=" O MET F 424 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 80 through 85 removed outlier: 5.734A pdb=" N VAL G 81 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA G 94 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN G 83 " --> pdb=" O TRP G 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU G 35 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL G 131 " --> pdb=" O LEU G 35 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL G 37 " --> pdb=" O LEU G 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 166 removed outlier: 6.443A pdb=" N LEU G 163 " --> pdb=" O PHE G 192 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N KCX G 194 " --> pdb=" O LEU G 163 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR G 165 " --> pdb=" O KCX G 194 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL G 193 " --> pdb=" O SER G 232 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ASN G 234 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N HIS G 231 " --> pdb=" O ALA G 261 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU G 263 " --> pdb=" O HIS G 231 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE G 233 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP G 265 " --> pdb=" O PHE G 233 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N TYR G 260 " --> pdb=" O PHE G 285 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N HIS G 287 " --> pdb=" O TYR G 260 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE G 262 " --> pdb=" O HIS G 287 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N HIS G 289 " --> pdb=" O PHE G 262 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE G 264 " --> pdb=" O HIS G 289 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE G 162 " --> pdb=" O THR G 422 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N MET G 424 " --> pdb=" O ILE G 162 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY G 164 " --> pdb=" O MET G 424 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 80 through 85 removed outlier: 5.731A pdb=" N VAL H 81 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA H 94 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN H 83 " --> pdb=" O TRP H 92 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU H 35 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL H 131 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL H 37 " --> pdb=" O LEU H 129 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 162 through 166 removed outlier: 6.447A pdb=" N LEU H 163 " --> pdb=" O PHE H 192 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N KCX H 194 " --> pdb=" O LEU H 163 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR H 165 " --> pdb=" O KCX H 194 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL H 193 " --> pdb=" O SER H 232 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN H 234 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N HIS H 231 " --> pdb=" O ALA H 261 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU H 263 " --> pdb=" O HIS H 231 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE H 233 " --> pdb=" O LEU H 263 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASP H 265 " --> pdb=" O PHE H 233 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N TYR H 260 " --> pdb=" O PHE H 285 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N HIS H 287 " --> pdb=" O TYR H 260 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE H 262 " --> pdb=" O HIS H 287 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N HIS H 289 " --> pdb=" O PHE H 262 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE H 264 " --> pdb=" O HIS H 289 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE H 162 " --> pdb=" O THR H 422 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N MET H 424 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLY H 164 " --> pdb=" O MET H 424 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 80 through 85 removed outlier: 5.667A pdb=" N VAL I 81 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA I 94 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN I 83 " --> pdb=" O TRP I 92 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR I 33 " --> pdb=" O TRP I 132 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP I 132 " --> pdb=" O TYR I 33 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU I 35 " --> pdb=" O ASP I 130 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP I 130 " --> pdb=" O LEU I 35 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL I 37 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU I 128 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS I 39 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU I 126 " --> pdb=" O HIS I 39 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE I 41 " --> pdb=" O SER I 124 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 162 through 166 removed outlier: 6.538A pdb=" N LEU I 163 " --> pdb=" O PHE I 192 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N KCX I 194 " --> pdb=" O LEU I 163 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR I 165 " --> pdb=" O KCX I 194 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL I 193 " --> pdb=" O SER I 232 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASN I 234 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N HIS I 231 " --> pdb=" O ALA I 261 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU I 263 " --> pdb=" O HIS I 231 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE I 233 " --> pdb=" O LEU I 263 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP I 265 " --> pdb=" O PHE I 233 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N TYR I 260 " --> pdb=" O PHE I 285 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N HIS I 287 " --> pdb=" O TYR I 260 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE I 262 " --> pdb=" O HIS I 287 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N HIS I 289 " --> pdb=" O PHE I 262 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE I 264 " --> pdb=" O HIS I 289 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 80 through 85 removed outlier: 5.758A pdb=" N VAL J 81 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA J 94 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN J 83 " --> pdb=" O TRP J 92 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP J 130 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N HIS J 39 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU J 128 " --> pdb=" O HIS J 39 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE J 41 " --> pdb=" O LEU J 126 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU J 126 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N GLY J 304 " --> pdb=" O SER J 124 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU J 126 " --> pdb=" O GLY J 304 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 162 through 166 removed outlier: 6.540A pdb=" N LEU J 163 " --> pdb=" O PHE J 192 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N KCX J 194 " --> pdb=" O LEU J 163 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR J 165 " --> pdb=" O KCX J 194 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL J 193 " --> pdb=" O SER J 232 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASN J 234 " --> pdb=" O VAL J 193 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N HIS J 231 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU J 263 " --> pdb=" O HIS J 231 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE J 233 " --> pdb=" O LEU J 263 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP J 265 " --> pdb=" O PHE J 233 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N TYR J 260 " --> pdb=" O PHE J 285 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N HIS J 287 " --> pdb=" O TYR J 260 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE J 262 " --> pdb=" O HIS J 287 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N HIS J 289 " --> pdb=" O PHE J 262 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE J 264 " --> pdb=" O HIS J 289 " (cutoff:3.500A) 1346 hydrogen bonds defined for protein. 3876 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.31 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10080 1.34 - 1.46: 7694 1.46 - 1.58: 14016 1.58 - 1.70: 0 1.70 - 1.82: 280 Bond restraints: 32070 Sorted by residual: bond pdb=" NZ KCX G 194 " pdb=" CX KCX G 194 " ideal model delta sigma weight residual 1.411 1.326 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" NZ KCX B 194 " pdb=" CX KCX B 194 " ideal model delta sigma weight residual 1.411 1.326 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" NZ KCX F 194 " pdb=" CX KCX F 194 " ideal model delta sigma weight residual 1.411 1.326 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" NZ KCX A 194 " pdb=" CX KCX A 194 " ideal model delta sigma weight residual 1.411 1.326 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" NZ KCX I 194 " pdb=" CX KCX I 194 " ideal model delta sigma weight residual 1.411 1.326 0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 32065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 43325 4.51 - 9.03: 73 9.03 - 13.54: 12 13.54 - 18.05: 0 18.05 - 22.57: 10 Bond angle restraints: 43420 Sorted by residual: angle pdb=" C SER B 361 " pdb=" N LYS B 362 " pdb=" CA LYS B 362 " ideal model delta sigma weight residual 121.70 144.27 -22.57 1.80e+00 3.09e-01 1.57e+02 angle pdb=" C SER E 361 " pdb=" N LYS E 362 " pdb=" CA LYS E 362 " ideal model delta sigma weight residual 121.70 144.14 -22.44 1.80e+00 3.09e-01 1.55e+02 angle pdb=" C SER D 361 " pdb=" N LYS D 362 " pdb=" CA LYS D 362 " ideal model delta sigma weight residual 121.70 144.14 -22.44 1.80e+00 3.09e-01 1.55e+02 angle pdb=" C SER C 361 " pdb=" N LYS C 362 " pdb=" CA LYS C 362 " ideal model delta sigma weight residual 121.70 144.05 -22.35 1.80e+00 3.09e-01 1.54e+02 angle pdb=" C SER A 361 " pdb=" N LYS A 362 " pdb=" CA LYS A 362 " ideal model delta sigma weight residual 121.70 144.03 -22.33 1.80e+00 3.09e-01 1.54e+02 ... (remaining 43415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16547 17.98 - 35.96: 1650 35.96 - 53.93: 451 53.93 - 71.91: 165 71.91 - 89.89: 17 Dihedral angle restraints: 18830 sinusoidal: 7440 harmonic: 11390 Sorted by residual: dihedral pdb=" CA TRP J 360 " pdb=" C TRP J 360 " pdb=" N SER J 361 " pdb=" CA SER J 361 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA TRP D 360 " pdb=" C TRP D 360 " pdb=" N SER D 361 " pdb=" CA SER D 361 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA TRP H 360 " pdb=" C TRP H 360 " pdb=" N SER H 361 " pdb=" CA SER H 361 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 18827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2924 0.031 - 0.063: 1099 0.063 - 0.094: 419 0.094 - 0.125: 231 0.125 - 0.157: 17 Chirality restraints: 4690 Sorted by residual: chirality pdb=" CA GLU G 197 " pdb=" N GLU G 197 " pdb=" C GLU G 197 " pdb=" CB GLU G 197 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA GLU I 197 " pdb=" N GLU I 197 " pdb=" C GLU I 197 " pdb=" CB GLU I 197 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA GLU J 197 " pdb=" N GLU J 197 " pdb=" C GLU J 197 " pdb=" CB GLU J 197 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 4687 not shown) Planarity restraints: 5590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 240 " -0.017 2.00e-02 2.50e+03 1.74e-02 5.27e+00 pdb=" CG PHE H 240 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE H 240 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE H 240 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE H 240 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE H 240 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 240 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 240 " 0.012 2.00e-02 2.50e+03 1.72e-02 5.19e+00 pdb=" CG PHE G 240 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE G 240 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE G 240 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE G 240 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE G 240 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE G 240 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 240 " 0.016 2.00e-02 2.50e+03 1.55e-02 4.20e+00 pdb=" CG PHE C 240 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE C 240 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 240 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 240 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 240 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 240 " 0.000 2.00e-02 2.50e+03 ... (remaining 5587 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 446 2.63 - 3.19: 27913 3.19 - 3.76: 56660 3.76 - 4.33: 80161 4.33 - 4.90: 123583 Nonbonded interactions: 288763 Sorted by model distance: nonbonded pdb=" OD1 ASP A 196 " pdb="MG MG A 501 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP J 196 " pdb="MG MG J 501 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP D 196 " pdb="MG MG D 501 " model vdw 2.062 2.170 nonbonded pdb=" OD1 ASP C 196 " pdb="MG MG C 501 " model vdw 2.064 2.170 nonbonded pdb=" OD1 ASP I 196 " pdb="MG MG I 501 " model vdw 2.099 2.170 ... (remaining 288758 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' selection = chain 'I' selection = chain 'J' } 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 30.110 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 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:9.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 : 0.003 0.085 32070 Z= 0.160 Angle : 0.697 22.566 43420 Z= 0.372 Chirality : 0.043 0.157 4690 Planarity : 0.003 0.027 5590 Dihedral : 16.581 89.891 11550 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.53 % Allowed : 15.58 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.53 % 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: 0.71 (0.14), residues: 3880 helix: 1.50 (0.13), residues: 1690 sheet: -0.67 (0.19), residues: 580 loop : -0.07 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 251 TYR 0.012 0.002 TYR H 141 PHE 0.040 0.002 PHE H 240 TRP 0.015 0.002 TRP I 97 HIS 0.004 0.001 HIS F 231 Details of bonding type rmsd covalent geometry : bond 0.00337 (32070) covalent geometry : angle 0.69683 (43420) hydrogen bonds : bond 0.15277 ( 1346) hydrogen bonds : angle 6.12221 ( 3876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 362 time to evaluate : 0.996 Fit side-chains REVERT: D 245 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7647 (tm-30) REVERT: F 11 LYS cc_start: 0.8178 (mttp) cc_final: 0.7937 (mtmm) REVERT: F 180 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: F 394 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8412 (mppt) REVERT: I 394 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8419 (mppt) outliers start: 83 outliers final: 65 residues processed: 442 average time/residue: 0.7226 time to fit residues: 372.1578 Evaluate side-chains 418 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 352 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 389 TRP Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 389 TRP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 389 TRP Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 422 THR Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 389 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 195 ASN B 107 GLN B 195 ASN C 8 GLN C 107 GLN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 107 GLN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN E 195 ASN F 156 ASN F 195 ASN G 8 GLN G 195 ASN H 195 ASN I 107 GLN I 195 ASN J 107 GLN J 195 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.155680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.118333 restraints weight = 27044.230| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.39 r_work: 0.3060 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 32070 Z= 0.193 Angle : 0.656 13.059 43420 Z= 0.359 Chirality : 0.046 0.154 4690 Planarity : 0.004 0.028 5590 Dihedral : 7.951 58.796 4397 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.54 % Allowed : 13.14 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.13), residues: 3880 helix: 1.59 (0.12), residues: 1670 sheet: -1.47 (0.18), residues: 640 loop : -0.22 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 298 TYR 0.015 0.002 TYR J 20 PHE 0.023 0.002 PHE G 240 TRP 0.011 0.002 TRP J 271 HIS 0.006 0.002 HIS F 231 Details of bonding type rmsd covalent geometry : bond 0.00416 (32070) covalent geometry : angle 0.65608 (43420) hydrogen bonds : bond 0.05098 ( 1346) hydrogen bonds : angle 5.24077 ( 3876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 366 time to evaluate : 1.217 Fit side-chains REVERT: A 151 MET cc_start: 0.8567 (ttm) cc_final: 0.8144 (ttm) REVERT: A 180 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7924 (tp30) REVERT: A 224 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: A 394 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8173 (mppt) REVERT: A 418 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8162 (pt) REVERT: B 394 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8239 (mppt) REVERT: B 418 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7396 (pp) REVERT: C 180 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7953 (tp30) REVERT: C 394 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8237 (mppt) REVERT: D 10 ILE cc_start: 0.8651 (mt) cc_final: 0.8424 (mm) REVERT: D 180 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7929 (tp30) REVERT: D 394 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8186 (mppt) REVERT: E 394 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8275 (mppt) REVERT: F 50 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8552 (mt0) REVERT: F 394 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8294 (mppt) REVERT: G 180 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: G 248 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8307 (mm-30) REVERT: G 394 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8278 (mppt) REVERT: H 180 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7648 (tp30) REVERT: H 394 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8279 (mppt) REVERT: I 8 GLN cc_start: 0.6275 (mm110) cc_final: 0.5929 (mm-40) REVERT: I 50 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8535 (mt0) REVERT: I 180 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: I 394 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8309 (mppt) REVERT: J 180 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: J 224 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: J 394 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8169 (mppt) REVERT: J 418 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8177 (pt) outliers start: 149 outliers final: 59 residues processed: 492 average time/residue: 0.7280 time to fit residues: 418.4977 Evaluate side-chains 412 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 339 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 418 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 288 optimal weight: 1.9990 chunk 365 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 328 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 354 HIS B 107 GLN C 8 GLN C 107 GLN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 107 GLN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 HIS E 107 GLN F 107 GLN G 354 HIS H 354 HIS I 107 GLN J 107 GLN J 354 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.155586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.118225 restraints weight = 27120.899| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.38 r_work: 0.3062 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 32070 Z= 0.192 Angle : 0.651 13.020 43420 Z= 0.354 Chirality : 0.046 0.156 4690 Planarity : 0.004 0.026 5590 Dihedral : 7.344 55.913 4355 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.78 % Allowed : 14.05 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.36 (0.13), residues: 3880 helix: 1.55 (0.12), residues: 1670 sheet: -1.58 (0.18), residues: 640 loop : -0.27 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 251 TYR 0.015 0.002 TYR A 20 PHE 0.018 0.003 PHE G 305 TRP 0.012 0.002 TRP E 271 HIS 0.007 0.001 HIS I 231 Details of bonding type rmsd covalent geometry : bond 0.00415 (32070) covalent geometry : angle 0.65105 (43420) hydrogen bonds : bond 0.04912 ( 1346) hydrogen bonds : angle 5.12418 ( 3876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 360 time to evaluate : 1.200 Fit side-chains REVERT: A 180 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: A 224 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: A 394 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8145 (mppt) REVERT: A 418 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8097 (pt) REVERT: B 394 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8265 (mppt) REVERT: B 418 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7434 (pp) REVERT: C 180 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7935 (tp30) REVERT: C 394 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8254 (mppt) REVERT: D 180 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: D 394 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8248 (mppt) REVERT: E 394 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8276 (mppt) REVERT: E 418 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7401 (pp) REVERT: F 50 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8543 (mt0) REVERT: F 180 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: F 394 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8307 (mppt) REVERT: G 83 GLN cc_start: 0.9082 (tt0) cc_final: 0.8719 (tt0) REVERT: G 180 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7653 (tp30) REVERT: G 394 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8309 (mppt) REVERT: H 180 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7639 (tp30) REVERT: H 224 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: H 394 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8314 (mppt) REVERT: I 50 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8545 (mt0) REVERT: I 180 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: I 394 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8320 (mppt) REVERT: I 424 MET cc_start: 0.7731 (ptp) cc_final: 0.7494 (ptm) REVERT: J 156 ASN cc_start: 0.7445 (t0) cc_final: 0.7213 (t0) REVERT: J 180 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7886 (tp30) REVERT: J 224 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: J 394 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8152 (mppt) REVERT: J 418 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8131 (pt) outliers start: 124 outliers final: 58 residues processed: 462 average time/residue: 0.7719 time to fit residues: 414.3292 Evaluate side-chains 423 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 348 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 171 MET Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 418 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 44 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 318 optimal weight: 0.0770 chunk 78 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN B 107 GLN C 8 GLN C 107 GLN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 107 GLN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN E 354 HIS F 107 GLN H 107 GLN I 107 GLN J 107 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.155528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.118331 restraints weight = 26983.273| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.39 r_work: 0.3059 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 32070 Z= 0.196 Angle : 0.656 13.009 43420 Z= 0.356 Chirality : 0.046 0.155 4690 Planarity : 0.004 0.026 5590 Dihedral : 7.264 54.415 4351 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.81 % Allowed : 14.18 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.30 (0.13), residues: 3880 helix: 1.55 (0.12), residues: 1660 sheet: -1.71 (0.17), residues: 690 loop : -0.25 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 98 TYR 0.015 0.003 TYR A 20 PHE 0.019 0.003 PHE H 305 TRP 0.012 0.002 TRP E 271 HIS 0.007 0.002 HIS F 231 Details of bonding type rmsd covalent geometry : bond 0.00427 (32070) covalent geometry : angle 0.65626 (43420) hydrogen bonds : bond 0.04856 ( 1346) hydrogen bonds : angle 5.10011 ( 3876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 357 time to evaluate : 1.260 Fit side-chains REVERT: A 156 ASN cc_start: 0.7483 (t0) cc_final: 0.7220 (t0) REVERT: A 180 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: A 224 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: A 394 LYS cc_start: 0.8758 (mtpt) cc_final: 0.8148 (mppt) REVERT: A 415 MET cc_start: 0.6097 (mmt) cc_final: 0.5864 (mmt) REVERT: A 418 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8053 (pt) REVERT: B 170 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8249 (mtpm) REVERT: B 394 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8336 (mppt) REVERT: B 418 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7398 (pp) REVERT: C 180 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: C 394 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8256 (mppt) REVERT: D 180 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7934 (tp30) REVERT: D 394 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8265 (mppt) REVERT: E 170 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8241 (mtpm) REVERT: E 394 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8259 (mppt) REVERT: E 418 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7369 (pp) REVERT: F 50 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8555 (mt0) REVERT: F 180 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: F 394 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8288 (mppt) REVERT: F 415 MET cc_start: 0.5615 (mtp) cc_final: 0.4757 (mtm) REVERT: G 83 GLN cc_start: 0.9092 (tt0) cc_final: 0.8730 (tt0) REVERT: G 180 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7675 (tp30) REVERT: G 394 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8314 (mppt) REVERT: H 180 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7679 (tp30) REVERT: H 394 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8318 (mppt) REVERT: I 50 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8539 (mt0) REVERT: I 180 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: I 394 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8324 (mppt) REVERT: I 424 MET cc_start: 0.7770 (ptp) cc_final: 0.7517 (ptm) REVERT: J 156 ASN cc_start: 0.7446 (t0) cc_final: 0.7173 (t0) REVERT: J 180 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: J 224 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: J 394 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8152 (mppt) REVERT: J 415 MET cc_start: 0.6170 (mmt) cc_final: 0.5945 (mmt) REVERT: J 418 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8064 (pt) outliers start: 125 outliers final: 66 residues processed: 462 average time/residue: 0.7690 time to fit residues: 411.8893 Evaluate side-chains 425 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 341 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 389 TRP Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 171 MET Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 418 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 85 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 chunk 232 optimal weight: 20.0000 chunk 271 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN B 107 GLN C 8 GLN C 107 GLN D 8 GLN D 107 GLN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN F 107 GLN G 8 GLN G 107 GLN H 107 GLN I 107 GLN J 107 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.153675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.115379 restraints weight = 26987.235| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.52 r_work: 0.3019 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 32070 Z= 0.279 Angle : 0.731 13.407 43420 Z= 0.398 Chirality : 0.049 0.168 4690 Planarity : 0.004 0.029 5590 Dihedral : 7.447 54.986 4349 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.45 % Allowed : 13.87 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 (0.13), residues: 3880 helix: 1.33 (0.12), residues: 1660 sheet: -1.85 (0.16), residues: 760 loop : -0.15 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 298 TYR 0.021 0.003 TYR A 20 PHE 0.023 0.003 PHE G 305 TRP 0.015 0.003 TRP A 271 HIS 0.010 0.002 HIS I 231 Details of bonding type rmsd covalent geometry : bond 0.00620 (32070) covalent geometry : angle 0.73116 (43420) hydrogen bonds : bond 0.05497 ( 1346) hydrogen bonds : angle 5.25146 ( 3876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 343 time to evaluate : 1.243 Fit side-chains REVERT: A 180 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: A 220 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7463 (ttpp) REVERT: A 224 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: A 394 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8143 (mppt) REVERT: A 415 MET cc_start: 0.5970 (mmt) cc_final: 0.5616 (mmt) REVERT: A 418 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8083 (pt) REVERT: B 50 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8668 (mt0) REVERT: B 394 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8344 (mppt) REVERT: B 418 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7275 (pp) REVERT: C 180 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: C 218 MET cc_start: 0.8459 (ttm) cc_final: 0.7815 (ttm) REVERT: C 394 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8186 (mppt) REVERT: D 70 GLU cc_start: 0.8046 (tt0) cc_final: 0.7770 (tt0) REVERT: D 180 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7996 (tp30) REVERT: D 218 MET cc_start: 0.8485 (ttm) cc_final: 0.7809 (ttm) REVERT: D 394 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8199 (mppt) REVERT: E 418 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7286 (pp) REVERT: F 50 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8596 (mt0) REVERT: F 180 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: F 394 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8276 (mppt) REVERT: F 415 MET cc_start: 0.5753 (mtp) cc_final: 0.4764 (mtm) REVERT: G 83 GLN cc_start: 0.9088 (tt0) cc_final: 0.8736 (tt0) REVERT: G 180 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7686 (tp30) REVERT: G 394 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8301 (mppt) REVERT: H 180 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7681 (tp30) REVERT: H 223 LYS cc_start: 0.6914 (mmtt) cc_final: 0.6643 (mtmt) REVERT: H 394 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8300 (mppt) REVERT: I 50 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8579 (mt0) REVERT: I 180 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: I 359 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6742 (mt-10) REVERT: I 394 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8290 (mppt) REVERT: I 424 MET cc_start: 0.7746 (ptp) cc_final: 0.7502 (ptm) REVERT: J 156 ASN cc_start: 0.7510 (t0) cc_final: 0.7208 (t0) REVERT: J 180 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: J 220 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7469 (ttpp) REVERT: J 224 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: J 394 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8144 (mppt) REVERT: J 415 MET cc_start: 0.5968 (mmt) cc_final: 0.5622 (mmt) REVERT: J 418 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8085 (pt) outliers start: 146 outliers final: 77 residues processed: 461 average time/residue: 0.7882 time to fit residues: 421.2188 Evaluate side-chains 429 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 332 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 389 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 389 TRP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 389 TRP Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 389 TRP Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 209 LYS Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 359 GLU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 180 GLU Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 220 LYS Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 418 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 146 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 352 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 260 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN C 8 GLN C 107 GLN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN F 107 GLN G 8 GLN I 107 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.156919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119388 restraints weight = 27082.965| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.40 r_work: 0.3084 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32070 Z= 0.146 Angle : 0.611 12.641 43420 Z= 0.333 Chirality : 0.044 0.154 4690 Planarity : 0.003 0.026 5590 Dihedral : 7.006 52.559 4347 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.29 % Allowed : 14.79 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.53 % 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: 0.35 (0.13), residues: 3880 helix: 1.61 (0.12), residues: 1660 sheet: -1.71 (0.18), residues: 640 loop : -0.30 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.012 0.002 TYR D 20 PHE 0.016 0.002 PHE G 305 TRP 0.013 0.002 TRP J 97 HIS 0.004 0.001 HIS F 293 Details of bonding type rmsd covalent geometry : bond 0.00310 (32070) covalent geometry : angle 0.61135 (43420) hydrogen bonds : bond 0.04257 ( 1346) hydrogen bonds : angle 4.94703 ( 3876) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 358 time to evaluate : 1.202 Fit side-chains REVERT: A 156 ASN cc_start: 0.7405 (t0) cc_final: 0.7189 (t0) REVERT: A 180 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: A 224 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: A 394 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8173 (mppt) REVERT: A 415 MET cc_start: 0.5971 (mmt) cc_final: 0.5651 (mmt) REVERT: A 418 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8094 (pt) REVERT: B 170 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8224 (mtpm) REVERT: B 394 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8316 (mppt) REVERT: B 418 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7687 (pt) REVERT: C 220 LYS cc_start: 0.7562 (mmtt) cc_final: 0.7323 (mmtt) REVERT: C 224 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: C 394 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8206 (mppt) REVERT: D 224 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: D 245 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7568 (tm-30) REVERT: D 394 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8184 (mppt) REVERT: E 170 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8219 (mtpm) REVERT: E 418 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7409 (pp) REVERT: F 50 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: F 180 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: F 394 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8282 (mppt) REVERT: F 415 MET cc_start: 0.5673 (mtp) cc_final: 0.4685 (mtm) REVERT: G 394 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8300 (mppt) REVERT: H 394 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8302 (mppt) REVERT: I 8 GLN cc_start: 0.6198 (mm110) cc_final: 0.5821 (mm-40) REVERT: I 180 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: I 359 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6702 (mt-10) REVERT: I 394 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8304 (mppt) REVERT: I 424 MET cc_start: 0.7712 (ptp) cc_final: 0.7510 (ptm) REVERT: J 156 ASN cc_start: 0.7441 (t0) cc_final: 0.7239 (t0) REVERT: J 224 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: J 394 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8167 (mppt) REVERT: J 415 MET cc_start: 0.5978 (mmt) cc_final: 0.5655 (mmt) REVERT: J 418 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8097 (pt) outliers start: 108 outliers final: 58 residues processed: 443 average time/residue: 0.7773 time to fit residues: 398.6988 Evaluate side-chains 422 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 349 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 389 TRP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 171 MET Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 359 GLU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 389 TRP Chi-restraints excluded: chain J residue 418 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 66 optimal weight: 1.9990 chunk 313 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 189 optimal weight: 0.0570 chunk 254 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN C 8 GLN ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 107 GLN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN F 107 GLN G 8 GLN I 107 GLN J 107 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.155995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.119569 restraints weight = 27108.192| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.38 r_work: 0.3070 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 32070 Z= 0.175 Angle : 0.637 12.802 43420 Z= 0.346 Chirality : 0.045 0.154 4690 Planarity : 0.004 0.025 5590 Dihedral : 6.930 51.968 4341 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.69 % Allowed : 14.54 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.53 % 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: 0.35 (0.13), residues: 3880 helix: 1.62 (0.12), residues: 1660 sheet: -1.74 (0.18), residues: 640 loop : -0.28 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 160 TYR 0.013 0.002 TYR A 20 PHE 0.017 0.002 PHE G 305 TRP 0.011 0.002 TRP G 97 HIS 0.006 0.001 HIS I 231 Details of bonding type rmsd covalent geometry : bond 0.00380 (32070) covalent geometry : angle 0.63651 (43420) hydrogen bonds : bond 0.04547 ( 1346) hydrogen bonds : angle 4.96962 ( 3876) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 352 time to evaluate : 1.188 Fit side-chains REVERT: A 156 ASN cc_start: 0.7492 (t0) cc_final: 0.7240 (t0) REVERT: A 180 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: A 220 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7258 (tttt) REVERT: A 224 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: A 394 LYS cc_start: 0.8764 (mtpt) cc_final: 0.8163 (mppt) REVERT: A 415 MET cc_start: 0.5926 (mmt) cc_final: 0.5621 (mmt) REVERT: A 418 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8073 (pt) REVERT: B 170 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8229 (mtpm) REVERT: B 394 LYS cc_start: 0.8903 (mtpt) cc_final: 0.8319 (mppt) REVERT: C 180 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: C 218 MET cc_start: 0.8464 (ttm) cc_final: 0.7743 (ttm) REVERT: D 102 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7885 (mmt90) REVERT: D 180 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: D 218 MET cc_start: 0.8460 (ttm) cc_final: 0.7759 (ttm) REVERT: D 224 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: E 170 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8224 (mtpm) REVERT: E 418 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7384 (pp) REVERT: F 50 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8538 (mt0) REVERT: F 180 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: F 394 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8286 (mppt) REVERT: F 415 MET cc_start: 0.5698 (mtp) cc_final: 0.4655 (mtm) REVERT: G 180 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: G 394 LYS cc_start: 0.8922 (mtpt) cc_final: 0.8317 (mppt) REVERT: H 180 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: H 394 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8326 (mppt) REVERT: I 8 GLN cc_start: 0.6217 (mm110) cc_final: 0.5862 (mm-40) REVERT: I 50 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8531 (mt0) REVERT: I 180 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: I 359 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: I 394 LYS cc_start: 0.8812 (mtpt) cc_final: 0.8310 (mppt) REVERT: I 415 MET cc_start: 0.5488 (mtp) cc_final: 0.4794 (mtm) REVERT: I 424 MET cc_start: 0.7721 (ptp) cc_final: 0.7496 (ptm) REVERT: J 156 ASN cc_start: 0.7480 (t0) cc_final: 0.7188 (t0) REVERT: J 224 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: J 394 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8173 (mppt) REVERT: J 415 MET cc_start: 0.5926 (mmt) cc_final: 0.5619 (mmt) REVERT: J 418 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8075 (pt) outliers start: 121 outliers final: 64 residues processed: 447 average time/residue: 0.7073 time to fit residues: 367.1022 Evaluate side-chains 430 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 347 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 389 TRP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 389 TRP Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 171 MET Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 359 GLU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 107 GLN Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 389 TRP Chi-restraints excluded: chain J residue 418 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 144 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 72 optimal weight: 0.0040 chunk 293 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 266 optimal weight: 0.3980 chunk 317 optimal weight: 0.7980 chunk 336 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN C 8 GLN C 107 GLN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 107 GLN E 107 GLN E 429 HIS F 107 GLN G 8 GLN H 107 GLN I 107 GLN J 107 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.157767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121559 restraints weight = 27108.519| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.38 r_work: 0.3102 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32070 Z= 0.136 Angle : 0.601 12.519 43420 Z= 0.326 Chirality : 0.043 0.153 4690 Planarity : 0.003 0.025 5590 Dihedral : 6.640 51.499 4337 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.96 % Allowed : 15.49 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.53 % 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: 0.50 (0.14), residues: 3880 helix: 1.76 (0.12), residues: 1660 sheet: -1.50 (0.19), residues: 590 loop : -0.36 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 278 TYR 0.011 0.002 TYR C 20 PHE 0.015 0.002 PHE C 411 TRP 0.013 0.001 TRP A 97 HIS 0.004 0.001 HIS F 293 Details of bonding type rmsd covalent geometry : bond 0.00288 (32070) covalent geometry : angle 0.60096 (43420) hydrogen bonds : bond 0.04069 ( 1346) hydrogen bonds : angle 4.83079 ( 3876) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 374 time to evaluate : 1.206 Fit side-chains REVERT: A 151 MET cc_start: 0.8590 (ttm) cc_final: 0.8232 (ttm) REVERT: A 156 ASN cc_start: 0.7458 (t0) cc_final: 0.7196 (t0) REVERT: A 220 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7190 (tttt) REVERT: A 224 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: A 394 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8158 (mppt) REVERT: A 415 MET cc_start: 0.5925 (mmt) cc_final: 0.5662 (mmt) REVERT: A 418 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8068 (pt) REVERT: B 394 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8326 (mppt) REVERT: C 283 ASP cc_start: 0.7840 (p0) cc_final: 0.7627 (p0) REVERT: C 394 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8177 (mppt) REVERT: D 102 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7914 (mmt90) REVERT: D 224 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: D 245 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7572 (tm-30) REVERT: D 394 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8180 (mppt) REVERT: D 418 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7491 (pp) REVERT: F 50 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: F 180 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: F 220 LYS cc_start: 0.7732 (tttt) cc_final: 0.7427 (ttpt) REVERT: F 394 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8273 (mppt) REVERT: F 415 MET cc_start: 0.5709 (mtp) cc_final: 0.4673 (mtm) REVERT: G 394 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8299 (mppt) REVERT: H 394 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8308 (mppt) REVERT: I 8 GLN cc_start: 0.6177 (mm110) cc_final: 0.5803 (mm-40) REVERT: I 11 LYS cc_start: 0.8150 (mttp) cc_final: 0.7924 (mtmm) REVERT: I 50 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8453 (mt0) REVERT: I 180 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: I 359 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6722 (mt-10) REVERT: I 394 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8288 (mppt) REVERT: I 424 MET cc_start: 0.7700 (ptp) cc_final: 0.7470 (ptm) REVERT: J 156 ASN cc_start: 0.7545 (t0) cc_final: 0.7252 (t0) REVERT: J 220 LYS cc_start: 0.7754 (ttpt) cc_final: 0.7201 (tttt) REVERT: J 224 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: J 415 MET cc_start: 0.5949 (mmt) cc_final: 0.5674 (mmt) REVERT: J 418 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8057 (pt) outliers start: 97 outliers final: 51 residues processed: 451 average time/residue: 0.7463 time to fit residues: 390.4283 Evaluate side-chains 427 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 364 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 171 MET Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 359 GLU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 389 TRP Chi-restraints excluded: chain J residue 418 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 8 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 302 optimal weight: 6.9990 chunk 360 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 161 optimal weight: 0.0010 chunk 229 optimal weight: 1.9990 chunk 330 optimal weight: 6.9990 chunk 296 optimal weight: 7.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN C 8 GLN ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN F 107 GLN G 8 GLN H 107 GLN I 107 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.156145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119267 restraints weight = 27109.529| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.42 r_work: 0.3072 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32070 Z= 0.174 Angle : 0.638 12.782 43420 Z= 0.346 Chirality : 0.045 0.153 4690 Planarity : 0.004 0.024 5590 Dihedral : 6.847 118.815 4332 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.74 % Allowed : 15.88 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.53 % 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: 0.45 (0.13), residues: 3880 helix: 1.67 (0.12), residues: 1660 sheet: -1.52 (0.19), residues: 590 loop : -0.34 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 160 TYR 0.014 0.002 TYR A 20 PHE 0.018 0.002 PHE G 240 TRP 0.011 0.002 TRP J 97 HIS 0.006 0.001 HIS F 231 Details of bonding type rmsd covalent geometry : bond 0.00377 (32070) covalent geometry : angle 0.63769 (43420) hydrogen bonds : bond 0.04479 ( 1346) hydrogen bonds : angle 4.91738 ( 3876) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 364 time to evaluate : 1.313 Fit side-chains REVERT: A 156 ASN cc_start: 0.7520 (t0) cc_final: 0.7286 (t0) REVERT: A 220 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7258 (tttt) REVERT: A 224 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: A 415 MET cc_start: 0.5874 (mmt) cc_final: 0.5614 (mmt) REVERT: A 418 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8081 (pt) REVERT: B 394 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8272 (mppt) REVERT: D 224 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: D 418 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7493 (pp) REVERT: F 50 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8533 (mt0) REVERT: F 180 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: F 394 LYS cc_start: 0.8793 (mtpt) cc_final: 0.8280 (mppt) REVERT: F 415 MET cc_start: 0.5747 (mtp) cc_final: 0.4635 (mtm) REVERT: G 180 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: G 394 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8333 (mppt) REVERT: H 180 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: H 394 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8338 (mppt) REVERT: I 8 GLN cc_start: 0.6219 (mm110) cc_final: 0.5856 (mm-40) REVERT: I 11 LYS cc_start: 0.8184 (mttp) cc_final: 0.7952 (mtmm) REVERT: I 50 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: I 180 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: I 359 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6696 (mt-10) REVERT: I 394 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8313 (mppt) REVERT: I 415 MET cc_start: 0.5659 (mtp) cc_final: 0.4984 (mtm) REVERT: I 424 MET cc_start: 0.7733 (ptp) cc_final: 0.7504 (ptm) REVERT: J 156 ASN cc_start: 0.7570 (t0) cc_final: 0.7251 (t0) REVERT: J 220 LYS cc_start: 0.7836 (ttpt) cc_final: 0.7295 (tttt) REVERT: J 224 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: J 415 MET cc_start: 0.5901 (mmt) cc_final: 0.5606 (mmt) REVERT: J 418 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8089 (pt) outliers start: 90 outliers final: 54 residues processed: 434 average time/residue: 0.7835 time to fit residues: 393.6707 Evaluate side-chains 427 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 360 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 389 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 389 TRP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 389 TRP Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 171 MET Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 359 GLU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 389 TRP Chi-restraints excluded: chain J residue 418 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 378 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 370 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 318 optimal weight: 5.9990 chunk 299 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN B 107 GLN C 8 GLN C 107 GLN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 107 GLN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN F 107 GLN G 107 GLN H 107 GLN I 107 GLN ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.155172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.117964 restraints weight = 26944.066| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.38 r_work: 0.3058 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32070 Z= 0.205 Angle : 0.674 13.019 43420 Z= 0.366 Chirality : 0.046 0.153 4690 Planarity : 0.004 0.037 5590 Dihedral : 6.709 49.067 4329 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.99 % Allowed : 15.73 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.27 (0.13), residues: 3880 helix: 1.55 (0.12), residues: 1660 sheet: -1.83 (0.17), residues: 690 loop : -0.23 (0.17), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 390 TYR 0.016 0.003 TYR A 20 PHE 0.019 0.003 PHE G 240 TRP 0.014 0.002 TRP B 271 HIS 0.007 0.002 HIS I 231 Details of bonding type rmsd covalent geometry : bond 0.00448 (32070) covalent geometry : angle 0.67410 (43420) hydrogen bonds : bond 0.04854 ( 1346) hydrogen bonds : angle 5.04766 ( 3876) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 354 time to evaluate : 1.105 Fit side-chains REVERT: A 156 ASN cc_start: 0.7547 (t0) cc_final: 0.7273 (t0) REVERT: A 180 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: A 220 LYS cc_start: 0.7826 (ttpt) cc_final: 0.7278 (tttt) REVERT: A 224 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: A 418 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8092 (pt) REVERT: B 394 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8330 (mppt) REVERT: C 180 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7944 (tp30) REVERT: D 180 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: D 220 LYS cc_start: 0.7651 (mmtt) cc_final: 0.7373 (mptt) REVERT: D 224 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: D 418 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7493 (pp) REVERT: F 50 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8557 (mt0) REVERT: F 180 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: F 394 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8300 (mppt) REVERT: F 415 MET cc_start: 0.5744 (mtp) cc_final: 0.4593 (mtm) REVERT: G 83 GLN cc_start: 0.9060 (tt0) cc_final: 0.8752 (tt0) REVERT: G 180 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: G 394 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8332 (mppt) REVERT: H 180 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7669 (tp30) REVERT: H 394 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8336 (mppt) REVERT: I 8 GLN cc_start: 0.6253 (mm110) cc_final: 0.5894 (mm-40) REVERT: I 50 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8545 (mt0) REVERT: I 180 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: I 359 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6695 (mt-10) REVERT: I 394 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8319 (mppt) REVERT: I 424 MET cc_start: 0.7706 (ptp) cc_final: 0.7481 (ptm) REVERT: J 156 ASN cc_start: 0.7567 (t0) cc_final: 0.7348 (t0) REVERT: J 415 MET cc_start: 0.5792 (mmt) cc_final: 0.5542 (mmt) REVERT: J 418 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8097 (pt) outliers start: 98 outliers final: 55 residues processed: 433 average time/residue: 0.7596 time to fit residues: 381.3364 Evaluate side-chains 411 residues out of total 3280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 341 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 389 TRP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 171 MET Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 171 MET Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 359 GLU Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 389 TRP Chi-restraints excluded: chain J residue 418 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 170 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 309 optimal weight: 8.9990 chunk 357 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 300 optimal weight: 0.0470 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN C 8 GLN C 107 GLN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN F 107 GLN G 8 GLN G 107 GLN H 107 GLN I 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.156825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.119738 restraints weight = 27203.971| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.51 r_work: 0.3079 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32070 Z= 0.149 Angle : 0.624 12.609 43420 Z= 0.338 Chirality : 0.044 0.153 4690 Planarity : 0.003 0.024 5590 Dihedral : 6.542 48.806 4329 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.53 % Allowed : 16.25 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.53 % 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: 0.41 (0.13), residues: 3880 helix: 1.67 (0.12), residues: 1660 sheet: -1.57 (0.19), residues: 590 loop : -0.38 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 160 TYR 0.012 0.002 TYR C 20 PHE 0.018 0.002 PHE G 240 TRP 0.013 0.002 TRP J 97 HIS 0.004 0.001 HIS I 293 Details of bonding type rmsd covalent geometry : bond 0.00319 (32070) covalent geometry : angle 0.62390 (43420) hydrogen bonds : bond 0.04270 ( 1346) hydrogen bonds : angle 4.92027 ( 3876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13521.38 seconds wall clock time: 231 minutes 21.61 seconds (13881.61 seconds total)