Starting phenix.real_space_refine on Sun Feb 8 09:56:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qgn_53139/02_2026/9qgn_53139.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qgn_53139/02_2026/9qgn_53139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qgn_53139/02_2026/9qgn_53139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qgn_53139/02_2026/9qgn_53139.map" model { file = "/net/cci-nas-00/data/ceres_data/9qgn_53139/02_2026/9qgn_53139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qgn_53139/02_2026/9qgn_53139.cif" } resolution = 2.46 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= 0.046 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 27654 2.51 5 N 7200 2.21 5 O 8526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s 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: 43476 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2225 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain breaks: 2 Chain: "B" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2225 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain breaks: 2 Chain: "C" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2225 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain breaks: 2 Chain: "D" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2225 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain breaks: 2 Chain: "E" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2225 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain breaks: 2 Chain: "F" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2225 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain breaks: 2 Chain: "1A" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1133 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "1B" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1133 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "1C" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1133 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "1D" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1133 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "1E" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1133 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "1F" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1133 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "1G" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1160 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain: "1H" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1160 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain: "1I" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1160 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain: "1J" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1160 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain: "1K" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1160 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain: "1L" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1160 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain: "2A" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2728 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 327} Chain: "2B" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2728 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 327} Chain: "2C" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2728 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 327} Chain: "2D" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2728 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 327} Chain: "2E" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2728 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 327} Chain: "2F" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2728 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 327} Time building chain proxies: 10.69, per 1000 atoms: 0.25 Number of scatterers: 43476 At special positions: 0 Unit cell: (174, 176.4, 139.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 8526 8.00 N 7200 7.00 C 27654 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: 3.58 Conformation dependent library (CDL) restraints added in 1.7 seconds 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10512 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 72 sheets defined 26.7% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 9 through 27 Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 113 through 129 Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 201 through 218 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 260 through 275 removed outlier: 4.281A pdb=" N GLN A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 27 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 113 through 129 Processing helix chain 'B' and resid 148 through 160 Processing helix chain 'B' and resid 201 through 218 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 260 through 275 removed outlier: 4.312A pdb=" N GLN B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 27 Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 113 through 129 Processing helix chain 'C' and resid 148 through 160 Processing helix chain 'C' and resid 201 through 218 Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 260 through 275 removed outlier: 4.276A pdb=" N GLN C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 27 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 113 through 129 Processing helix chain 'D' and resid 148 through 160 Processing helix chain 'D' and resid 201 through 218 Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 260 through 275 removed outlier: 4.269A pdb=" N GLN D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 27 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 113 through 129 Processing helix chain 'E' and resid 148 through 160 Processing helix chain 'E' and resid 201 through 218 Processing helix chain 'E' and resid 220 through 227 Processing helix chain 'E' and resid 260 through 275 removed outlier: 4.374A pdb=" N GLN E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 27 Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 113 through 129 Processing helix chain 'F' and resid 148 through 160 Processing helix chain 'F' and resid 201 through 218 Processing helix chain 'F' and resid 220 through 227 Processing helix chain 'F' and resid 260 through 275 removed outlier: 4.275A pdb=" N GLN F 264 " --> pdb=" O THR F 260 " (cutoff:3.500A) Processing helix chain '1A' and resid 75 through 83 Processing helix chain '1B' and resid 75 through 83 Processing helix chain '1C' and resid 75 through 83 Processing helix chain '1D' and resid 75 through 83 Processing helix chain '1E' and resid 75 through 83 Processing helix chain '1F' and resid 75 through 83 Processing helix chain '1G' and resid 4 through 12 Processing helix chain '1G' and resid 75 through 82 Processing helix chain '1H' and resid 4 through 12 Processing helix chain '1H' and resid 75 through 82 Processing helix chain '1I' and resid 4 through 12 Processing helix chain '1I' and resid 75 through 83 Processing helix chain '1J' and resid 4 through 12 Processing helix chain '1J' and resid 75 through 82 Processing helix chain '1K' and resid 4 through 12 Processing helix chain '1K' and resid 75 through 82 Processing helix chain '1L' and resid 4 through 12 Processing helix chain '1L' and resid 75 through 83 Processing helix chain '2A' and resid 51 through 60 Processing helix chain '2A' and resid 67 through 79 removed outlier: 3.890A pdb=" N ILE2A 71 " --> pdb=" O ASN2A 67 " (cutoff:3.500A) Processing helix chain '2A' and resid 91 through 96 Processing helix chain '2A' and resid 97 through 99 No H-bonds generated for 'chain '2A' and resid 97 through 99' Processing helix chain '2A' and resid 112 through 120 Processing helix chain '2A' and resid 171 through 187 removed outlier: 4.169A pdb=" N ALA2A 175 " --> pdb=" O PRO2A 171 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY2A 178 " --> pdb=" O ALA2A 174 " (cutoff:3.500A) Processing helix chain '2A' and resid 198 through 202 removed outlier: 4.167A pdb=" N GLY2A 201 " --> pdb=" O ILE2A 198 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU2A 202 " --> pdb=" O GLN2A 199 " (cutoff:3.500A) No H-bonds generated for 'chain '2A' and resid 198 through 202' Processing helix chain '2A' and resid 209 through 215 removed outlier: 3.685A pdb=" N GLN2A 215 " --> pdb=" O ASP2A 211 " (cutoff:3.500A) Processing helix chain '2A' and resid 249 through 267 Processing helix chain '2A' and resid 268 through 271 removed outlier: 3.710A pdb=" N VAL2A 271 " --> pdb=" O SER2A 268 " (cutoff:3.500A) No H-bonds generated for 'chain '2A' and resid 268 through 271' Processing helix chain '2A' and resid 276 through 298 Processing helix chain '2A' and resid 304 through 307 Processing helix chain '2A' and resid 320 through 326 Processing helix chain '2B' and resid 51 through 60 Processing helix chain '2B' and resid 67 through 79 removed outlier: 3.888A pdb=" N ILE2B 71 " --> pdb=" O ASN2B 67 " (cutoff:3.500A) Processing helix chain '2B' and resid 91 through 96 Processing helix chain '2B' and resid 97 through 99 No H-bonds generated for 'chain '2B' and resid 97 through 99' Processing helix chain '2B' and resid 112 through 120 Processing helix chain '2B' and resid 171 through 187 removed outlier: 4.179A pdb=" N ALA2B 175 " --> pdb=" O PRO2B 171 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY2B 178 " --> pdb=" O ALA2B 174 " (cutoff:3.500A) Processing helix chain '2B' and resid 198 through 202 removed outlier: 4.195A pdb=" N GLY2B 201 " --> pdb=" O ILE2B 198 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU2B 202 " --> pdb=" O GLN2B 199 " (cutoff:3.500A) No H-bonds generated for 'chain '2B' and resid 198 through 202' Processing helix chain '2B' and resid 209 through 216 removed outlier: 3.731A pdb=" N GLN2B 215 " --> pdb=" O ASP2B 211 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR2B 216 " --> pdb=" O LEU2B 212 " (cutoff:3.500A) Processing helix chain '2B' and resid 249 through 267 Processing helix chain '2B' and resid 268 through 271 removed outlier: 3.678A pdb=" N VAL2B 271 " --> pdb=" O SER2B 268 " (cutoff:3.500A) No H-bonds generated for 'chain '2B' and resid 268 through 271' Processing helix chain '2B' and resid 276 through 298 Processing helix chain '2B' and resid 304 through 307 Processing helix chain '2B' and resid 320 through 326 Processing helix chain '2C' and resid 51 through 60 Processing helix chain '2C' and resid 67 through 79 removed outlier: 3.899A pdb=" N ILE2C 71 " --> pdb=" O ASN2C 67 " (cutoff:3.500A) Processing helix chain '2C' and resid 91 through 96 Processing helix chain '2C' and resid 97 through 99 No H-bonds generated for 'chain '2C' and resid 97 through 99' Processing helix chain '2C' and resid 112 through 120 Processing helix chain '2C' and resid 171 through 187 removed outlier: 4.161A pdb=" N ALA2C 175 " --> pdb=" O PRO2C 171 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY2C 178 " --> pdb=" O ALA2C 174 " (cutoff:3.500A) Processing helix chain '2C' and resid 198 through 202 removed outlier: 4.170A pdb=" N GLY2C 201 " --> pdb=" O ILE2C 198 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU2C 202 " --> pdb=" O GLN2C 199 " (cutoff:3.500A) No H-bonds generated for 'chain '2C' and resid 198 through 202' Processing helix chain '2C' and resid 209 through 216 removed outlier: 3.673A pdb=" N GLN2C 215 " --> pdb=" O ASP2C 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR2C 216 " --> pdb=" O LEU2C 212 " (cutoff:3.500A) Processing helix chain '2C' and resid 249 through 267 Processing helix chain '2C' and resid 268 through 271 removed outlier: 3.732A pdb=" N VAL2C 271 " --> pdb=" O SER2C 268 " (cutoff:3.500A) No H-bonds generated for 'chain '2C' and resid 268 through 271' Processing helix chain '2C' and resid 276 through 297 Processing helix chain '2C' and resid 304 through 308 removed outlier: 3.525A pdb=" N ALA2C 308 " --> pdb=" O LYS2C 304 " (cutoff:3.500A) No H-bonds generated for 'chain '2C' and resid 304 through 308' Processing helix chain '2C' and resid 320 through 326 Processing helix chain '2D' and resid 51 through 60 Processing helix chain '2D' and resid 67 through 79 removed outlier: 3.683A pdb=" N ILE2D 71 " --> pdb=" O ASN2D 67 " (cutoff:3.500A) Processing helix chain '2D' and resid 91 through 96 Processing helix chain '2D' and resid 97 through 99 No H-bonds generated for 'chain '2D' and resid 97 through 99' Processing helix chain '2D' and resid 112 through 120 Processing helix chain '2D' and resid 171 through 187 removed outlier: 4.167A pdb=" N ALA2D 175 " --> pdb=" O PRO2D 171 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY2D 178 " --> pdb=" O ALA2D 174 " (cutoff:3.500A) Processing helix chain '2D' and resid 198 through 202 removed outlier: 4.165A pdb=" N GLY2D 201 " --> pdb=" O ILE2D 198 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU2D 202 " --> pdb=" O GLN2D 199 " (cutoff:3.500A) No H-bonds generated for 'chain '2D' and resid 198 through 202' Processing helix chain '2D' and resid 209 through 215 removed outlier: 3.688A pdb=" N GLN2D 215 " --> pdb=" O ASP2D 211 " (cutoff:3.500A) Processing helix chain '2D' and resid 249 through 268 Processing helix chain '2D' and resid 269 through 271 No H-bonds generated for 'chain '2D' and resid 269 through 271' Processing helix chain '2D' and resid 276 through 297 Processing helix chain '2D' and resid 304 through 307 Processing helix chain '2D' and resid 320 through 326 Processing helix chain '2E' and resid 51 through 60 Processing helix chain '2E' and resid 67 through 79 removed outlier: 3.889A pdb=" N ILE2E 71 " --> pdb=" O ASN2E 67 " (cutoff:3.500A) Processing helix chain '2E' and resid 91 through 96 Processing helix chain '2E' and resid 97 through 99 No H-bonds generated for 'chain '2E' and resid 97 through 99' Processing helix chain '2E' and resid 112 through 120 Processing helix chain '2E' and resid 171 through 187 removed outlier: 4.179A pdb=" N ALA2E 175 " --> pdb=" O PRO2E 171 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY2E 178 " --> pdb=" O ALA2E 174 " (cutoff:3.500A) Processing helix chain '2E' and resid 198 through 202 removed outlier: 4.242A pdb=" N GLY2E 201 " --> pdb=" O ILE2E 198 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU2E 202 " --> pdb=" O GLN2E 199 " (cutoff:3.500A) No H-bonds generated for 'chain '2E' and resid 198 through 202' Processing helix chain '2E' and resid 209 through 216 removed outlier: 3.732A pdb=" N GLN2E 215 " --> pdb=" O ASP2E 211 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR2E 216 " --> pdb=" O LEU2E 212 " (cutoff:3.500A) Processing helix chain '2E' and resid 249 through 268 Processing helix chain '2E' and resid 269 through 271 No H-bonds generated for 'chain '2E' and resid 269 through 271' Processing helix chain '2E' and resid 276 through 298 Processing helix chain '2E' and resid 304 through 307 Processing helix chain '2E' and resid 320 through 326 Processing helix chain '2F' and resid 51 through 60 Processing helix chain '2F' and resid 67 through 79 removed outlier: 3.706A pdb=" N ILE2F 71 " --> pdb=" O ASN2F 67 " (cutoff:3.500A) Processing helix chain '2F' and resid 91 through 96 Processing helix chain '2F' and resid 97 through 99 No H-bonds generated for 'chain '2F' and resid 97 through 99' Processing helix chain '2F' and resid 112 through 120 Processing helix chain '2F' and resid 171 through 187 removed outlier: 4.164A pdb=" N ALA2F 175 " --> pdb=" O PRO2F 171 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY2F 178 " --> pdb=" O ALA2F 174 " (cutoff:3.500A) Processing helix chain '2F' and resid 198 through 202 removed outlier: 4.170A pdb=" N GLY2F 201 " --> pdb=" O ILE2F 198 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU2F 202 " --> pdb=" O GLN2F 199 " (cutoff:3.500A) No H-bonds generated for 'chain '2F' and resid 198 through 202' Processing helix chain '2F' and resid 209 through 216 removed outlier: 3.659A pdb=" N GLN2F 215 " --> pdb=" O ASP2F 211 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR2F 216 " --> pdb=" O LEU2F 212 " (cutoff:3.500A) Processing helix chain '2F' and resid 249 through 267 Processing helix chain '2F' and resid 268 through 271 removed outlier: 3.730A pdb=" N VAL2F 271 " --> pdb=" O SER2F 268 " (cutoff:3.500A) No H-bonds generated for 'chain '2F' and resid 268 through 271' Processing helix chain '2F' and resid 276 through 297 Processing helix chain '2F' and resid 304 through 308 removed outlier: 3.525A pdb=" N ALA2F 308 " --> pdb=" O LYS2F 304 " (cutoff:3.500A) No H-bonds generated for 'chain '2F' and resid 304 through 308' Processing helix chain '2F' and resid 320 through 326 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.526A pdb=" N ASP A 34 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL A 53 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG A 36 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU A 55 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL A 51 " --> pdb=" O TRP A 95 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TRP A 95 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL A 53 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N THR A 93 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU A 55 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 91 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU A 57 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 196 Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 236 removed outlier: 5.798A pdb=" N GLU A 247 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER A 290 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL A 249 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU A 292 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 251 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ALA A 294 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 253 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS A 296 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 255 " --> pdb=" O LYS A 296 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 280 " --> pdb=" O ILE A 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 36 removed outlier: 6.520A pdb=" N ASP B 34 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL B 53 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG B 36 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU B 55 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASN B 89 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE B 58 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN B 87 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU B 60 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ASN B 85 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AA9, first strand: chain 'B' and resid 189 through 196 Processing sheet with id=AB1, first strand: chain 'B' and resid 230 through 236 removed outlier: 6.362A pdb=" N GLU B 247 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL B 289 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL B 249 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 291 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP B 295 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N GLY B 255 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU B 297 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 280 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 34 through 36 removed outlier: 6.527A pdb=" N ASP C 34 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL C 53 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG C 36 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU C 55 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN C 89 " --> pdb=" O TYR C 56 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE C 58 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN C 87 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU C 60 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASN C 85 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 72 through 73 Processing sheet with id=AB5, first strand: chain 'C' and resid 189 through 196 Processing sheet with id=AB6, first strand: chain 'C' and resid 230 through 236 removed outlier: 11.897A pdb=" N GLU C 247 " --> pdb=" O SER C 290 " (cutoff:3.500A) removed outlier: 11.762A pdb=" N GLU C 292 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N VAL C 249 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 11.624A pdb=" N ALA C 294 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 11.607A pdb=" N VAL C 251 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N LYS C 296 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL C 253 " --> pdb=" O LYS C 296 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE C 298 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLY C 255 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL C 280 " --> pdb=" O ILE C 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB8, first strand: chain 'D' and resid 34 through 36 removed outlier: 6.525A pdb=" N ASP D 34 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL D 53 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG D 36 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU D 55 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL D 51 " --> pdb=" O TRP D 95 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TRP D 95 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL D 53 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N THR D 93 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU D 55 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU D 91 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU D 57 " --> pdb=" O ASN D 89 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 72 through 73 Processing sheet with id=AC1, first strand: chain 'D' and resid 189 through 196 Processing sheet with id=AC2, first strand: chain 'D' and resid 230 through 236 removed outlier: 5.798A pdb=" N GLU D 247 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER D 290 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL D 249 " --> pdb=" O SER D 290 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU D 292 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 251 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA D 294 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL D 253 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS D 296 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY D 255 " --> pdb=" O LYS D 296 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL D 280 " --> pdb=" O ILE D 287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AC4, first strand: chain 'E' and resid 34 through 36 removed outlier: 6.520A pdb=" N ASP E 34 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL E 53 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG E 36 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU E 55 " --> pdb=" O ARG E 36 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN E 89 " --> pdb=" O TYR E 56 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE E 58 " --> pdb=" O ASN E 87 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN E 87 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU E 60 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASN E 85 " --> pdb=" O GLU E 60 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 72 through 73 Processing sheet with id=AC6, first strand: chain 'E' and resid 189 through 196 Processing sheet with id=AC7, first strand: chain 'E' and resid 230 through 236 removed outlier: 6.352A pdb=" N GLU E 247 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL E 289 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL E 249 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS E 291 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP E 295 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLY E 255 " --> pdb=" O ASP E 295 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU E 297 " --> pdb=" O GLY E 255 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL E 280 " --> pdb=" O ILE E 287 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AC9, first strand: chain 'F' and resid 34 through 36 removed outlier: 6.529A pdb=" N ASP F 34 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL F 53 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG F 36 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU F 55 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN F 89 " --> pdb=" O TYR F 56 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE F 58 " --> pdb=" O ASN F 87 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN F 87 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU F 60 " --> pdb=" O ASN F 85 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASN F 85 " --> pdb=" O GLU F 60 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 72 through 73 Processing sheet with id=AD2, first strand: chain 'F' and resid 189 through 196 Processing sheet with id=AD3, first strand: chain 'F' and resid 230 through 236 removed outlier: 5.760A pdb=" N GLU F 247 " --> pdb=" O VAL F 288 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER F 290 " --> pdb=" O GLU F 247 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL F 249 " --> pdb=" O SER F 290 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLU F 292 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL F 251 " --> pdb=" O GLU F 292 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ALA F 294 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL F 253 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS F 296 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY F 255 " --> pdb=" O LYS F 296 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL F 280 " --> pdb=" O ILE F 287 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '1A' and resid 26 through 27 removed outlier: 7.084A pdb=" N LYS1A 92 " --> pdb=" O ALA1A 113 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ALA1A 113 " --> pdb=" O LYS1A 92 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE1A 94 " --> pdb=" O ASN1A 111 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN1A 111 " --> pdb=" O ILE1A 94 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE1A 96 " --> pdb=" O THR1A 109 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR1A 109 " --> pdb=" O ILE1A 96 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU1A 98 " --> pdb=" O LEU1A 107 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N THR1A 140 " --> pdb=" O PRO1A 117 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER1A 119 " --> pdb=" O ALA1A 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '1A' and resid 143 through 148 removed outlier: 4.070A pdb=" N ARG1A 143 " --> pdb=" O ALA1A 113 " (cutoff:3.500A) removed outlier: 23.511A pdb=" N VAL1A 112 " --> pdb=" O LYS1F 46 " (cutoff:3.500A) removed outlier: 20.507A pdb=" N LYS1F 46 " --> pdb=" O VAL1A 112 " (cutoff:3.500A) removed outlier: 17.411A pdb=" N ASN1A 114 " --> pdb=" O GLU1F 44 " (cutoff:3.500A) removed outlier: 12.787A pdb=" N GLU1F 44 " --> pdb=" O ASN1A 114 " (cutoff:3.500A) removed outlier: 12.695A pdb=" N PHE1A 116 " --> pdb=" O VAL1F 42 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N VAL1F 42 " --> pdb=" O PHE1A 116 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR1A 118 " --> pdb=" O TYR1F 40 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N HIS1F 39 " --> pdb=" O ARG1F 59 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG1F 59 " --> pdb=" O HIS1F 39 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP1F 41 " --> pdb=" O GLY1F 57 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '1A' and resid 52 through 59 removed outlier: 5.186A pdb=" N ASP1A 41 " --> pdb=" O GLY1A 57 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ARG1A 59 " --> pdb=" O HIS1A 39 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N HIS1A 39 " --> pdb=" O ARG1A 59 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N THR1B 118 " --> pdb=" O TYR1A 40 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N VAL1A 42 " --> pdb=" O PHE1B 116 " (cutoff:3.500A) removed outlier: 12.660A pdb=" N PHE1B 116 " --> pdb=" O VAL1A 42 " (cutoff:3.500A) removed outlier: 12.709A pdb=" N GLU1A 44 " --> pdb=" O ASN1B 114 " (cutoff:3.500A) removed outlier: 17.365A pdb=" N ASN1B 114 " --> pdb=" O GLU1A 44 " (cutoff:3.500A) removed outlier: 20.498A pdb=" N LYS1A 46 " --> pdb=" O VAL1B 112 " (cutoff:3.500A) removed outlier: 23.509A pdb=" N VAL1B 112 " --> pdb=" O LYS1A 46 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG1B 143 " --> pdb=" O ALA1B 113 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '1B' and resid 26 through 27 removed outlier: 5.783A pdb=" N LYS1B 92 " --> pdb=" O ASN1B 114 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N THR1B 140 " --> pdb=" O PRO1B 117 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER1B 119 " --> pdb=" O ALA1B 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '1A' and resid 125 through 126 removed outlier: 6.721A pdb=" N GLU1F 136 " --> pdb=" O PHE1F 120 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE1F 120 " --> pdb=" O GLU1F 136 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA1F 138 " --> pdb=" O THR1F 118 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS1F 92 " --> pdb=" O ASN1F 114 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '1E' and resid 52 through 59 removed outlier: 5.172A pdb=" N ASP1E 41 " --> pdb=" O GLY1E 57 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG1E 59 " --> pdb=" O HIS1E 39 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N HIS1E 39 " --> pdb=" O ARG1E 59 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N THR1F 118 " --> pdb=" O TYR1E 40 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N VAL1E 42 " --> pdb=" O PHE1F 116 " (cutoff:3.500A) removed outlier: 12.647A pdb=" N PHE1F 116 " --> pdb=" O VAL1E 42 " (cutoff:3.500A) removed outlier: 12.738A pdb=" N GLU1E 44 " --> pdb=" O ASN1F 114 " (cutoff:3.500A) removed outlier: 17.406A pdb=" N ASN1F 114 " --> pdb=" O GLU1E 44 " (cutoff:3.500A) removed outlier: 20.484A pdb=" N LYS1E 46 " --> pdb=" O VAL1F 112 " (cutoff:3.500A) removed outlier: 23.515A pdb=" N VAL1F 112 " --> pdb=" O LYS1E 46 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG1F 143 " --> pdb=" O ALA1F 113 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '1B' and resid 52 through 59 removed outlier: 5.169A pdb=" N ASP1B 41 " --> pdb=" O GLY1B 57 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARG1B 59 " --> pdb=" O HIS1B 39 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N HIS1B 39 " --> pdb=" O ARG1B 59 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR1C 118 " --> pdb=" O TYR1B 40 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N VAL1B 42 " --> pdb=" O PHE1C 116 " (cutoff:3.500A) removed outlier: 12.650A pdb=" N PHE1C 116 " --> pdb=" O VAL1B 42 " (cutoff:3.500A) removed outlier: 12.744A pdb=" N GLU1B 44 " --> pdb=" O ASN1C 114 " (cutoff:3.500A) removed outlier: 17.409A pdb=" N ASN1C 114 " --> pdb=" O GLU1B 44 " (cutoff:3.500A) removed outlier: 20.479A pdb=" N LYS1B 46 " --> pdb=" O VAL1C 112 " (cutoff:3.500A) removed outlier: 23.515A pdb=" N VAL1C 112 " --> pdb=" O LYS1B 46 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG1C 143 " --> pdb=" O ALA1C 113 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '1C' and resid 26 through 27 removed outlier: 5.840A pdb=" N LYS1C 92 " --> pdb=" O ASN1C 114 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N THR1C 140 " --> pdb=" O PRO1C 117 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '1C' and resid 52 through 59 removed outlier: 5.216A pdb=" N ASP1C 41 " --> pdb=" O GLY1C 57 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG1C 59 " --> pdb=" O HIS1C 39 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N HIS1C 39 " --> pdb=" O ARG1C 59 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR1D 118 " --> pdb=" O TYR1C 40 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N VAL1C 42 " --> pdb=" O PHE1D 116 " (cutoff:3.500A) removed outlier: 12.694A pdb=" N PHE1D 116 " --> pdb=" O VAL1C 42 " (cutoff:3.500A) removed outlier: 12.787A pdb=" N GLU1C 44 " --> pdb=" O ASN1D 114 " (cutoff:3.500A) removed outlier: 17.415A pdb=" N ASN1D 114 " --> pdb=" O GLU1C 44 " (cutoff:3.500A) removed outlier: 20.503A pdb=" N LYS1C 46 " --> pdb=" O VAL1D 112 " (cutoff:3.500A) removed outlier: 23.516A pdb=" N VAL1D 112 " --> pdb=" O LYS1C 46 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG1D 143 " --> pdb=" O ALA1D 113 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '1D' and resid 26 through 27 removed outlier: 7.083A pdb=" N LYS1D 92 " --> pdb=" O ALA1D 113 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA1D 113 " --> pdb=" O LYS1D 92 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE1D 94 " --> pdb=" O ASN1D 111 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN1D 111 " --> pdb=" O ILE1D 94 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE1D 96 " --> pdb=" O THR1D 109 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR1D 109 " --> pdb=" O ILE1D 96 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU1D 98 " --> pdb=" O LEU1D 107 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THR1D 140 " --> pdb=" O PRO1D 117 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER1D 119 " --> pdb=" O ALA1D 138 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '1D' and resid 52 through 59 removed outlier: 5.174A pdb=" N ASP1D 41 " --> pdb=" O GLY1D 57 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG1D 59 " --> pdb=" O HIS1D 39 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N HIS1D 39 " --> pdb=" O ARG1D 59 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N THR1E 118 " --> pdb=" O TYR1D 40 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N VAL1D 42 " --> pdb=" O PHE1E 116 " (cutoff:3.500A) removed outlier: 12.665A pdb=" N PHE1E 116 " --> pdb=" O VAL1D 42 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N GLU1D 44 " --> pdb=" O ASN1E 114 " (cutoff:3.500A) removed outlier: 17.358A pdb=" N ASN1E 114 " --> pdb=" O GLU1D 44 " (cutoff:3.500A) removed outlier: 20.497A pdb=" N LYS1D 46 " --> pdb=" O VAL1E 112 " (cutoff:3.500A) removed outlier: 23.504A pdb=" N VAL1E 112 " --> pdb=" O LYS1D 46 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG1E 143 " --> pdb=" O ALA1E 113 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '1E' and resid 26 through 27 removed outlier: 5.810A pdb=" N LYS1E 92 " --> pdb=" O ASN1E 114 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N THR1E 140 " --> pdb=" O PRO1E 117 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER1E 119 " --> pdb=" O ALA1E 138 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '1G' and resid 26 through 27 removed outlier: 7.051A pdb=" N LYS1G 92 " --> pdb=" O ALA1G 113 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ALA1G 113 " --> pdb=" O LYS1G 92 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE1G 94 " --> pdb=" O ASN1G 111 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN1G 111 " --> pdb=" O ILE1G 94 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE1G 96 " --> pdb=" O THR1G 109 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR1G 109 " --> pdb=" O ILE1G 96 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU1G 98 " --> pdb=" O LEU1G 107 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA1G 138 " --> pdb=" O THR1G 118 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE1G 120 " --> pdb=" O GLU1G 136 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU1G 136 " --> pdb=" O PHE1G 120 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '1G' and resid 144 through 148 removed outlier: 23.775A pdb=" N VAL1G 112 " --> pdb=" O LYS1L 46 " (cutoff:3.500A) removed outlier: 20.452A pdb=" N LYS1L 46 " --> pdb=" O VAL1G 112 " (cutoff:3.500A) removed outlier: 17.354A pdb=" N ASN1G 114 " --> pdb=" O GLU1L 44 " (cutoff:3.500A) removed outlier: 12.728A pdb=" N GLU1L 44 " --> pdb=" O ASN1G 114 " (cutoff:3.500A) removed outlier: 12.678A pdb=" N PHE1G 116 " --> pdb=" O VAL1L 42 " (cutoff:3.500A) removed outlier: 9.550A pdb=" N VAL1L 42 " --> pdb=" O PHE1G 116 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR1G 118 " --> pdb=" O TYR1L 40 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N HIS1L 39 " --> pdb=" O ARG1L 59 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG1L 59 " --> pdb=" O HIS1L 39 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP1L 41 " --> pdb=" O GLY1L 57 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '1G' and resid 52 through 59 removed outlier: 4.789A pdb=" N ASP1G 41 " --> pdb=" O GLY1G 57 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ARG1G 59 " --> pdb=" O HIS1G 39 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N HIS1G 39 " --> pdb=" O ARG1G 59 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N THR1H 118 " --> pdb=" O TYR1G 40 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N VAL1G 42 " --> pdb=" O PHE1H 116 " (cutoff:3.500A) removed outlier: 12.733A pdb=" N PHE1H 116 " --> pdb=" O VAL1G 42 " (cutoff:3.500A) removed outlier: 12.709A pdb=" N GLU1G 44 " --> pdb=" O ASN1H 114 " (cutoff:3.500A) removed outlier: 17.354A pdb=" N ASN1H 114 " --> pdb=" O GLU1G 44 " (cutoff:3.500A) removed outlier: 20.409A pdb=" N LYS1G 46 " --> pdb=" O VAL1H 112 " (cutoff:3.500A) removed outlier: 23.556A pdb=" N VAL1H 112 " --> pdb=" O LYS1G 46 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '1H' and resid 26 through 27 removed outlier: 7.116A pdb=" N LYS1H 92 " --> pdb=" O ALA1H 113 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA1H 113 " --> pdb=" O LYS1H 92 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE1H 94 " --> pdb=" O ASN1H 111 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN1H 111 " --> pdb=" O ILE1H 94 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE1H 96 " --> pdb=" O THR1H 109 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR1H 109 " --> pdb=" O ILE1H 96 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU1H 98 " --> pdb=" O LEU1H 107 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N THR1H 140 " --> pdb=" O PRO1H 117 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER1H 119 " --> pdb=" O ALA1H 138 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '1G' and resid 125 through 126 removed outlier: 3.562A pdb=" N SER1L 119 " --> pdb=" O ALA1L 138 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N THR1L 140 " --> pdb=" O PRO1L 117 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU1L 98 " --> pdb=" O LEU1L 107 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR1L 109 " --> pdb=" O ILE1L 96 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE1L 96 " --> pdb=" O THR1L 109 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN1L 111 " --> pdb=" O ILE1L 94 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE1L 94 " --> pdb=" O ASN1L 111 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ALA1L 113 " --> pdb=" O LYS1L 92 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS1L 92 " --> pdb=" O ALA1L 113 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '1K' and resid 52 through 59 removed outlier: 4.806A pdb=" N ASP1K 41 " --> pdb=" O GLY1K 57 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG1K 59 " --> pdb=" O HIS1K 39 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N HIS1K 39 " --> pdb=" O ARG1K 59 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N THR1L 118 " --> pdb=" O TYR1K 40 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N VAL1K 42 " --> pdb=" O PHE1L 116 " (cutoff:3.500A) removed outlier: 12.771A pdb=" N PHE1L 116 " --> pdb=" O VAL1K 42 " (cutoff:3.500A) removed outlier: 12.811A pdb=" N GLU1K 44 " --> pdb=" O ASN1L 114 " (cutoff:3.500A) removed outlier: 17.420A pdb=" N ASN1L 114 " --> pdb=" O GLU1K 44 " (cutoff:3.500A) removed outlier: 20.331A pdb=" N LYS1K 46 " --> pdb=" O VAL1L 112 " (cutoff:3.500A) removed outlier: 23.435A pdb=" N VAL1L 112 " --> pdb=" O LYS1K 46 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '1H' and resid 52 through 59 removed outlier: 4.799A pdb=" N ASP1H 41 " --> pdb=" O GLY1H 57 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ARG1H 59 " --> pdb=" O HIS1H 39 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N HIS1H 39 " --> pdb=" O ARG1H 59 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR1I 118 " --> pdb=" O TYR1H 40 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL1H 42 " --> pdb=" O PHE1I 116 " (cutoff:3.500A) removed outlier: 12.769A pdb=" N PHE1I 116 " --> pdb=" O VAL1H 42 " (cutoff:3.500A) removed outlier: 12.810A pdb=" N GLU1H 44 " --> pdb=" O ASN1I 114 " (cutoff:3.500A) removed outlier: 17.422A pdb=" N ASN1I 114 " --> pdb=" O GLU1H 44 " (cutoff:3.500A) removed outlier: 20.331A pdb=" N LYS1H 46 " --> pdb=" O VAL1I 112 " (cutoff:3.500A) removed outlier: 23.437A pdb=" N VAL1I 112 " --> pdb=" O LYS1H 46 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '1I' and resid 26 through 27 removed outlier: 7.081A pdb=" N LYS1I 92 " --> pdb=" O ALA1I 113 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ALA1I 113 " --> pdb=" O LYS1I 92 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE1I 94 " --> pdb=" O ASN1I 111 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN1I 111 " --> pdb=" O ILE1I 94 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE1I 96 " --> pdb=" O THR1I 109 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR1I 109 " --> pdb=" O ILE1I 96 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU1I 98 " --> pdb=" O LEU1I 107 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR1I 140 " --> pdb=" O PRO1I 117 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER1I 119 " --> pdb=" O ALA1I 138 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '1I' and resid 52 through 59 removed outlier: 4.725A pdb=" N ASP1I 41 " --> pdb=" O GLY1I 57 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ARG1I 59 " --> pdb=" O HIS1I 39 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N HIS1I 39 " --> pdb=" O ARG1I 59 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR1J 118 " --> pdb=" O TYR1I 40 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N VAL1I 42 " --> pdb=" O PHE1J 116 " (cutoff:3.500A) removed outlier: 12.677A pdb=" N PHE1J 116 " --> pdb=" O VAL1I 42 " (cutoff:3.500A) removed outlier: 12.738A pdb=" N GLU1I 44 " --> pdb=" O ASN1J 114 " (cutoff:3.500A) removed outlier: 17.376A pdb=" N ASN1J 114 " --> pdb=" O GLU1I 44 " (cutoff:3.500A) removed outlier: 20.318A pdb=" N LYS1I 46 " --> pdb=" O VAL1J 112 " (cutoff:3.500A) removed outlier: 23.451A pdb=" N VAL1J 112 " --> pdb=" O LYS1I 46 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '1J' and resid 26 through 27 removed outlier: 7.053A pdb=" N LYS1J 92 " --> pdb=" O ALA1J 113 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ALA1J 113 " --> pdb=" O LYS1J 92 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE1J 94 " --> pdb=" O ASN1J 111 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASN1J 111 " --> pdb=" O ILE1J 94 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE1J 96 " --> pdb=" O THR1J 109 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR1J 109 " --> pdb=" O ILE1J 96 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU1J 98 " --> pdb=" O LEU1J 107 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA1J 138 " --> pdb=" O THR1J 118 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE1J 120 " --> pdb=" O GLU1J 136 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU1J 136 " --> pdb=" O PHE1J 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain '1J' and resid 52 through 59 removed outlier: 4.780A pdb=" N ASP1J 41 " --> pdb=" O GLY1J 57 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ARG1J 59 " --> pdb=" O HIS1J 39 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N HIS1J 39 " --> pdb=" O ARG1J 59 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR1K 118 " --> pdb=" O TYR1J 40 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N VAL1J 42 " --> pdb=" O PHE1K 116 " (cutoff:3.500A) removed outlier: 12.736A pdb=" N PHE1K 116 " --> pdb=" O VAL1J 42 " (cutoff:3.500A) removed outlier: 12.710A pdb=" N GLU1J 44 " --> pdb=" O ASN1K 114 " (cutoff:3.500A) removed outlier: 17.354A pdb=" N ASN1K 114 " --> pdb=" O GLU1J 44 " (cutoff:3.500A) removed outlier: 20.409A pdb=" N LYS1J 46 " --> pdb=" O VAL1K 112 " (cutoff:3.500A) removed outlier: 23.558A pdb=" N VAL1K 112 " --> pdb=" O LYS1J 46 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain '1K' and resid 26 through 27 removed outlier: 7.112A pdb=" N LYS1K 92 " --> pdb=" O ALA1K 113 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ALA1K 113 " --> pdb=" O LYS1K 92 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE1K 94 " --> pdb=" O ASN1K 111 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN1K 111 " --> pdb=" O ILE1K 94 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE1K 96 " --> pdb=" O THR1K 109 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR1K 109 " --> pdb=" O ILE1K 96 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU1K 98 " --> pdb=" O LEU1K 107 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N THR1K 140 " --> pdb=" O PRO1K 117 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER1K 119 " --> pdb=" O ALA1K 138 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '2A' and resid 9 through 13 Processing sheet with id=AG2, first strand: chain '2A' and resid 46 through 49 removed outlier: 5.882A pdb=" N VAL2A 31 " --> pdb=" O VAL2A 106 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR2A 156 " --> pdb=" O PHE2A 130 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ASN2A 223 " --> pdb=" O ALA2A 153 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL2A 155 " --> pdb=" O ASN2A 223 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE2A 225 " --> pdb=" O VAL2A 155 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR2A 157 " --> pdb=" O ILE2A 225 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N THR2A 227 " --> pdb=" O TYR2A 157 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N MET2A 224 " --> pdb=" O TRP2A 236 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '2A' and resid 160 through 161 Processing sheet with id=AG4, first strand: chain '2A' and resid 343 through 347 Processing sheet with id=AG5, first strand: chain '2B' and resid 46 through 49 removed outlier: 5.821A pdb=" N VAL2B 31 " --> pdb=" O VAL2B 106 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR2B 156 " --> pdb=" O PHE2B 130 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ASN2B 223 " --> pdb=" O ALA2B 153 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL2B 155 " --> pdb=" O ASN2B 223 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE2B 225 " --> pdb=" O VAL2B 155 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR2B 157 " --> pdb=" O ILE2B 225 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N THR2B 227 " --> pdb=" O TYR2B 157 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET2B 224 " --> pdb=" O TRP2B 236 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '2B' and resid 160 through 161 Processing sheet with id=AG7, first strand: chain '2B' and resid 343 through 347 removed outlier: 6.480A pdb=" N ILE2B 344 " --> pdb=" O TYR2C 11 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU2C 13 " --> pdb=" O ILE2B 344 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU2B 346 " --> pdb=" O GLU2C 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain '2C' and resid 46 through 49 removed outlier: 5.828A pdb=" N VAL2C 31 " --> pdb=" O VAL2C 106 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR2C 156 " --> pdb=" O PHE2C 130 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ASN2C 223 " --> pdb=" O ALA2C 153 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL2C 155 " --> pdb=" O ASN2C 223 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE2C 225 " --> pdb=" O VAL2C 155 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR2C 157 " --> pdb=" O ILE2C 225 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N THR2C 227 " --> pdb=" O TYR2C 157 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET2C 224 " --> pdb=" O TRP2C 236 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '2C' and resid 160 through 161 Processing sheet with id=AH1, first strand: chain '2C' and resid 343 through 347 removed outlier: 6.461A pdb=" N ILE2C 344 " --> pdb=" O TYR2D 11 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLU2D 13 " --> pdb=" O ILE2C 344 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU2C 346 " --> pdb=" O GLU2D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain '2D' and resid 46 through 49 removed outlier: 5.869A pdb=" N VAL2D 31 " --> pdb=" O VAL2D 106 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR2D 156 " --> pdb=" O PHE2D 130 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N ASN2D 223 " --> pdb=" O ALA2D 153 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL2D 155 " --> pdb=" O ASN2D 223 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE2D 225 " --> pdb=" O VAL2D 155 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR2D 157 " --> pdb=" O ILE2D 225 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N THR2D 227 " --> pdb=" O TYR2D 157 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET2D 224 " --> pdb=" O TRP2D 236 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '2D' and resid 160 through 161 Processing sheet with id=AH4, first strand: chain '2D' and resid 343 through 347 Processing sheet with id=AH5, first strand: chain '2E' and resid 46 through 49 removed outlier: 5.820A pdb=" N VAL2E 31 " --> pdb=" O VAL2E 106 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR2E 156 " --> pdb=" O PHE2E 130 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ASN2E 223 " --> pdb=" O ALA2E 153 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL2E 155 " --> pdb=" O ASN2E 223 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE2E 225 " --> pdb=" O VAL2E 155 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR2E 157 " --> pdb=" O ILE2E 225 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N THR2E 227 " --> pdb=" O TYR2E 157 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET2E 224 " --> pdb=" O TRP2E 236 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '2E' and resid 160 through 161 Processing sheet with id=AH7, first strand: chain '2E' and resid 343 through 347 removed outlier: 6.479A pdb=" N ILE2E 344 " --> pdb=" O TYR2F 11 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU2F 13 " --> pdb=" O ILE2E 344 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU2E 346 " --> pdb=" O GLU2F 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain '2F' and resid 46 through 49 removed outlier: 5.827A pdb=" N VAL2F 31 " --> pdb=" O VAL2F 106 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR2F 156 " --> pdb=" O PHE2F 130 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ASN2F 223 " --> pdb=" O ALA2F 153 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL2F 155 " --> pdb=" O ASN2F 223 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE2F 225 " --> pdb=" O VAL2F 155 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR2F 157 " --> pdb=" O ILE2F 225 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N THR2F 227 " --> pdb=" O TYR2F 157 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET2F 224 " --> pdb=" O TRP2F 236 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '2F' and resid 160 through 161 1770 hydrogen bonds defined for protein. 5031 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: 10.66 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14304 1.34 - 1.46: 8355 1.46 - 1.57: 21537 1.57 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 44358 Sorted by residual: bond pdb=" CA THR1J 75 " pdb=" CB THR1J 75 " ideal model delta sigma weight residual 1.533 1.560 -0.026 2.15e-02 2.16e+03 1.51e+00 bond pdb=" CA THR1G 75 " pdb=" CB THR1G 75 " ideal model delta sigma weight residual 1.533 1.559 -0.025 2.15e-02 2.16e+03 1.39e+00 bond pdb=" CB GLN2F 62 " pdb=" CG GLN2F 62 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.26e-01 bond pdb=" CB GLU B 277 " pdb=" CG GLU B 277 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.89e-01 bond pdb=" CB GLU1I 6 " pdb=" CG GLU1I 6 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.84e-01 ... (remaining 44353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 59696 1.35 - 2.71: 550 2.71 - 4.06: 270 4.06 - 5.41: 32 5.41 - 6.77: 4 Bond angle restraints: 60552 Sorted by residual: angle pdb=" C ILE C 142 " pdb=" N ILE C 143 " pdb=" CA ILE C 143 " ideal model delta sigma weight residual 122.13 126.69 -4.56 1.85e+00 2.92e-01 6.07e+00 angle pdb=" C ILE B 142 " pdb=" N ILE B 143 " pdb=" CA ILE B 143 " ideal model delta sigma weight residual 122.13 126.66 -4.53 1.85e+00 2.92e-01 5.99e+00 angle pdb=" C ILE F 142 " pdb=" N ILE F 143 " pdb=" CA ILE F 143 " ideal model delta sigma weight residual 122.13 126.65 -4.52 1.85e+00 2.92e-01 5.97e+00 angle pdb=" C ILE E 142 " pdb=" N ILE E 143 " pdb=" CA ILE E 143 " ideal model delta sigma weight residual 122.13 126.64 -4.51 1.85e+00 2.92e-01 5.95e+00 angle pdb=" C ILE A 142 " pdb=" N ILE A 143 " pdb=" CA ILE A 143 " ideal model delta sigma weight residual 122.13 126.50 -4.37 1.85e+00 2.92e-01 5.57e+00 ... (remaining 60547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 23456 17.93 - 35.85: 2373 35.85 - 53.78: 641 53.78 - 71.71: 128 71.71 - 89.64: 90 Dihedral angle restraints: 26688 sinusoidal: 10428 harmonic: 16260 Sorted by residual: dihedral pdb=" CB GLU B 252 " pdb=" CG GLU B 252 " pdb=" CD GLU B 252 " pdb=" OE1 GLU B 252 " ideal model delta sinusoidal sigma weight residual 0.00 88.94 -88.94 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU1F 101 " pdb=" CG GLU1F 101 " pdb=" CD GLU1F 101 " pdb=" OE1 GLU1F 101 " ideal model delta sinusoidal sigma weight residual 0.00 88.92 -88.92 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU1C 101 " pdb=" CG GLU1C 101 " pdb=" CD GLU1C 101 " pdb=" OE1 GLU1C 101 " ideal model delta sinusoidal sigma weight residual 0.00 88.91 -88.91 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 26685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 4447 0.030 - 0.059: 1507 0.059 - 0.089: 387 0.089 - 0.118: 608 0.118 - 0.148: 95 Chirality restraints: 7044 Sorted by residual: chirality pdb=" CA VAL2D 87 " pdb=" N VAL2D 87 " pdb=" C VAL2D 87 " pdb=" CB VAL2D 87 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE2F 225 " pdb=" N ILE2F 225 " pdb=" C ILE2F 225 " pdb=" CB ILE2F 225 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE2C 225 " pdb=" N ILE2C 225 " pdb=" C ILE2C 225 " pdb=" CB ILE2C 225 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 7041 not shown) Planarity restraints: 7854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG1A 143 " 0.162 9.50e-02 1.11e+02 7.32e-02 3.83e+00 pdb=" NE ARG1A 143 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG1A 143 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG1A 143 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG1A 143 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR1J 75 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C THR1J 75 " 0.034 2.00e-02 2.50e+03 pdb=" O THR1J 75 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS1J 76 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR1G 75 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C THR1G 75 " -0.033 2.00e-02 2.50e+03 pdb=" O THR1G 75 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS1G 76 " 0.011 2.00e-02 2.50e+03 ... (remaining 7851 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2169 2.73 - 3.27: 40264 3.27 - 3.81: 71125 3.81 - 4.36: 86550 4.36 - 4.90: 151389 Nonbonded interactions: 351497 Sorted by model distance: nonbonded pdb=" N GLU1G 6 " pdb=" OE1 GLU1G 6 " model vdw 2.186 3.120 nonbonded pdb=" N GLU1J 6 " pdb=" OE1 GLU1J 6 " model vdw 2.191 3.120 nonbonded pdb=" O ASP2F 131 " pdb=" OH TYR2F 147 " model vdw 2.200 3.040 nonbonded pdb=" O ASP2C 131 " pdb=" OH TYR2C 147 " model vdw 2.201 3.040 nonbonded pdb=" O ASP2D 131 " pdb=" OH TYR2D 147 " model vdw 2.206 3.040 ... (remaining 351492 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 '1A' selection = chain '1B' selection = chain '1C' selection = chain '1D' selection = chain '1E' selection = chain '1F' selection = (chain '1G' and resid 6 through 149) selection = (chain '1H' and resid 6 through 149) selection = (chain '1I' and resid 6 through 149) selection = (chain '1J' and resid 6 through 149) selection = (chain '1K' and resid 6 through 149) selection = (chain '1L' and resid 6 through 149) } ncs_group { reference = chain '2A' selection = chain '2B' selection = chain '2C' selection = chain '2D' selection = chain '2E' selection = chain '2F' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 21.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 43.180 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.140 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 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 : 0.002 0.037 44358 Z= 0.103 Angle : 0.424 6.766 60552 Z= 0.217 Chirality : 0.044 0.148 7044 Planarity : 0.003 0.073 7854 Dihedral : 16.523 89.636 16176 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.05 % Allowed : 19.50 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.11), residues: 5490 helix: 2.41 (0.14), residues: 1344 sheet: 1.12 (0.15), residues: 1338 loop : 0.05 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG1A 143 TYR 0.008 0.001 TYR2F 83 PHE 0.010 0.001 PHE1D 78 TRP 0.009 0.001 TRP B 156 HIS 0.001 0.000 HIS1A 39 Details of bonding type rmsd covalent geometry : bond 0.00244 (44358) covalent geometry : angle 0.42416 (60552) hydrogen bonds : bond 0.16810 ( 1770) hydrogen bonds : angle 6.46150 ( 5031) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 410 time to evaluate : 1.697 Fit side-chains REVERT: A 201 ASP cc_start: 0.7407 (t0) cc_final: 0.7143 (t0) REVERT: B 201 ASP cc_start: 0.7670 (t0) cc_final: 0.7429 (t0) REVERT: B 220 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7869 (p) REVERT: C 201 ASP cc_start: 0.7833 (t0) cc_final: 0.7457 (t0) REVERT: D 201 ASP cc_start: 0.7540 (t0) cc_final: 0.7202 (t0) REVERT: E 201 ASP cc_start: 0.7583 (t0) cc_final: 0.7304 (t0) REVERT: E 220 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.7894 (p) REVERT: F 201 ASP cc_start: 0.7911 (t0) cc_final: 0.7524 (t0) REVERT: 1B 90 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: 1B 126 ASP cc_start: 0.9122 (t0) cc_final: 0.8898 (t0) REVERT: 1C 126 ASP cc_start: 0.9043 (t0) cc_final: 0.8816 (t0) REVERT: 1E 67 ARG cc_start: 0.8982 (ttp80) cc_final: 0.8666 (mmm-85) REVERT: 1E 90 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: 1E 126 ASP cc_start: 0.9104 (t0) cc_final: 0.8878 (t0) REVERT: 1F 126 ASP cc_start: 0.9060 (t0) cc_final: 0.8792 (t0) REVERT: 1G 7 GLN cc_start: 0.9085 (mt0) cc_final: 0.8808 (mt0) REVERT: 1H 76 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8528 (mtmm) REVERT: 1I 105 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8643 (mt-10) REVERT: 1K 67 ARG cc_start: 0.8901 (mtm-85) cc_final: 0.8680 (mtm110) REVERT: 1K 76 LYS cc_start: 0.8850 (mtpp) cc_final: 0.8632 (mtmm) REVERT: 1K 90 GLU cc_start: 0.9018 (tp30) cc_final: 0.8325 (tm-30) REVERT: 1L 67 ARG cc_start: 0.8968 (mtp-110) cc_final: 0.8587 (mtp85) REVERT: 1L 105 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8646 (mt-10) REVERT: 2B 329 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9172 (ttp) REVERT: 2C 164 TRP cc_start: 0.9229 (OUTLIER) cc_final: 0.7571 (p-90) REVERT: 2C 230 LYS cc_start: 0.4474 (ptpt) cc_final: 0.3911 (ptpt) REVERT: 2D 62 GLN cc_start: 0.8301 (mm110) cc_final: 0.7980 (pm20) REVERT: 2D 88 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7020 (mm-40) REVERT: 2F 62 GLN cc_start: 0.7567 (pm20) cc_final: 0.7168 (pm20) REVERT: 2F 164 TRP cc_start: 0.9226 (OUTLIER) cc_final: 0.7553 (p-90) REVERT: 2F 230 LYS cc_start: 0.5177 (ptpt) cc_final: 0.4602 (ptpt) outliers start: 51 outliers final: 38 residues processed: 454 average time/residue: 0.8775 time to fit residues: 474.1324 Evaluate side-chains 451 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 405 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain 1A residue 7 GLN Chi-restraints excluded: chain 1B residue 90 GLU Chi-restraints excluded: chain 1B residue 124 SER Chi-restraints excluded: chain 1C residue 38 VAL Chi-restraints excluded: chain 1E residue 90 GLU Chi-restraints excluded: chain 1F residue 38 VAL Chi-restraints excluded: chain 1G residue 124 SER Chi-restraints excluded: chain 1G residue 129 SER Chi-restraints excluded: chain 1H residue 75 THR Chi-restraints excluded: chain 1I residue 144 VAL Chi-restraints excluded: chain 1J residue 124 SER Chi-restraints excluded: chain 1J residue 129 SER Chi-restraints excluded: chain 1K residue 75 THR Chi-restraints excluded: chain 1K residue 122 SER Chi-restraints excluded: chain 1L residue 7 GLN Chi-restraints excluded: chain 1L residue 144 VAL Chi-restraints excluded: chain 2A residue 212 LEU Chi-restraints excluded: chain 2B residue 22 VAL Chi-restraints excluded: chain 2B residue 212 LEU Chi-restraints excluded: chain 2B residue 329 MET Chi-restraints excluded: chain 2C residue 164 TRP Chi-restraints excluded: chain 2C residue 189 VAL Chi-restraints excluded: chain 2C residue 317 ILE Chi-restraints excluded: chain 2D residue 88 GLN Chi-restraints excluded: chain 2D residue 101 ASP Chi-restraints excluded: chain 2D residue 164 TRP Chi-restraints excluded: chain 2D residue 212 LEU Chi-restraints excluded: chain 2E residue 22 VAL Chi-restraints excluded: chain 2E residue 212 LEU Chi-restraints excluded: chain 2F residue 164 TRP Chi-restraints excluded: chain 2F residue 189 VAL Chi-restraints excluded: chain 2F residue 317 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 0.5980 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 31 ASN 1D 31 ASN ** 2E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.080943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.060263 restraints weight = 78042.744| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.37 r_work: 0.2645 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 44358 Z= 0.107 Angle : 0.456 5.370 60552 Z= 0.243 Chirality : 0.045 0.145 7044 Planarity : 0.003 0.039 7854 Dihedral : 4.790 61.214 6004 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.26 % Allowed : 19.11 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.12), residues: 5490 helix: 2.37 (0.14), residues: 1374 sheet: 0.99 (0.14), residues: 1416 loop : 0.12 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG1A 143 TYR 0.008 0.001 TYR1J 17 PHE 0.011 0.001 PHE1E 78 TRP 0.010 0.001 TRP E 156 HIS 0.001 0.000 HIS C 59 Details of bonding type rmsd covalent geometry : bond 0.00240 (44358) covalent geometry : angle 0.45615 (60552) hydrogen bonds : bond 0.04386 ( 1770) hydrogen bonds : angle 5.04656 ( 5031) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 415 time to evaluate : 1.706 Fit side-chains REVERT: A 201 ASP cc_start: 0.7121 (t0) cc_final: 0.6815 (t0) REVERT: B 201 ASP cc_start: 0.7635 (t0) cc_final: 0.7200 (t0) REVERT: 1B 90 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8137 (tm-30) REVERT: 1B 119 SER cc_start: 0.9471 (t) cc_final: 0.9170 (m) REVERT: 1B 126 ASP cc_start: 0.9111 (t0) cc_final: 0.8864 (t0) REVERT: 1C 126 ASP cc_start: 0.9043 (t0) cc_final: 0.8807 (t0) REVERT: 1E 31 ASN cc_start: 0.8747 (t0) cc_final: 0.8523 (t0) REVERT: 1E 119 SER cc_start: 0.9479 (t) cc_final: 0.9177 (m) REVERT: 1E 126 ASP cc_start: 0.9095 (t0) cc_final: 0.8825 (t0) REVERT: 1F 105 GLU cc_start: 0.8859 (tt0) cc_final: 0.8607 (tt0) REVERT: 1F 126 ASP cc_start: 0.9047 (t0) cc_final: 0.8820 (t0) REVERT: 1G 7 GLN cc_start: 0.9021 (mt0) cc_final: 0.8790 (mt0) REVERT: 1H 63 ASN cc_start: 0.9367 (m110) cc_final: 0.9165 (m-40) REVERT: 1H 76 LYS cc_start: 0.8753 (mtpp) cc_final: 0.8492 (mtmm) REVERT: 1I 67 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8563 (mtp180) REVERT: 1I 105 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8563 (mt-10) REVERT: 1K 63 ASN cc_start: 0.9383 (m110) cc_final: 0.9136 (m-40) REVERT: 1K 67 ARG cc_start: 0.8915 (mtm-85) cc_final: 0.8591 (mtm110) REVERT: 1K 76 LYS cc_start: 0.8744 (mtpp) cc_final: 0.8476 (mtmm) REVERT: 1K 90 GLU cc_start: 0.9060 (tp30) cc_final: 0.8288 (tm-30) REVERT: 1L 67 ARG cc_start: 0.8890 (mtp-110) cc_final: 0.8557 (mtp85) REVERT: 1L 105 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8563 (mt-10) REVERT: 2B 61 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: 2C 230 LYS cc_start: 0.5008 (ptpt) cc_final: 0.4553 (ptpt) REVERT: 2D 62 GLN cc_start: 0.8315 (mm110) cc_final: 0.7876 (pm20) REVERT: 2E 88 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6740 (mm-40) REVERT: 2E 267 MET cc_start: 0.9510 (ptp) cc_final: 0.8951 (ptm) REVERT: 2F 61 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: 2F 62 GLN cc_start: 0.7596 (pm20) cc_final: 0.7072 (pm20) outliers start: 61 outliers final: 21 residues processed: 468 average time/residue: 0.8866 time to fit residues: 492.9850 Evaluate side-chains 430 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 406 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain 1F residue 119 SER Chi-restraints excluded: chain 1H residue 68 LYS Chi-restraints excluded: chain 1H residue 129 SER Chi-restraints excluded: chain 1I residue 34 SER Chi-restraints excluded: chain 1I residue 132 ILE Chi-restraints excluded: chain 1I residue 144 VAL Chi-restraints excluded: chain 1K residue 129 SER Chi-restraints excluded: chain 1L residue 75 THR Chi-restraints excluded: chain 1L residue 132 ILE Chi-restraints excluded: chain 1L residue 144 VAL Chi-restraints excluded: chain 2A residue 134 THR Chi-restraints excluded: chain 2A residue 164 TRP Chi-restraints excluded: chain 2A residue 212 LEU Chi-restraints excluded: chain 2B residue 61 GLU Chi-restraints excluded: chain 2C residue 134 THR Chi-restraints excluded: chain 2D residue 134 THR Chi-restraints excluded: chain 2D residue 164 TRP Chi-restraints excluded: chain 2D residue 212 LEU Chi-restraints excluded: chain 2E residue 88 GLN Chi-restraints excluded: chain 2F residue 61 GLU Chi-restraints excluded: chain 2F residue 134 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 72 optimal weight: 4.9990 chunk 518 optimal weight: 4.9990 chunk 463 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 449 optimal weight: 0.8980 chunk 231 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 46 GLN 1A 31 ASN 1D 31 ASN 1I 135 GLN 1L 135 GLN 2A 88 GLN ** 2B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.081529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.060878 restraints weight = 77719.444| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.36 r_work: 0.2654 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 44358 Z= 0.102 Angle : 0.441 5.802 60552 Z= 0.232 Chirality : 0.045 0.141 7044 Planarity : 0.003 0.037 7854 Dihedral : 3.819 58.749 5936 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.70 % Allowed : 18.63 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.11), residues: 5490 helix: 2.39 (0.14), residues: 1374 sheet: 1.03 (0.14), residues: 1446 loop : 0.11 (0.12), residues: 2670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG1E 143 TYR 0.008 0.001 TYR1J 17 PHE 0.012 0.001 PHE1E 78 TRP 0.009 0.001 TRP B 156 HIS 0.001 0.000 HIS C 59 Details of bonding type rmsd covalent geometry : bond 0.00235 (44358) covalent geometry : angle 0.44134 (60552) hydrogen bonds : bond 0.03891 ( 1770) hydrogen bonds : angle 4.70979 ( 5031) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 418 time to evaluate : 1.836 Fit side-chains REVERT: B 201 ASP cc_start: 0.7631 (t0) cc_final: 0.7138 (t0) REVERT: B 248 SER cc_start: 0.9179 (m) cc_final: 0.8471 (p) REVERT: B 252 GLU cc_start: 0.7647 (tp30) cc_final: 0.7398 (tp30) REVERT: 1B 90 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8025 (tm-30) REVERT: 1B 93 ASP cc_start: 0.9084 (m-30) cc_final: 0.8874 (m-30) REVERT: 1B 119 SER cc_start: 0.9496 (t) cc_final: 0.9198 (m) REVERT: 1B 126 ASP cc_start: 0.9118 (t0) cc_final: 0.8840 (t0) REVERT: 1C 67 ARG cc_start: 0.8830 (ttp80) cc_final: 0.8451 (ttp-110) REVERT: 1C 105 GLU cc_start: 0.8872 (tt0) cc_final: 0.8620 (tt0) REVERT: 1D 76 LYS cc_start: 0.8700 (mtmm) cc_final: 0.8483 (mttp) REVERT: 1E 90 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: 1E 93 ASP cc_start: 0.9116 (m-30) cc_final: 0.8904 (m-30) REVERT: 1E 119 SER cc_start: 0.9497 (t) cc_final: 0.9206 (m) REVERT: 1E 126 ASP cc_start: 0.9093 (t0) cc_final: 0.8818 (t0) REVERT: 1E 143 ARG cc_start: 0.8626 (ttp-110) cc_final: 0.8366 (ttp-110) REVERT: 1F 67 ARG cc_start: 0.8810 (ttp80) cc_final: 0.8425 (ttp-110) REVERT: 1F 105 GLU cc_start: 0.8872 (tt0) cc_final: 0.8620 (tt0) REVERT: 1F 119 SER cc_start: 0.9221 (OUTLIER) cc_final: 0.8846 (m) REVERT: 1F 126 ASP cc_start: 0.9048 (t0) cc_final: 0.8821 (t0) REVERT: 1G 7 GLN cc_start: 0.9051 (mt0) cc_final: 0.8824 (mt0) REVERT: 1H 76 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8494 (mtmm) REVERT: 1I 67 ARG cc_start: 0.8880 (mtm-85) cc_final: 0.8617 (mtp180) REVERT: 1I 105 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8549 (mt-10) REVERT: 1K 63 ASN cc_start: 0.9393 (m110) cc_final: 0.9147 (m-40) REVERT: 1K 67 ARG cc_start: 0.8912 (mtm-85) cc_final: 0.8618 (mtm110) REVERT: 1K 76 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8493 (mtmm) REVERT: 1K 90 GLU cc_start: 0.9052 (tp30) cc_final: 0.8287 (tm-30) REVERT: 1L 67 ARG cc_start: 0.8858 (mtp-110) cc_final: 0.8597 (mtp85) REVERT: 1L 105 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8548 (mt-10) REVERT: 2A 88 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6781 (mm-40) REVERT: 2B 61 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8366 (mt-10) REVERT: 2B 88 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6658 (tp-100) REVERT: 2C 277 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: 2D 62 GLN cc_start: 0.8316 (mm110) cc_final: 0.7940 (pm20) REVERT: 2D 88 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6708 (mm-40) REVERT: 2E 88 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6653 (tp-100) REVERT: 2E 199 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.8781 (mm-40) REVERT: 2F 277 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7825 (tm-30) outliers start: 82 outliers final: 28 residues processed: 487 average time/residue: 0.9146 time to fit residues: 530.7499 Evaluate side-chains 444 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 406 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain 1E residue 90 GLU Chi-restraints excluded: chain 1E residue 105 GLU Chi-restraints excluded: chain 1F residue 119 SER Chi-restraints excluded: chain 1H residue 68 LYS Chi-restraints excluded: chain 1H residue 119 SER Chi-restraints excluded: chain 1H residue 129 SER Chi-restraints excluded: chain 1I residue 34 SER Chi-restraints excluded: chain 1I residue 132 ILE Chi-restraints excluded: chain 1K residue 66 LEU Chi-restraints excluded: chain 1K residue 129 SER Chi-restraints excluded: chain 1L residue 75 THR Chi-restraints excluded: chain 1L residue 132 ILE Chi-restraints excluded: chain 2A residue 88 GLN Chi-restraints excluded: chain 2A residue 134 THR Chi-restraints excluded: chain 2A residue 164 TRP Chi-restraints excluded: chain 2A residue 212 LEU Chi-restraints excluded: chain 2B residue 61 GLU Chi-restraints excluded: chain 2B residue 88 GLN Chi-restraints excluded: chain 2C residue 134 THR Chi-restraints excluded: chain 2C residue 277 GLN Chi-restraints excluded: chain 2D residue 88 GLN Chi-restraints excluded: chain 2D residue 134 THR Chi-restraints excluded: chain 2D residue 212 LEU Chi-restraints excluded: chain 2D residue 267 MET Chi-restraints excluded: chain 2E residue 88 GLN Chi-restraints excluded: chain 2E residue 136 GLU Chi-restraints excluded: chain 2E residue 199 GLN Chi-restraints excluded: chain 2F residue 134 THR Chi-restraints excluded: chain 2F residue 277 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 467 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 295 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 415 optimal weight: 0.7980 chunk 464 optimal weight: 4.9990 chunk 472 optimal weight: 5.9990 chunk 329 optimal weight: 2.9990 chunk 436 optimal weight: 3.9990 chunk 383 optimal weight: 7.9990 chunk 382 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN D 202 ASN 1A 31 ASN 1D 31 ASN 1L 135 GLN ** 2B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2B 246 ASN ** 2E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.060445 restraints weight = 77678.997| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.38 r_work: 0.2630 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 44358 Z= 0.134 Angle : 0.459 6.423 60552 Z= 0.241 Chirality : 0.045 0.139 7044 Planarity : 0.003 0.036 7854 Dihedral : 3.863 57.826 5932 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.39 % Allowed : 18.36 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.11), residues: 5490 helix: 2.39 (0.14), residues: 1374 sheet: 0.97 (0.14), residues: 1446 loop : 0.07 (0.12), residues: 2670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG1E 143 TYR 0.009 0.001 TYR1J 17 PHE 0.013 0.001 PHE1E 78 TRP 0.009 0.001 TRP B 156 HIS 0.001 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00320 (44358) covalent geometry : angle 0.45924 (60552) hydrogen bonds : bond 0.03965 ( 1770) hydrogen bonds : angle 4.61107 ( 5031) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 417 time to evaluate : 1.299 Fit side-chains REVERT: B 201 ASP cc_start: 0.7713 (t0) cc_final: 0.7217 (t0) REVERT: B 248 SER cc_start: 0.9012 (m) cc_final: 0.8317 (p) REVERT: B 252 GLU cc_start: 0.7668 (tp30) cc_final: 0.7406 (tp30) REVERT: E 252 GLU cc_start: 0.7680 (tp30) cc_final: 0.7424 (tp30) REVERT: 1B 90 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: 1B 93 ASP cc_start: 0.9074 (m-30) cc_final: 0.8874 (m-30) REVERT: 1B 126 ASP cc_start: 0.9140 (t0) cc_final: 0.8866 (t0) REVERT: 1C 67 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8596 (ttp-110) REVERT: 1C 105 GLU cc_start: 0.8872 (tt0) cc_final: 0.8629 (tt0) REVERT: 1E 90 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: 1E 119 SER cc_start: 0.9501 (t) cc_final: 0.9200 (m) REVERT: 1E 126 ASP cc_start: 0.9125 (t0) cc_final: 0.8851 (t0) REVERT: 1E 143 ARG cc_start: 0.8642 (ttp-110) cc_final: 0.8399 (ttp-110) REVERT: 1F 67 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8470 (ttp-110) REVERT: 1F 105 GLU cc_start: 0.8880 (tt0) cc_final: 0.8651 (tt0) REVERT: 1G 7 GLN cc_start: 0.9083 (mt0) cc_final: 0.8834 (mt0) REVERT: 1H 76 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8518 (mtmm) REVERT: 1I 67 ARG cc_start: 0.8960 (mtm-85) cc_final: 0.8539 (mtp85) REVERT: 1I 105 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8562 (mt-10) REVERT: 1K 67 ARG cc_start: 0.8935 (mtm-85) cc_final: 0.8658 (mtm110) REVERT: 1K 76 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8515 (mtmm) REVERT: 1K 90 GLU cc_start: 0.9061 (tp30) cc_final: 0.8306 (tm-30) REVERT: 1L 67 ARG cc_start: 0.8891 (mtp-110) cc_final: 0.8613 (mtp85) REVERT: 1L 105 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8566 (mt-10) REVERT: 2B 61 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: 2B 88 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6702 (tp-100) REVERT: 2B 329 MET cc_start: 0.9530 (ttp) cc_final: 0.9236 (ttp) REVERT: 2C 277 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: 2D 62 GLN cc_start: 0.8328 (mm110) cc_final: 0.7919 (pm20) REVERT: 2D 88 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6883 (mm-40) REVERT: 2E 199 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8695 (mm-40) REVERT: 2F 61 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8297 (mt-10) REVERT: 2F 62 GLN cc_start: 0.7571 (pm20) cc_final: 0.7024 (pm20) REVERT: 2F 277 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7854 (tm-30) outliers start: 67 outliers final: 35 residues processed: 472 average time/residue: 0.9021 time to fit residues: 506.5481 Evaluate side-chains 452 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 408 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain 1A residue 34 SER Chi-restraints excluded: chain 1B residue 90 GLU Chi-restraints excluded: chain 1D residue 34 SER Chi-restraints excluded: chain 1E residue 90 GLU Chi-restraints excluded: chain 1F residue 99 THR Chi-restraints excluded: chain 1F residue 119 SER Chi-restraints excluded: chain 1H residue 68 LYS Chi-restraints excluded: chain 1H residue 119 SER Chi-restraints excluded: chain 1H residue 129 SER Chi-restraints excluded: chain 1I residue 34 SER Chi-restraints excluded: chain 1I residue 132 ILE Chi-restraints excluded: chain 1I residue 144 VAL Chi-restraints excluded: chain 1K residue 66 LEU Chi-restraints excluded: chain 1K residue 129 SER Chi-restraints excluded: chain 1L residue 34 SER Chi-restraints excluded: chain 1L residue 75 THR Chi-restraints excluded: chain 1L residue 132 ILE Chi-restraints excluded: chain 1L residue 144 VAL Chi-restraints excluded: chain 2A residue 134 THR Chi-restraints excluded: chain 2A residue 164 TRP Chi-restraints excluded: chain 2A residue 212 LEU Chi-restraints excluded: chain 2B residue 61 GLU Chi-restraints excluded: chain 2B residue 88 GLN Chi-restraints excluded: chain 2B residue 136 GLU Chi-restraints excluded: chain 2B residue 212 LEU Chi-restraints excluded: chain 2C residue 134 THR Chi-restraints excluded: chain 2C residue 277 GLN Chi-restraints excluded: chain 2D residue 88 GLN Chi-restraints excluded: chain 2D residue 134 THR Chi-restraints excluded: chain 2D residue 164 TRP Chi-restraints excluded: chain 2D residue 212 LEU Chi-restraints excluded: chain 2E residue 136 GLU Chi-restraints excluded: chain 2E residue 199 GLN Chi-restraints excluded: chain 2E residue 212 LEU Chi-restraints excluded: chain 2F residue 61 GLU Chi-restraints excluded: chain 2F residue 134 THR Chi-restraints excluded: chain 2F residue 277 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 324 optimal weight: 0.5980 chunk 539 optimal weight: 0.9980 chunk 486 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 510 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 347 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 206 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 31 ASN 1D 31 ASN 1L 135 GLN ** 2B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2E 246 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.061221 restraints weight = 77285.715| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.37 r_work: 0.2658 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 44358 Z= 0.105 Angle : 0.443 6.032 60552 Z= 0.232 Chirality : 0.045 0.139 7044 Planarity : 0.003 0.037 7854 Dihedral : 3.805 56.557 5932 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.57 % Allowed : 18.57 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.11), residues: 5490 helix: 2.40 (0.14), residues: 1374 sheet: 0.94 (0.13), residues: 1476 loop : 0.13 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG1G 67 TYR 0.008 0.001 TYR1J 17 PHE 0.012 0.001 PHE1E 78 TRP 0.009 0.001 TRP B 156 HIS 0.001 0.000 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00246 (44358) covalent geometry : angle 0.44258 (60552) hydrogen bonds : bond 0.03648 ( 1770) hydrogen bonds : angle 4.47772 ( 5031) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 418 time to evaluate : 1.722 Fit side-chains REVERT: B 201 ASP cc_start: 0.7711 (t0) cc_final: 0.7189 (t0) REVERT: B 248 SER cc_start: 0.8936 (m) cc_final: 0.8219 (p) REVERT: B 252 GLU cc_start: 0.7683 (tp30) cc_final: 0.7406 (tp30) REVERT: E 248 SER cc_start: 0.9131 (m) cc_final: 0.8370 (p) REVERT: 1B 31 ASN cc_start: 0.8856 (t0) cc_final: 0.8587 (t0) REVERT: 1B 90 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: 1B 93 ASP cc_start: 0.9054 (m-30) cc_final: 0.8853 (m-30) REVERT: 1B 126 ASP cc_start: 0.9128 (t0) cc_final: 0.8854 (t0) REVERT: 1C 67 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8638 (ttp-110) REVERT: 1C 105 GLU cc_start: 0.8884 (tt0) cc_final: 0.8623 (tt0) REVERT: 1E 90 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: 1E 119 SER cc_start: 0.9500 (t) cc_final: 0.9210 (m) REVERT: 1E 126 ASP cc_start: 0.9112 (t0) cc_final: 0.8867 (t0) REVERT: 1E 143 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8377 (ttp-110) REVERT: 1F 67 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8593 (ttp-110) REVERT: 1F 105 GLU cc_start: 0.8893 (tt0) cc_final: 0.8645 (tt0) REVERT: 1F 119 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8862 (m) REVERT: 1F 126 ASP cc_start: 0.9068 (t0) cc_final: 0.8828 (t0) REVERT: 1G 7 GLN cc_start: 0.9082 (mt0) cc_final: 0.8849 (mt0) REVERT: 1H 136 GLU cc_start: 0.8955 (tt0) cc_final: 0.8593 (mm-30) REVERT: 1I 67 ARG cc_start: 0.8995 (mtm-85) cc_final: 0.8591 (mtp85) REVERT: 1I 105 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8579 (mt-10) REVERT: 1K 67 ARG cc_start: 0.8939 (mtm-85) cc_final: 0.8702 (mtm110) REVERT: 1K 90 GLU cc_start: 0.9072 (tp30) cc_final: 0.8342 (tm-30) REVERT: 1K 136 GLU cc_start: 0.8903 (tt0) cc_final: 0.8644 (mm-30) REVERT: 1L 67 ARG cc_start: 0.8901 (mtp-110) cc_final: 0.8620 (mtp85) REVERT: 1L 105 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8572 (mt-10) REVERT: 2A 326 GLN cc_start: 0.8792 (mt0) cc_final: 0.8488 (mt0) REVERT: 2B 61 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: 2B 88 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6822 (tp-100) REVERT: 2C 277 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: 2D 62 GLN cc_start: 0.8329 (mm110) cc_final: 0.7971 (pm20) REVERT: 2D 88 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6850 (mm-40) REVERT: 2D 277 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: 2D 322 ASP cc_start: 0.8491 (t70) cc_final: 0.8251 (t70) REVERT: 2D 326 GLN cc_start: 0.8780 (mt0) cc_final: 0.8476 (mt0) REVERT: 2E 88 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6773 (tp-100) REVERT: 2E 199 GLN cc_start: 0.9326 (OUTLIER) cc_final: 0.8719 (mm-40) REVERT: 2E 329 MET cc_start: 0.9518 (ttp) cc_final: 0.9166 (ttp) REVERT: 2F 277 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7833 (tm-30) outliers start: 76 outliers final: 34 residues processed: 482 average time/residue: 0.9077 time to fit residues: 520.3345 Evaluate side-chains 456 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 411 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain 1A residue 34 SER Chi-restraints excluded: chain 1B residue 90 GLU Chi-restraints excluded: chain 1D residue 34 SER Chi-restraints excluded: chain 1E residue 90 GLU Chi-restraints excluded: chain 1F residue 99 THR Chi-restraints excluded: chain 1F residue 119 SER Chi-restraints excluded: chain 1H residue 119 SER Chi-restraints excluded: chain 1H residue 129 SER Chi-restraints excluded: chain 1H residue 132 ILE Chi-restraints excluded: chain 1I residue 34 SER Chi-restraints excluded: chain 1I residue 132 ILE Chi-restraints excluded: chain 1I residue 144 VAL Chi-restraints excluded: chain 1K residue 66 LEU Chi-restraints excluded: chain 1K residue 129 SER Chi-restraints excluded: chain 1L residue 34 SER Chi-restraints excluded: chain 1L residue 75 THR Chi-restraints excluded: chain 1L residue 132 ILE Chi-restraints excluded: chain 1L residue 144 VAL Chi-restraints excluded: chain 2A residue 134 THR Chi-restraints excluded: chain 2A residue 164 TRP Chi-restraints excluded: chain 2A residue 212 LEU Chi-restraints excluded: chain 2B residue 61 GLU Chi-restraints excluded: chain 2B residue 88 GLN Chi-restraints excluded: chain 2B residue 136 GLU Chi-restraints excluded: chain 2C residue 134 THR Chi-restraints excluded: chain 2C residue 277 GLN Chi-restraints excluded: chain 2D residue 88 GLN Chi-restraints excluded: chain 2D residue 134 THR Chi-restraints excluded: chain 2D residue 164 TRP Chi-restraints excluded: chain 2D residue 212 LEU Chi-restraints excluded: chain 2D residue 277 GLN Chi-restraints excluded: chain 2E residue 88 GLN Chi-restraints excluded: chain 2E residue 136 GLU Chi-restraints excluded: chain 2E residue 199 GLN Chi-restraints excluded: chain 2E residue 212 LEU Chi-restraints excluded: chain 2F residue 134 THR Chi-restraints excluded: chain 2F residue 277 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 107 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 166 optimal weight: 0.0170 chunk 91 optimal weight: 5.9990 chunk 195 optimal weight: 0.2980 chunk 198 optimal weight: 4.9990 chunk 361 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 539 optimal weight: 0.9980 chunk 494 optimal weight: 1.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN 1A 31 ASN 1C 111 ASN 1D 31 ASN 1F 111 ASN 1L 7 GLN ** 2B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.081693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.061099 restraints weight = 77657.956| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.35 r_work: 0.2658 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 44358 Z= 0.102 Angle : 0.447 7.156 60552 Z= 0.233 Chirality : 0.045 0.138 7044 Planarity : 0.003 0.035 7854 Dihedral : 3.770 55.526 5932 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.45 % Allowed : 19.19 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.11), residues: 5490 helix: 2.42 (0.14), residues: 1374 sheet: 0.96 (0.13), residues: 1476 loop : 0.14 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG1J 67 TYR 0.008 0.001 TYR1J 17 PHE 0.012 0.001 PHE1E 78 TRP 0.009 0.001 TRP A 156 HIS 0.001 0.000 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00239 (44358) covalent geometry : angle 0.44678 (60552) hydrogen bonds : bond 0.03551 ( 1770) hydrogen bonds : angle 4.41075 ( 5031) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 408 time to evaluate : 1.901 Fit side-chains REVERT: B 201 ASP cc_start: 0.7640 (t0) cc_final: 0.7104 (t0) REVERT: B 248 SER cc_start: 0.8958 (m) cc_final: 0.8234 (p) REVERT: E 248 SER cc_start: 0.9109 (m) cc_final: 0.8313 (p) REVERT: 1B 31 ASN cc_start: 0.8774 (t0) cc_final: 0.8480 (t0) REVERT: 1B 90 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: 1B 126 ASP cc_start: 0.9103 (t0) cc_final: 0.8849 (t0) REVERT: 1C 67 ARG cc_start: 0.8853 (ttp80) cc_final: 0.8632 (ttp-110) REVERT: 1C 105 GLU cc_start: 0.8846 (tt0) cc_final: 0.8611 (tt0) REVERT: 1C 126 ASP cc_start: 0.9045 (t0) cc_final: 0.8752 (t0) REVERT: 1E 90 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: 1E 93 ASP cc_start: 0.9085 (m-30) cc_final: 0.8880 (m-30) REVERT: 1E 119 SER cc_start: 0.9499 (t) cc_final: 0.9196 (m) REVERT: 1E 126 ASP cc_start: 0.9090 (t0) cc_final: 0.8833 (t0) REVERT: 1F 67 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8603 (ttp-110) REVERT: 1F 105 GLU cc_start: 0.8855 (tt0) cc_final: 0.8635 (tt0) REVERT: 1F 119 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8867 (m) REVERT: 1F 126 ASP cc_start: 0.9038 (t0) cc_final: 0.8786 (t0) REVERT: 1I 67 ARG cc_start: 0.8972 (mtm-85) cc_final: 0.8539 (mtp85) REVERT: 1I 105 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8556 (mt-10) REVERT: 1J 136 GLU cc_start: 0.9040 (tt0) cc_final: 0.8785 (mt-10) REVERT: 1K 67 ARG cc_start: 0.8903 (mtm-85) cc_final: 0.8647 (mtm110) REVERT: 1K 90 GLU cc_start: 0.9061 (tp30) cc_final: 0.8307 (tm-30) REVERT: 1L 67 ARG cc_start: 0.8869 (mtp-110) cc_final: 0.8578 (mtp85) REVERT: 1L 105 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8542 (mt-10) REVERT: 2A 322 ASP cc_start: 0.8484 (t70) cc_final: 0.8242 (t70) REVERT: 2A 326 GLN cc_start: 0.8768 (mt0) cc_final: 0.8446 (mt0) REVERT: 2B 61 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8307 (mt-10) REVERT: 2B 88 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6751 (tp-100) REVERT: 2C 61 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: 2C 261 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8336 (ttm110) REVERT: 2C 277 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: 2D 62 GLN cc_start: 0.8339 (mm110) cc_final: 0.7971 (pm20) REVERT: 2D 88 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6845 (mm-40) REVERT: 2D 277 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: 2D 326 GLN cc_start: 0.8747 (mt0) cc_final: 0.8401 (mt0) REVERT: 2E 199 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8664 (mm-40) REVERT: 2F 62 GLN cc_start: 0.7565 (pm20) cc_final: 0.7090 (pm20) REVERT: 2F 261 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8343 (ttm110) REVERT: 2F 277 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7795 (tm-30) outliers start: 70 outliers final: 42 residues processed: 469 average time/residue: 0.8240 time to fit residues: 461.6988 Evaluate side-chains 458 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 403 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain 1A residue 34 SER Chi-restraints excluded: chain 1B residue 90 GLU Chi-restraints excluded: chain 1D residue 34 SER Chi-restraints excluded: chain 1E residue 90 GLU Chi-restraints excluded: chain 1F residue 99 THR Chi-restraints excluded: chain 1F residue 119 SER Chi-restraints excluded: chain 1H residue 129 SER Chi-restraints excluded: chain 1H residue 132 ILE Chi-restraints excluded: chain 1I residue 34 SER Chi-restraints excluded: chain 1I residue 68 LYS Chi-restraints excluded: chain 1I residue 132 ILE Chi-restraints excluded: chain 1I residue 144 VAL Chi-restraints excluded: chain 1K residue 66 LEU Chi-restraints excluded: chain 1K residue 129 SER Chi-restraints excluded: chain 1L residue 7 GLN Chi-restraints excluded: chain 1L residue 34 SER Chi-restraints excluded: chain 1L residue 75 THR Chi-restraints excluded: chain 1L residue 132 ILE Chi-restraints excluded: chain 1L residue 144 VAL Chi-restraints excluded: chain 2A residue 134 THR Chi-restraints excluded: chain 2A residue 164 TRP Chi-restraints excluded: chain 2A residue 212 LEU Chi-restraints excluded: chain 2B residue 61 GLU Chi-restraints excluded: chain 2B residue 88 GLN Chi-restraints excluded: chain 2B residue 136 GLU Chi-restraints excluded: chain 2B residue 212 LEU Chi-restraints excluded: chain 2C residue 61 GLU Chi-restraints excluded: chain 2C residue 134 THR Chi-restraints excluded: chain 2C residue 261 ARG Chi-restraints excluded: chain 2C residue 277 GLN Chi-restraints excluded: chain 2D residue 88 GLN Chi-restraints excluded: chain 2D residue 134 THR Chi-restraints excluded: chain 2D residue 164 TRP Chi-restraints excluded: chain 2D residue 196 VAL Chi-restraints excluded: chain 2D residue 212 LEU Chi-restraints excluded: chain 2D residue 277 GLN Chi-restraints excluded: chain 2E residue 136 GLU Chi-restraints excluded: chain 2E residue 199 GLN Chi-restraints excluded: chain 2F residue 134 THR Chi-restraints excluded: chain 2F residue 261 ARG Chi-restraints excluded: chain 2F residue 277 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 121 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 343 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 375 optimal weight: 5.9990 chunk 393 optimal weight: 4.9990 chunk 339 optimal weight: 0.2980 chunk 302 optimal weight: 2.9990 chunk 414 optimal weight: 0.9990 chunk 437 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS D 59 HIS 1A 31 ASN 1C 111 ASN 1D 31 ASN 1F 111 ASN 1G 7 GLN 1L 7 GLN 1L 135 GLN ** 2B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.061280 restraints weight = 77161.134| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.37 r_work: 0.2660 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44358 Z= 0.112 Angle : 0.451 5.816 60552 Z= 0.236 Chirality : 0.045 0.138 7044 Planarity : 0.003 0.041 7854 Dihedral : 3.777 54.843 5932 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.43 % Allowed : 19.29 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.11), residues: 5490 helix: 2.43 (0.14), residues: 1374 sheet: 0.96 (0.13), residues: 1476 loop : 0.13 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG1B 143 TYR 0.008 0.001 TYR1J 17 PHE 0.012 0.001 PHE1E 78 TRP 0.009 0.001 TRP D 156 HIS 0.001 0.000 HIS C 59 Details of bonding type rmsd covalent geometry : bond 0.00266 (44358) covalent geometry : angle 0.45115 (60552) hydrogen bonds : bond 0.03614 ( 1770) hydrogen bonds : angle 4.40473 ( 5031) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 399 time to evaluate : 1.263 Fit side-chains REVERT: B 201 ASP cc_start: 0.7672 (t0) cc_final: 0.7126 (t0) REVERT: B 248 SER cc_start: 0.8954 (m) cc_final: 0.8233 (p) REVERT: E 248 SER cc_start: 0.9095 (m) cc_final: 0.8302 (p) REVERT: 1B 31 ASN cc_start: 0.8796 (t0) cc_final: 0.8490 (t0) REVERT: 1B 90 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: 1B 126 ASP cc_start: 0.9109 (t0) cc_final: 0.8859 (t0) REVERT: 1C 67 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8647 (ttp-110) REVERT: 1C 105 GLU cc_start: 0.8858 (tt0) cc_final: 0.8635 (tt0) REVERT: 1C 126 ASP cc_start: 0.9050 (t0) cc_final: 0.8740 (t0) REVERT: 1E 90 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7972 (tm-30) REVERT: 1E 119 SER cc_start: 0.9504 (t) cc_final: 0.9201 (m) REVERT: 1E 126 ASP cc_start: 0.9101 (t0) cc_final: 0.8813 (t0) REVERT: 1F 67 ARG cc_start: 0.8831 (ttp80) cc_final: 0.8609 (ttp-110) REVERT: 1F 105 GLU cc_start: 0.8874 (tt0) cc_final: 0.8668 (tt0) REVERT: 1F 119 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.8855 (m) REVERT: 1F 126 ASP cc_start: 0.9051 (t0) cc_final: 0.8797 (t0) REVERT: 1H 76 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8486 (mtmm) REVERT: 1I 67 ARG cc_start: 0.8989 (mtm-85) cc_final: 0.8552 (mtp85) REVERT: 1I 105 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8571 (mt-10) REVERT: 1K 67 ARG cc_start: 0.8960 (mtm-85) cc_final: 0.8686 (mtm110) REVERT: 1K 76 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8505 (mtmm) REVERT: 1K 90 GLU cc_start: 0.9072 (tp30) cc_final: 0.8335 (tm-30) REVERT: 1L 67 ARG cc_start: 0.8909 (mtp-110) cc_final: 0.8644 (mtp85) REVERT: 1L 105 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8569 (mt-10) REVERT: 2A 326 GLN cc_start: 0.8771 (mt0) cc_final: 0.8426 (mt0) REVERT: 2B 61 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: 2C 61 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: 2C 261 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8372 (ttm110) REVERT: 2C 277 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: 2D 62 GLN cc_start: 0.8335 (mm110) cc_final: 0.7985 (pm20) REVERT: 2D 88 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6938 (mm-40) REVERT: 2D 277 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: 2D 326 GLN cc_start: 0.8743 (mt0) cc_final: 0.8403 (mt0) REVERT: 2E 88 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6771 (tp-100) REVERT: 2E 199 GLN cc_start: 0.9319 (OUTLIER) cc_final: 0.8693 (mm-40) REVERT: 2E 329 MET cc_start: 0.9512 (ttp) cc_final: 0.9181 (ttp) REVERT: 2F 62 GLN cc_start: 0.7580 (pm20) cc_final: 0.7036 (pm20) REVERT: 2F 164 TRP cc_start: 0.9137 (OUTLIER) cc_final: 0.7401 (p-90) REVERT: 2F 261 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8383 (ttm110) REVERT: 2F 277 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7822 (tm-30) outliers start: 69 outliers final: 46 residues processed: 458 average time/residue: 0.7128 time to fit residues: 389.6484 Evaluate side-chains 460 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 400 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain 1A residue 34 SER Chi-restraints excluded: chain 1B residue 90 GLU Chi-restraints excluded: chain 1C residue 99 THR Chi-restraints excluded: chain 1D residue 34 SER Chi-restraints excluded: chain 1D residue 143 ARG Chi-restraints excluded: chain 1E residue 90 GLU Chi-restraints excluded: chain 1F residue 99 THR Chi-restraints excluded: chain 1F residue 119 SER Chi-restraints excluded: chain 1H residue 129 SER Chi-restraints excluded: chain 1H residue 132 ILE Chi-restraints excluded: chain 1I residue 34 SER Chi-restraints excluded: chain 1I residue 68 LYS Chi-restraints excluded: chain 1I residue 132 ILE Chi-restraints excluded: chain 1I residue 144 VAL Chi-restraints excluded: chain 1K residue 66 LEU Chi-restraints excluded: chain 1K residue 129 SER Chi-restraints excluded: chain 1K residue 132 ILE Chi-restraints excluded: chain 1L residue 34 SER Chi-restraints excluded: chain 1L residue 75 THR Chi-restraints excluded: chain 1L residue 132 ILE Chi-restraints excluded: chain 1L residue 144 VAL Chi-restraints excluded: chain 2A residue 134 THR Chi-restraints excluded: chain 2A residue 164 TRP Chi-restraints excluded: chain 2A residue 196 VAL Chi-restraints excluded: chain 2A residue 212 LEU Chi-restraints excluded: chain 2B residue 61 GLU Chi-restraints excluded: chain 2B residue 136 GLU Chi-restraints excluded: chain 2B residue 212 LEU Chi-restraints excluded: chain 2C residue 61 GLU Chi-restraints excluded: chain 2C residue 134 THR Chi-restraints excluded: chain 2C residue 261 ARG Chi-restraints excluded: chain 2C residue 277 GLN Chi-restraints excluded: chain 2D residue 88 GLN Chi-restraints excluded: chain 2D residue 134 THR Chi-restraints excluded: chain 2D residue 164 TRP Chi-restraints excluded: chain 2D residue 196 VAL Chi-restraints excluded: chain 2D residue 212 LEU Chi-restraints excluded: chain 2D residue 277 GLN Chi-restraints excluded: chain 2E residue 88 GLN Chi-restraints excluded: chain 2E residue 136 GLU Chi-restraints excluded: chain 2E residue 199 GLN Chi-restraints excluded: chain 2E residue 212 LEU Chi-restraints excluded: chain 2F residue 134 THR Chi-restraints excluded: chain 2F residue 164 TRP Chi-restraints excluded: chain 2F residue 261 ARG Chi-restraints excluded: chain 2F residue 277 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 50 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 278 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 40 optimal weight: 0.0870 chunk 297 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 191 optimal weight: 0.2980 chunk 115 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 31 ASN 1D 31 ASN ** 1G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1L 7 GLN 1L 135 GLN 2A 88 GLN ** 2B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.082213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.061603 restraints weight = 77549.608| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.36 r_work: 0.2673 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 44358 Z= 0.094 Angle : 0.444 6.511 60552 Z= 0.232 Chirality : 0.045 0.138 7044 Planarity : 0.003 0.034 7854 Dihedral : 3.703 53.490 5932 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.51 % Allowed : 19.46 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.11), residues: 5490 helix: 2.45 (0.14), residues: 1374 sheet: 0.96 (0.13), residues: 1500 loop : 0.16 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG1H 67 TYR 0.007 0.001 TYR1J 17 PHE 0.011 0.001 PHE1E 78 TRP 0.009 0.001 TRP E 156 HIS 0.002 0.000 HIS1G 39 Details of bonding type rmsd covalent geometry : bond 0.00219 (44358) covalent geometry : angle 0.44387 (60552) hydrogen bonds : bond 0.03386 ( 1770) hydrogen bonds : angle 4.32298 ( 5031) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 409 time to evaluate : 1.332 Fit side-chains REVERT: B 201 ASP cc_start: 0.7666 (t0) cc_final: 0.7120 (t0) REVERT: B 248 SER cc_start: 0.8823 (m) cc_final: 0.8132 (p) REVERT: E 248 SER cc_start: 0.9006 (m) cc_final: 0.8251 (p) REVERT: 1B 31 ASN cc_start: 0.8776 (t0) cc_final: 0.8537 (t0) REVERT: 1B 90 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: 1B 93 ASP cc_start: 0.9055 (m-30) cc_final: 0.8844 (m-30) REVERT: 1B 126 ASP cc_start: 0.9095 (t0) cc_final: 0.8844 (t0) REVERT: 1C 67 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8654 (ttp-110) REVERT: 1C 105 GLU cc_start: 0.8859 (tt0) cc_final: 0.8639 (tt0) REVERT: 1C 126 ASP cc_start: 0.9035 (t0) cc_final: 0.8800 (t0) REVERT: 1E 90 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: 1E 119 SER cc_start: 0.9495 (t) cc_final: 0.9204 (m) REVERT: 1E 126 ASP cc_start: 0.9086 (t0) cc_final: 0.8835 (t0) REVERT: 1F 67 ARG cc_start: 0.8825 (ttp80) cc_final: 0.8513 (ttp-110) REVERT: 1F 105 GLU cc_start: 0.8874 (tt0) cc_final: 0.8669 (tt0) REVERT: 1F 119 SER cc_start: 0.9151 (OUTLIER) cc_final: 0.8913 (m) REVERT: 1F 126 ASP cc_start: 0.9042 (t0) cc_final: 0.8780 (t0) REVERT: 1G 136 GLU cc_start: 0.9053 (tt0) cc_final: 0.8824 (mt-10) REVERT: 1H 76 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8481 (mtmm) REVERT: 1I 67 ARG cc_start: 0.8981 (mtm-85) cc_final: 0.8519 (mtp85) REVERT: 1I 105 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8574 (mt-10) REVERT: 1K 67 ARG cc_start: 0.8938 (mtm-85) cc_final: 0.8714 (mtm110) REVERT: 1K 76 LYS cc_start: 0.8756 (mtpp) cc_final: 0.8478 (mtmm) REVERT: 1K 90 GLU cc_start: 0.9059 (tp30) cc_final: 0.8331 (tm-30) REVERT: 1K 136 GLU cc_start: 0.8923 (tt0) cc_final: 0.8650 (mm-30) REVERT: 1L 67 ARG cc_start: 0.8904 (mtp-110) cc_final: 0.8650 (mtp85) REVERT: 1L 105 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8565 (mt-10) REVERT: 2A 88 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6849 (mm-40) REVERT: 2A 326 GLN cc_start: 0.8753 (mt0) cc_final: 0.8415 (mt0) REVERT: 2B 61 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8268 (mt-10) REVERT: 2B 88 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6848 (tp-100) REVERT: 2C 62 GLN cc_start: 0.8448 (mm110) cc_final: 0.8233 (pm20) REVERT: 2C 261 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8367 (ttm110) REVERT: 2C 277 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: 2D 60 ASN cc_start: 0.9471 (t0) cc_final: 0.9243 (t0) REVERT: 2D 62 GLN cc_start: 0.8343 (mm110) cc_final: 0.7968 (pm20) REVERT: 2D 88 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6880 (mm-40) REVERT: 2D 277 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: 2D 322 ASP cc_start: 0.8505 (t70) cc_final: 0.8250 (t70) REVERT: 2D 326 GLN cc_start: 0.8722 (mt0) cc_final: 0.8384 (mt0) REVERT: 2E 88 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6786 (tp-100) REVERT: 2E 329 MET cc_start: 0.9521 (ttp) cc_final: 0.9177 (ttp) REVERT: 2F 61 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: 2F 62 GLN cc_start: 0.7543 (pm20) cc_final: 0.7009 (pm20) REVERT: 2F 261 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8375 (ttm110) REVERT: 2F 277 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7800 (tm-30) outliers start: 73 outliers final: 39 residues processed: 470 average time/residue: 0.7389 time to fit residues: 414.8666 Evaluate side-chains 457 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 404 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain 1A residue 34 SER Chi-restraints excluded: chain 1B residue 90 GLU Chi-restraints excluded: chain 1D residue 34 SER Chi-restraints excluded: chain 1D residue 143 ARG Chi-restraints excluded: chain 1E residue 90 GLU Chi-restraints excluded: chain 1F residue 99 THR Chi-restraints excluded: chain 1F residue 119 SER Chi-restraints excluded: chain 1H residue 129 SER Chi-restraints excluded: chain 1H residue 132 ILE Chi-restraints excluded: chain 1I residue 34 SER Chi-restraints excluded: chain 1I residue 132 ILE Chi-restraints excluded: chain 1I residue 144 VAL Chi-restraints excluded: chain 1K residue 66 LEU Chi-restraints excluded: chain 1K residue 129 SER Chi-restraints excluded: chain 1K residue 132 ILE Chi-restraints excluded: chain 1L residue 34 SER Chi-restraints excluded: chain 1L residue 75 THR Chi-restraints excluded: chain 1L residue 144 VAL Chi-restraints excluded: chain 2A residue 88 GLN Chi-restraints excluded: chain 2A residue 134 THR Chi-restraints excluded: chain 2A residue 164 TRP Chi-restraints excluded: chain 2A residue 212 LEU Chi-restraints excluded: chain 2B residue 61 GLU Chi-restraints excluded: chain 2B residue 88 GLN Chi-restraints excluded: chain 2B residue 136 GLU Chi-restraints excluded: chain 2C residue 117 SER Chi-restraints excluded: chain 2C residue 134 THR Chi-restraints excluded: chain 2C residue 261 ARG Chi-restraints excluded: chain 2C residue 277 GLN Chi-restraints excluded: chain 2D residue 88 GLN Chi-restraints excluded: chain 2D residue 134 THR Chi-restraints excluded: chain 2D residue 164 TRP Chi-restraints excluded: chain 2D residue 196 VAL Chi-restraints excluded: chain 2D residue 212 LEU Chi-restraints excluded: chain 2D residue 277 GLN Chi-restraints excluded: chain 2E residue 88 GLN Chi-restraints excluded: chain 2E residue 136 GLU Chi-restraints excluded: chain 2F residue 61 GLU Chi-restraints excluded: chain 2F residue 134 THR Chi-restraints excluded: chain 2F residue 261 ARG Chi-restraints excluded: chain 2F residue 277 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 393 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 144 optimal weight: 0.0870 chunk 463 optimal weight: 1.9990 chunk 239 optimal weight: 0.3980 chunk 263 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 31 ASN 1D 31 ASN 1G 7 GLN 1L 7 GLN 2A 88 GLN ** 2B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.082137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.061306 restraints weight = 77224.071| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.37 r_work: 0.2660 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44358 Z= 0.117 Angle : 0.463 6.708 60552 Z= 0.242 Chirality : 0.045 0.137 7044 Planarity : 0.003 0.032 7854 Dihedral : 3.746 52.831 5932 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.36 % Allowed : 19.83 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.11), residues: 5490 helix: 2.46 (0.14), residues: 1374 sheet: 0.99 (0.13), residues: 1476 loop : 0.15 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG1H 67 TYR 0.009 0.001 TYR1J 17 PHE 0.012 0.001 PHE1E 78 TRP 0.009 0.001 TRP A 156 HIS 0.001 0.000 HIS1G 39 Details of bonding type rmsd covalent geometry : bond 0.00278 (44358) covalent geometry : angle 0.46335 (60552) hydrogen bonds : bond 0.03604 ( 1770) hydrogen bonds : angle 4.36332 ( 5031) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 399 time to evaluate : 1.070 Fit side-chains REVERT: B 201 ASP cc_start: 0.7687 (t0) cc_final: 0.7136 (t0) REVERT: B 248 SER cc_start: 0.8979 (m) cc_final: 0.8255 (p) REVERT: E 248 SER cc_start: 0.9103 (m) cc_final: 0.8311 (p) REVERT: 1B 31 ASN cc_start: 0.8826 (t0) cc_final: 0.8596 (t0) REVERT: 1B 90 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: 1B 93 ASP cc_start: 0.9073 (m-30) cc_final: 0.8858 (m-30) REVERT: 1B 126 ASP cc_start: 0.9114 (t0) cc_final: 0.8866 (t0) REVERT: 1C 67 ARG cc_start: 0.8881 (ttp80) cc_final: 0.8677 (ttp-110) REVERT: 1C 105 GLU cc_start: 0.8850 (tt0) cc_final: 0.8627 (tt0) REVERT: 1C 126 ASP cc_start: 0.9051 (t0) cc_final: 0.8808 (t0) REVERT: 1E 90 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: 1E 119 SER cc_start: 0.9518 (t) cc_final: 0.9211 (m) REVERT: 1E 126 ASP cc_start: 0.9098 (t0) cc_final: 0.8839 (t0) REVERT: 1F 67 ARG cc_start: 0.8863 (ttp80) cc_final: 0.8558 (ttp-110) REVERT: 1F 105 GLU cc_start: 0.8871 (tt0) cc_final: 0.8665 (tt0) REVERT: 1F 119 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.8869 (m) REVERT: 1F 126 ASP cc_start: 0.9057 (t0) cc_final: 0.8790 (t0) REVERT: 1H 76 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8480 (mtmm) REVERT: 1I 67 ARG cc_start: 0.8952 (mtm-85) cc_final: 0.8523 (mtp85) REVERT: 1I 105 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8575 (mt-10) REVERT: 1K 67 ARG cc_start: 0.8958 (mtm-85) cc_final: 0.8468 (mtp85) REVERT: 1K 76 LYS cc_start: 0.8754 (mtpp) cc_final: 0.8488 (mtmm) REVERT: 1K 90 GLU cc_start: 0.9065 (tp30) cc_final: 0.8332 (tm-30) REVERT: 1K 136 GLU cc_start: 0.8925 (tt0) cc_final: 0.8687 (mm-30) REVERT: 1L 67 ARG cc_start: 0.8898 (mtp-110) cc_final: 0.8646 (mtp85) REVERT: 1L 105 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8589 (mt-10) REVERT: 2A 88 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7168 (mm-40) REVERT: 2A 326 GLN cc_start: 0.8769 (mt0) cc_final: 0.8426 (mt0) REVERT: 2B 61 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: 2B 88 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6862 (tp-100) REVERT: 2C 261 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8373 (ttm110) REVERT: 2C 277 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: 2D 60 ASN cc_start: 0.9467 (t0) cc_final: 0.9245 (t0) REVERT: 2D 62 GLN cc_start: 0.8356 (mm110) cc_final: 0.7972 (pm20) REVERT: 2D 88 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6979 (mm-40) REVERT: 2D 277 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8332 (tm-30) REVERT: 2D 326 GLN cc_start: 0.8728 (mt0) cc_final: 0.8375 (mt0) REVERT: 2F 62 GLN cc_start: 0.7531 (pm20) cc_final: 0.7009 (pm20) REVERT: 2F 261 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8386 (ttm110) REVERT: 2F 277 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7850 (tm-30) outliers start: 66 outliers final: 50 residues processed: 453 average time/residue: 0.5780 time to fit residues: 313.5850 Evaluate side-chains 463 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 401 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain 1A residue 34 SER Chi-restraints excluded: chain 1B residue 90 GLU Chi-restraints excluded: chain 1C residue 99 THR Chi-restraints excluded: chain 1D residue 34 SER Chi-restraints excluded: chain 1D residue 143 ARG Chi-restraints excluded: chain 1E residue 90 GLU Chi-restraints excluded: chain 1F residue 99 THR Chi-restraints excluded: chain 1F residue 119 SER Chi-restraints excluded: chain 1H residue 129 SER Chi-restraints excluded: chain 1H residue 132 ILE Chi-restraints excluded: chain 1H residue 136 GLU Chi-restraints excluded: chain 1I residue 34 SER Chi-restraints excluded: chain 1I residue 132 ILE Chi-restraints excluded: chain 1I residue 144 VAL Chi-restraints excluded: chain 1K residue 66 LEU Chi-restraints excluded: chain 1K residue 129 SER Chi-restraints excluded: chain 1K residue 132 ILE Chi-restraints excluded: chain 1L residue 7 GLN Chi-restraints excluded: chain 1L residue 34 SER Chi-restraints excluded: chain 1L residue 47 ASP Chi-restraints excluded: chain 1L residue 75 THR Chi-restraints excluded: chain 1L residue 144 VAL Chi-restraints excluded: chain 2A residue 88 GLN Chi-restraints excluded: chain 2A residue 134 THR Chi-restraints excluded: chain 2A residue 164 TRP Chi-restraints excluded: chain 2A residue 196 VAL Chi-restraints excluded: chain 2A residue 212 LEU Chi-restraints excluded: chain 2B residue 61 GLU Chi-restraints excluded: chain 2B residue 88 GLN Chi-restraints excluded: chain 2B residue 136 GLU Chi-restraints excluded: chain 2C residue 117 SER Chi-restraints excluded: chain 2C residue 134 THR Chi-restraints excluded: chain 2C residue 261 ARG Chi-restraints excluded: chain 2C residue 277 GLN Chi-restraints excluded: chain 2D residue 88 GLN Chi-restraints excluded: chain 2D residue 134 THR Chi-restraints excluded: chain 2D residue 164 TRP Chi-restraints excluded: chain 2D residue 196 VAL Chi-restraints excluded: chain 2D residue 212 LEU Chi-restraints excluded: chain 2D residue 267 MET Chi-restraints excluded: chain 2D residue 277 GLN Chi-restraints excluded: chain 2E residue 136 GLU Chi-restraints excluded: chain 2E residue 212 LEU Chi-restraints excluded: chain 2E residue 267 MET Chi-restraints excluded: chain 2F residue 117 SER Chi-restraints excluded: chain 2F residue 134 THR Chi-restraints excluded: chain 2F residue 261 ARG Chi-restraints excluded: chain 2F residue 277 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 134 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 221 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 339 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 384 optimal weight: 0.0170 chunk 323 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 533 optimal weight: 3.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 31 ASN 1D 31 ASN 1G 7 GLN 1L 7 GLN ** 2B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.081661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.060810 restraints weight = 77816.461| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.38 r_work: 0.2631 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44358 Z= 0.137 Angle : 0.475 7.123 60552 Z= 0.248 Chirality : 0.045 0.138 7044 Planarity : 0.003 0.032 7854 Dihedral : 3.796 52.696 5932 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.30 % Allowed : 19.85 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.11), residues: 5490 helix: 2.45 (0.14), residues: 1374 sheet: 0.97 (0.13), residues: 1476 loop : 0.13 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG1H 67 TYR 0.009 0.001 TYR1J 17 PHE 0.012 0.001 PHE1F 78 TRP 0.008 0.001 TRP F 156 HIS 0.001 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00331 (44358) covalent geometry : angle 0.47509 (60552) hydrogen bonds : bond 0.03757 ( 1770) hydrogen bonds : angle 4.39595 ( 5031) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 397 time to evaluate : 1.105 Fit side-chains REVERT: B 201 ASP cc_start: 0.7683 (t0) cc_final: 0.7128 (t0) REVERT: B 248 SER cc_start: 0.8989 (m) cc_final: 0.8264 (p) REVERT: E 248 SER cc_start: 0.9138 (m) cc_final: 0.8355 (p) REVERT: 1B 31 ASN cc_start: 0.8829 (t0) cc_final: 0.8592 (t0) REVERT: 1B 90 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: 1B 93 ASP cc_start: 0.9073 (m-30) cc_final: 0.8859 (m-30) REVERT: 1B 126 ASP cc_start: 0.9125 (t0) cc_final: 0.8877 (t0) REVERT: 1C 67 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8666 (ttp-110) REVERT: 1C 105 GLU cc_start: 0.8852 (tt0) cc_final: 0.8626 (tt0) REVERT: 1C 126 ASP cc_start: 0.9050 (t0) cc_final: 0.8811 (t0) REVERT: 1E 90 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: 1E 126 ASP cc_start: 0.9103 (t0) cc_final: 0.8842 (t0) REVERT: 1F 67 ARG cc_start: 0.8842 (ttp80) cc_final: 0.8633 (ttp-110) REVERT: 1F 105 GLU cc_start: 0.8870 (tt0) cc_final: 0.8662 (tt0) REVERT: 1F 119 SER cc_start: 0.9236 (OUTLIER) cc_final: 0.8843 (m) REVERT: 1F 126 ASP cc_start: 0.9056 (t0) cc_final: 0.8791 (t0) REVERT: 1H 76 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8461 (mtmm) REVERT: 1I 67 ARG cc_start: 0.8897 (mtm-85) cc_final: 0.8469 (mtp85) REVERT: 1I 105 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8584 (mt-10) REVERT: 1K 67 ARG cc_start: 0.8961 (mtm-85) cc_final: 0.8460 (mtp85) REVERT: 1K 76 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8476 (mtmm) REVERT: 1K 90 GLU cc_start: 0.9072 (tp30) cc_final: 0.8326 (tm-30) REVERT: 1L 67 ARG cc_start: 0.8887 (mtp-110) cc_final: 0.8635 (mtp85) REVERT: 1L 105 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8581 (mt-10) REVERT: 2A 326 GLN cc_start: 0.8760 (mt0) cc_final: 0.8412 (mt0) REVERT: 2B 61 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: 2C 230 LYS cc_start: 0.4934 (ptpt) cc_final: 0.4379 (ptpt) REVERT: 2C 261 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8352 (ttm110) REVERT: 2C 277 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: 2D 60 ASN cc_start: 0.9465 (t0) cc_final: 0.9255 (t0) REVERT: 2D 62 GLN cc_start: 0.8353 (mm110) cc_final: 0.7964 (pm20) REVERT: 2D 88 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6951 (mm-40) REVERT: 2D 326 GLN cc_start: 0.8739 (mt0) cc_final: 0.8389 (mt0) REVERT: 2F 62 GLN cc_start: 0.7517 (pm20) cc_final: 0.6992 (pm20) REVERT: 2F 230 LYS cc_start: 0.4958 (ptpt) cc_final: 0.4350 (ptpt) REVERT: 2F 261 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8361 (ttm110) REVERT: 2F 277 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7855 (tm-30) outliers start: 63 outliers final: 48 residues processed: 450 average time/residue: 0.5804 time to fit residues: 312.8342 Evaluate side-chains 453 residues out of total 4836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 396 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain 1A residue 34 SER Chi-restraints excluded: chain 1B residue 90 GLU Chi-restraints excluded: chain 1C residue 99 THR Chi-restraints excluded: chain 1D residue 34 SER Chi-restraints excluded: chain 1D residue 143 ARG Chi-restraints excluded: chain 1E residue 90 GLU Chi-restraints excluded: chain 1F residue 99 THR Chi-restraints excluded: chain 1F residue 119 SER Chi-restraints excluded: chain 1H residue 129 SER Chi-restraints excluded: chain 1H residue 132 ILE Chi-restraints excluded: chain 1H residue 136 GLU Chi-restraints excluded: chain 1I residue 34 SER Chi-restraints excluded: chain 1I residue 75 THR Chi-restraints excluded: chain 1I residue 132 ILE Chi-restraints excluded: chain 1I residue 144 VAL Chi-restraints excluded: chain 1K residue 66 LEU Chi-restraints excluded: chain 1K residue 129 SER Chi-restraints excluded: chain 1K residue 132 ILE Chi-restraints excluded: chain 1L residue 34 SER Chi-restraints excluded: chain 1L residue 75 THR Chi-restraints excluded: chain 1L residue 144 VAL Chi-restraints excluded: chain 2A residue 134 THR Chi-restraints excluded: chain 2A residue 164 TRP Chi-restraints excluded: chain 2A residue 196 VAL Chi-restraints excluded: chain 2A residue 212 LEU Chi-restraints excluded: chain 2B residue 61 GLU Chi-restraints excluded: chain 2B residue 136 GLU Chi-restraints excluded: chain 2B residue 212 LEU Chi-restraints excluded: chain 2C residue 117 SER Chi-restraints excluded: chain 2C residue 134 THR Chi-restraints excluded: chain 2C residue 261 ARG Chi-restraints excluded: chain 2C residue 277 GLN Chi-restraints excluded: chain 2D residue 88 GLN Chi-restraints excluded: chain 2D residue 134 THR Chi-restraints excluded: chain 2D residue 164 TRP Chi-restraints excluded: chain 2D residue 196 VAL Chi-restraints excluded: chain 2D residue 212 LEU Chi-restraints excluded: chain 2D residue 267 MET Chi-restraints excluded: chain 2E residue 136 GLU Chi-restraints excluded: chain 2E residue 212 LEU Chi-restraints excluded: chain 2E residue 267 MET Chi-restraints excluded: chain 2F residue 117 SER Chi-restraints excluded: chain 2F residue 134 THR Chi-restraints excluded: chain 2F residue 261 ARG Chi-restraints excluded: chain 2F residue 277 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 534 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 489 optimal weight: 5.9990 chunk 344 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 269 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 290 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 31 ASN 1D 31 ASN 1L 7 GLN ** 2B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.081646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.060801 restraints weight = 77888.638| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.38 r_work: 0.2646 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 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 0.046 44358 Z= 0.123 Angle : 0.470 7.110 60552 Z= 0.246 Chirality : 0.045 0.138 7044 Planarity : 0.003 0.032 7854 Dihedral : 3.812 52.285 5932 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.32 % Allowed : 19.83 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.11), residues: 5490 helix: 2.44 (0.14), residues: 1374 sheet: 0.96 (0.13), residues: 1476 loop : 0.13 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG1H 67 TYR 0.009 0.001 TYR1J 17 PHE 0.012 0.001 PHE1E 78 TRP 0.008 0.001 TRP E 156 HIS 0.001 0.000 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00296 (44358) covalent geometry : angle 0.46958 (60552) hydrogen bonds : bond 0.03711 ( 1770) hydrogen bonds : angle 4.39845 ( 5031) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15438.59 seconds wall clock time: 262 minutes 38.69 seconds (15758.69 seconds total)