Starting phenix.real_space_refine on Fri Jan 16 23:45:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ecy_28025/01_2026/8ecy_28025.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ecy_28025/01_2026/8ecy_28025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ecy_28025/01_2026/8ecy_28025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ecy_28025/01_2026/8ecy_28025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ecy_28025/01_2026/8ecy_28025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ecy_28025/01_2026/8ecy_28025.map" } resolution = 2.0 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= 0.002 sd= 0.057 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 Mn 20 7.51 5 S 315 5.16 5 Cl 11 4.86 5 C 28360 2.51 5 N 7675 2.21 5 O 10099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46485 Number of models: 1 Model: "" Number of chains: 45 Chain: "E" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "C" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "G" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "K" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "N" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "A" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2937 Classifications: {'peptide': 371} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 347} Chain: "J" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2937 Classifications: {'peptide': 371} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 347} Chain: "L" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2937 Classifications: {'peptide': 371} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 347} Chain: "Q" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2937 Classifications: {'peptide': 371} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 347} Chain: "H" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2937 Classifications: {'peptide': 371} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 347} Chain: "D" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2937 Classifications: {'peptide': 371} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 347} Chain: "B" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2937 Classifications: {'peptide': 371} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 347} Chain: "F" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2937 Classifications: {'peptide': 371} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 347} Chain: "I" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2937 Classifications: {'peptide': 371} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 347} Chain: "M" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2937 Classifications: {'peptide': 371} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 347} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "G" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "N" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 179 Classifications: {'water': 179} Link IDs: {None: 178} Chain: "J" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 171 Classifications: {'water': 171} Link IDs: {None: 170} Chain: "Q" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 170 Classifications: {'water': 170} Link IDs: {None: 169} Chain: "H" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 168 Classifications: {'water': 168} Link IDs: {None: 167} Chain: "D" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Chain: "B" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 184 Classifications: {'water': 184} Link IDs: {None: 183} Chain: "F" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 186 Classifications: {'water': 186} Link IDs: {None: 185} Chain: "I" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Chain: "M" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Time building chain proxies: 10.55, per 1000 atoms: 0.23 Number of scatterers: 46485 At special positions: 0 Unit cell: (133.63, 131.14, 200.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 20 24.99 Ca 5 19.99 Cl 11 17.00 S 315 16.00 O 10099 8.00 N 7675 7.00 C 28360 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: 3.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10170 Finding SS restraints... Secondary structure from input PDB file: 223 helices and 20 sheets defined 47.8% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.849A pdb=" N LEU E 20 " --> pdb=" O GLY E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 27 through 52 removed outlier: 3.570A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 removed outlier: 3.641A pdb=" N ARG E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 99 removed outlier: 3.787A pdb=" N SER E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE E 80 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.530A pdb=" N ALA E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 removed outlier: 3.635A pdb=" N LEU E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.555A pdb=" N PHE E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.621A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.849A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 348 through 353 removed outlier: 4.636A pdb=" N PHE E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 52 removed outlier: 3.570A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 removed outlier: 3.642A pdb=" N ARG C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 99 removed outlier: 3.787A pdb=" N SER C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.529A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 removed outlier: 3.634A pdb=" N LEU C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.556A pdb=" N PHE C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.622A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.849A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 348 through 353 removed outlier: 4.636A pdb=" N PHE C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 20 removed outlier: 3.848A pdb=" N LEU G 20 " --> pdb=" O GLY G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 23 No H-bonds generated for 'chain 'G' and resid 21 through 23' Processing helix chain 'G' and resid 27 through 52 removed outlier: 3.570A pdb=" N LEU G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 72 removed outlier: 3.641A pdb=" N ARG G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR G 72 " --> pdb=" O TYR G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 99 removed outlier: 3.786A pdb=" N SER G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE G 80 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL G 81 " --> pdb=" O PRO G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 114 Processing helix chain 'G' and resid 118 through 144 removed outlier: 3.530A pdb=" N ALA G 132 " --> pdb=" O LEU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 153 through 160 Processing helix chain 'G' and resid 164 through 174 removed outlier: 3.636A pdb=" N LEU G 174 " --> pdb=" O LYS G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 198 Processing helix chain 'G' and resid 203 through 230 removed outlier: 3.556A pdb=" N PHE G 207 " --> pdb=" O ASP G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 255 removed outlier: 3.622A pdb=" N ILE G 253 " --> pdb=" O LEU G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 263 Processing helix chain 'G' and resid 274 through 295 removed outlier: 3.849A pdb=" N ALA G 291 " --> pdb=" O TRP G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 324 Processing helix chain 'G' and resid 348 through 353 removed outlier: 4.636A pdb=" N PHE G 353 " --> pdb=" O ALA G 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 23 Processing helix chain 'K' and resid 27 through 52 removed outlier: 3.570A pdb=" N LEU K 31 " --> pdb=" O SER K 27 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG K 34 " --> pdb=" O LYS K 30 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 72 removed outlier: 3.642A pdb=" N ARG K 60 " --> pdb=" O GLU K 56 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR K 61 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR K 72 " --> pdb=" O TYR K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 99 removed outlier: 3.787A pdb=" N SER K 79 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE K 80 " --> pdb=" O ILE K 76 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL K 81 " --> pdb=" O PRO K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 114 Processing helix chain 'K' and resid 118 through 144 removed outlier: 3.530A pdb=" N ALA K 132 " --> pdb=" O LEU K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 151 Processing helix chain 'K' and resid 153 through 160 Processing helix chain 'K' and resid 164 through 174 removed outlier: 3.635A pdb=" N LEU K 174 " --> pdb=" O LYS K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 198 Processing helix chain 'K' and resid 203 through 230 removed outlier: 3.555A pdb=" N PHE K 207 " --> pdb=" O ASP K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 255 removed outlier: 3.621A pdb=" N ILE K 253 " --> pdb=" O LEU K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 263 Processing helix chain 'K' and resid 274 through 295 removed outlier: 3.849A pdb=" N ALA K 291 " --> pdb=" O TRP K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 324 Processing helix chain 'K' and resid 348 through 353 removed outlier: 4.636A pdb=" N PHE K 353 " --> pdb=" O ALA K 349 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 20 removed outlier: 3.848A pdb=" N LEU N 20 " --> pdb=" O GLY N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 23 No H-bonds generated for 'chain 'N' and resid 21 through 23' Processing helix chain 'N' and resid 27 through 52 removed outlier: 3.570A pdb=" N LEU N 31 " --> pdb=" O SER N 27 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG N 34 " --> pdb=" O LYS N 30 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU N 35 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 72 removed outlier: 3.641A pdb=" N ARG N 60 " --> pdb=" O GLU N 56 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR N 61 " --> pdb=" O GLU N 57 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR N 72 " --> pdb=" O TYR N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 99 removed outlier: 3.786A pdb=" N SER N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE N 80 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL N 81 " --> pdb=" O PRO N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 114 Processing helix chain 'N' and resid 118 through 144 removed outlier: 3.530A pdb=" N ALA N 132 " --> pdb=" O LEU N 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 151 Processing helix chain 'N' and resid 153 through 160 Processing helix chain 'N' and resid 164 through 174 removed outlier: 3.635A pdb=" N LEU N 174 " --> pdb=" O LYS N 170 " (cutoff:3.500A) Processing helix chain 'N' and resid 182 through 198 Processing helix chain 'N' and resid 203 through 230 removed outlier: 3.555A pdb=" N PHE N 207 " --> pdb=" O ASP N 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 255 removed outlier: 3.621A pdb=" N ILE N 253 " --> pdb=" O LEU N 249 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 263 Processing helix chain 'N' and resid 274 through 295 removed outlier: 3.849A pdb=" N ALA N 291 " --> pdb=" O TRP N 287 " (cutoff:3.500A) Processing helix chain 'N' and resid 306 through 324 Processing helix chain 'N' and resid 348 through 353 removed outlier: 4.636A pdb=" N PHE N 353 " --> pdb=" O ALA N 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.680A pdb=" N LYS A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.601A pdb=" N ARG A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 128 Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.644A pdb=" N VAL A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.527A pdb=" N ASP A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.646A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'J' and resid 5 through 9 Processing helix chain 'J' and resid 10 through 19 removed outlier: 3.681A pdb=" N LYS J 14 " --> pdb=" O ASN J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 57 Processing helix chain 'J' and resid 65 through 67 No H-bonds generated for 'chain 'J' and resid 65 through 67' Processing helix chain 'J' and resid 113 through 124 removed outlier: 3.602A pdb=" N ARG J 119 " --> pdb=" O HIS J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 128 Processing helix chain 'J' and resid 172 through 187 removed outlier: 3.644A pdb=" N VAL J 176 " --> pdb=" O GLY J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 233 removed outlier: 3.526A pdb=" N ASP J 216 " --> pdb=" O ILE J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 263 Processing helix chain 'J' and resid 266 through 279 removed outlier: 3.646A pdb=" N LYS J 279 " --> pdb=" O GLU J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 288 Processing helix chain 'J' and resid 294 through 298 Processing helix chain 'J' and resid 326 through 333 Processing helix chain 'J' and resid 347 through 360 Processing helix chain 'L' and resid 5 through 9 Processing helix chain 'L' and resid 10 through 19 removed outlier: 3.681A pdb=" N LYS L 14 " --> pdb=" O ASN L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 57 Processing helix chain 'L' and resid 65 through 67 No H-bonds generated for 'chain 'L' and resid 65 through 67' Processing helix chain 'L' and resid 113 through 124 removed outlier: 3.602A pdb=" N ARG L 119 " --> pdb=" O HIS L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 128 Processing helix chain 'L' and resid 172 through 187 removed outlier: 3.645A pdb=" N VAL L 176 " --> pdb=" O GLY L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 233 removed outlier: 3.526A pdb=" N ASP L 216 " --> pdb=" O ILE L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 263 Processing helix chain 'L' and resid 266 through 279 removed outlier: 3.646A pdb=" N LYS L 279 " --> pdb=" O GLU L 275 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 288 Processing helix chain 'L' and resid 294 through 298 Processing helix chain 'L' and resid 326 through 333 Processing helix chain 'L' and resid 347 through 360 Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 10 through 19 removed outlier: 3.681A pdb=" N LYS Q 14 " --> pdb=" O ASN Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 57 Processing helix chain 'Q' and resid 65 through 67 No H-bonds generated for 'chain 'Q' and resid 65 through 67' Processing helix chain 'Q' and resid 113 through 124 removed outlier: 3.602A pdb=" N ARG Q 119 " --> pdb=" O HIS Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 128 Processing helix chain 'Q' and resid 172 through 187 removed outlier: 3.645A pdb=" N VAL Q 176 " --> pdb=" O GLY Q 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 212 through 233 removed outlier: 3.526A pdb=" N ASP Q 216 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) Processing helix chain 'Q' and resid 258 through 263 Processing helix chain 'Q' and resid 266 through 279 removed outlier: 3.647A pdb=" N LYS Q 279 " --> pdb=" O GLU Q 275 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 288 Processing helix chain 'Q' and resid 294 through 298 Processing helix chain 'Q' and resid 326 through 333 Processing helix chain 'Q' and resid 347 through 360 Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 10 through 19 removed outlier: 3.680A pdb=" N LYS H 14 " --> pdb=" O ASN H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 113 through 124 removed outlier: 3.601A pdb=" N ARG H 119 " --> pdb=" O HIS H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 128 Processing helix chain 'H' and resid 172 through 187 removed outlier: 3.645A pdb=" N VAL H 176 " --> pdb=" O GLY H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 233 removed outlier: 3.527A pdb=" N ASP H 216 " --> pdb=" O ILE H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 266 through 279 removed outlier: 3.646A pdb=" N LYS H 279 " --> pdb=" O GLU H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 288 Processing helix chain 'H' and resid 294 through 298 Processing helix chain 'H' and resid 326 through 333 Processing helix chain 'H' and resid 347 through 360 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 10 through 19 removed outlier: 3.680A pdb=" N LYS D 14 " --> pdb=" O ASN D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.602A pdb=" N ARG D 119 " --> pdb=" O HIS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 128 Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.645A pdb=" N VAL D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 233 removed outlier: 3.526A pdb=" N ASP D 216 " --> pdb=" O ILE D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 266 through 279 removed outlier: 3.646A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 288 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 347 through 360 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 10 through 19 removed outlier: 3.680A pdb=" N LYS B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 113 through 124 removed outlier: 3.602A pdb=" N ARG B 119 " --> pdb=" O HIS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 128 Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.644A pdb=" N VAL B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 233 removed outlier: 3.526A pdb=" N ASP B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.646A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 288 Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 10 through 19 removed outlier: 3.681A pdb=" N LYS F 14 " --> pdb=" O ASN F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing helix chain 'F' and resid 113 through 124 removed outlier: 3.602A pdb=" N ARG F 119 " --> pdb=" O HIS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 128 Processing helix chain 'F' and resid 172 through 187 removed outlier: 3.644A pdb=" N VAL F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 233 removed outlier: 3.527A pdb=" N ASP F 216 " --> pdb=" O ILE F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 266 through 279 removed outlier: 3.646A pdb=" N LYS F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 288 Processing helix chain 'F' and resid 294 through 298 Processing helix chain 'F' and resid 326 through 333 Processing helix chain 'F' and resid 347 through 360 Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 10 through 19 removed outlier: 3.681A pdb=" N LYS I 14 " --> pdb=" O ASN I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 113 through 124 removed outlier: 3.603A pdb=" N ARG I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 128 Processing helix chain 'I' and resid 172 through 187 removed outlier: 3.644A pdb=" N VAL I 176 " --> pdb=" O GLY I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 233 removed outlier: 3.526A pdb=" N ASP I 216 " --> pdb=" O ILE I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 263 Processing helix chain 'I' and resid 266 through 279 removed outlier: 3.646A pdb=" N LYS I 279 " --> pdb=" O GLU I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 288 Processing helix chain 'I' and resid 294 through 298 Processing helix chain 'I' and resid 326 through 333 Processing helix chain 'I' and resid 347 through 360 Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 10 through 19 removed outlier: 3.680A pdb=" N LYS M 14 " --> pdb=" O ASN M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 57 Processing helix chain 'M' and resid 65 through 67 No H-bonds generated for 'chain 'M' and resid 65 through 67' Processing helix chain 'M' and resid 113 through 124 removed outlier: 3.601A pdb=" N ARG M 119 " --> pdb=" O HIS M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 128 Processing helix chain 'M' and resid 172 through 187 removed outlier: 3.645A pdb=" N VAL M 176 " --> pdb=" O GLY M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 233 removed outlier: 3.527A pdb=" N ASP M 216 " --> pdb=" O ILE M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 263 Processing helix chain 'M' and resid 266 through 279 removed outlier: 3.647A pdb=" N LYS M 279 " --> pdb=" O GLU M 275 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 288 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 326 through 333 Processing helix chain 'M' and resid 347 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 5.507A pdb=" N LEU A 79 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE A 102 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU A 100 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN A 27 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL A 97 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET A 29 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS A 99 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 31 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL A 101 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE A 33 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS A 42 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA J 195 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLY J 191 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN J 205 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR J 193 " --> pdb=" O GLU J 203 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU J 203 " --> pdb=" O THR J 193 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA J 195 " --> pdb=" O GLN J 201 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLN J 201 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE J 131 " --> pdb=" O PRO J 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 5.507A pdb=" N LEU A 79 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE A 102 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU A 100 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN A 27 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL A 97 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET A 29 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS A 99 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 31 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL A 101 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE A 33 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS A 42 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA J 195 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLY J 191 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN J 205 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR J 193 " --> pdb=" O GLU J 203 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU J 203 " --> pdb=" O THR J 193 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA J 195 " --> pdb=" O GLN J 201 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLN J 201 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE J 131 " --> pdb=" O PRO J 208 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY J 315 " --> pdb=" O ILE J 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.598A pdb=" N GLY A 315 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.088A pdb=" N PHE A 131 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLN A 201 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA A 195 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU A 203 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR A 193 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN A 205 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY A 191 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA A 195 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N CYS D 42 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN D 27 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL D 97 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N MET D 29 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N CYS D 99 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE D 31 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL D 101 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE D 33 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU D 100 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE D 102 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU D 79 " --> pdb=" O PHE D 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 60 through 63 removed outlier: 5.507A pdb=" N LEU J 79 " --> pdb=" O PHE J 102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE J 102 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU J 100 " --> pdb=" O PRO J 81 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN J 27 " --> pdb=" O LYS J 95 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL J 97 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET J 29 " --> pdb=" O VAL J 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS J 99 " --> pdb=" O MET J 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE J 31 " --> pdb=" O CYS J 99 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL J 101 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE J 33 " --> pdb=" O VAL J 101 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N CYS J 42 " --> pdb=" O ALA L 195 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA L 195 " --> pdb=" O CYS J 42 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY L 191 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN L 205 " --> pdb=" O GLY L 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR L 193 " --> pdb=" O GLU L 203 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU L 203 " --> pdb=" O THR L 193 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA L 195 " --> pdb=" O GLN L 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN L 201 " --> pdb=" O ALA L 195 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE L 131 " --> pdb=" O PRO L 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 60 through 63 removed outlier: 5.507A pdb=" N LEU J 79 " --> pdb=" O PHE J 102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE J 102 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU J 100 " --> pdb=" O PRO J 81 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN J 27 " --> pdb=" O LYS J 95 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL J 97 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET J 29 " --> pdb=" O VAL J 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS J 99 " --> pdb=" O MET J 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE J 31 " --> pdb=" O CYS J 99 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL J 101 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE J 33 " --> pdb=" O VAL J 101 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N CYS J 42 " --> pdb=" O ALA L 195 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA L 195 " --> pdb=" O CYS J 42 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY L 191 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN L 205 " --> pdb=" O GLY L 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR L 193 " --> pdb=" O GLU L 203 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU L 203 " --> pdb=" O THR L 193 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA L 195 " --> pdb=" O GLN L 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN L 201 " --> pdb=" O ALA L 195 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE L 131 " --> pdb=" O PRO L 208 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY L 315 " --> pdb=" O ILE L 325 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 60 through 63 removed outlier: 5.506A pdb=" N LEU L 79 " --> pdb=" O PHE L 102 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE L 102 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU L 100 " --> pdb=" O PRO L 81 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN L 27 " --> pdb=" O LYS L 95 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL L 97 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET L 29 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS L 99 " --> pdb=" O MET L 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE L 31 " --> pdb=" O CYS L 99 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL L 101 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE L 33 " --> pdb=" O VAL L 101 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS L 42 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA H 195 " --> pdb=" O CYS L 42 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY H 191 " --> pdb=" O THR L 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN H 205 " --> pdb=" O GLY H 191 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR H 193 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU H 203 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA H 195 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLN H 201 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE H 131 " --> pdb=" O PRO H 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 60 through 63 removed outlier: 5.506A pdb=" N LEU L 79 " --> pdb=" O PHE L 102 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE L 102 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU L 100 " --> pdb=" O PRO L 81 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN L 27 " --> pdb=" O LYS L 95 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL L 97 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET L 29 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS L 99 " --> pdb=" O MET L 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE L 31 " --> pdb=" O CYS L 99 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL L 101 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE L 33 " --> pdb=" O VAL L 101 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS L 42 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA H 195 " --> pdb=" O CYS L 42 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY H 191 " --> pdb=" O THR L 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN H 205 " --> pdb=" O GLY H 191 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR H 193 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU H 203 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA H 195 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLN H 201 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE H 131 " --> pdb=" O PRO H 208 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY H 315 " --> pdb=" O ILE H 325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 60 through 63 removed outlier: 5.507A pdb=" N LEU Q 79 " --> pdb=" O PHE Q 102 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE Q 102 " --> pdb=" O LEU Q 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU Q 100 " --> pdb=" O PRO Q 81 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN Q 27 " --> pdb=" O LYS Q 95 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL Q 97 " --> pdb=" O GLN Q 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET Q 29 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS Q 99 " --> pdb=" O MET Q 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE Q 31 " --> pdb=" O CYS Q 99 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 31 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE Q 33 " --> pdb=" O VAL Q 101 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N CYS Q 42 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ALA B 195 " --> pdb=" O CYS Q 42 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY B 191 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN B 205 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 193 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU B 203 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA B 195 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN B 201 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE B 131 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 60 through 63 removed outlier: 5.507A pdb=" N LEU Q 79 " --> pdb=" O PHE Q 102 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE Q 102 " --> pdb=" O LEU Q 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU Q 100 " --> pdb=" O PRO Q 81 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN Q 27 " --> pdb=" O LYS Q 95 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL Q 97 " --> pdb=" O GLN Q 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET Q 29 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS Q 99 " --> pdb=" O MET Q 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE Q 31 " --> pdb=" O CYS Q 99 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 31 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE Q 33 " --> pdb=" O VAL Q 101 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N CYS Q 42 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ALA B 195 " --> pdb=" O CYS Q 42 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY B 191 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN B 205 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 193 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU B 203 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA B 195 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN B 201 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE B 131 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY B 315 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 235 through 237 removed outlier: 6.598A pdb=" N GLY Q 315 " --> pdb=" O ILE Q 325 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 235 through 237 removed outlier: 6.088A pdb=" N PHE Q 131 " --> pdb=" O PRO Q 208 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN Q 201 " --> pdb=" O ALA Q 195 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA Q 195 " --> pdb=" O GLN Q 201 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU Q 203 " --> pdb=" O THR Q 193 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR Q 193 " --> pdb=" O GLU Q 203 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN Q 205 " --> pdb=" O GLY Q 191 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY Q 191 " --> pdb=" O THR M 46 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ALA Q 195 " --> pdb=" O CYS M 42 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS M 42 " --> pdb=" O ALA Q 195 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN M 27 " --> pdb=" O LYS M 95 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL M 97 " --> pdb=" O GLN M 27 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N MET M 29 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS M 99 " --> pdb=" O MET M 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE M 31 " --> pdb=" O CYS M 99 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL M 101 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE M 33 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU M 100 " --> pdb=" O PRO M 81 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE M 102 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU M 79 " --> pdb=" O PHE M 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 63 removed outlier: 5.506A pdb=" N LEU H 79 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE H 102 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU H 100 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN H 27 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL H 97 " --> pdb=" O GLN H 27 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N MET H 29 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS H 99 " --> pdb=" O MET H 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE H 31 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL H 101 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE H 33 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N CYS H 42 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA D 195 " --> pdb=" O CYS H 42 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY D 191 " --> pdb=" O THR H 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN D 205 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR D 193 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU D 203 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA D 195 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN D 201 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE D 131 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 60 through 63 removed outlier: 5.506A pdb=" N LEU H 79 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE H 102 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU H 100 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN H 27 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL H 97 " --> pdb=" O GLN H 27 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N MET H 29 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS H 99 " --> pdb=" O MET H 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE H 31 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL H 101 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE H 33 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N CYS H 42 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA D 195 " --> pdb=" O CYS H 42 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY D 191 " --> pdb=" O THR H 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN D 205 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR D 193 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU D 203 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA D 195 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN D 201 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE D 131 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY D 315 " --> pdb=" O ILE D 325 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 60 through 63 removed outlier: 5.506A pdb=" N LEU B 79 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE B 102 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU B 100 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN B 27 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL B 97 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET B 29 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS B 99 " --> pdb=" O MET B 29 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE B 31 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL B 101 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE B 33 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N CYS B 42 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ALA F 195 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY F 191 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN F 205 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR F 193 " --> pdb=" O GLU F 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU F 203 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA F 195 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN F 201 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE F 131 " --> pdb=" O PRO F 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 60 through 63 removed outlier: 5.506A pdb=" N LEU B 79 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE B 102 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU B 100 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN B 27 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL B 97 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET B 29 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS B 99 " --> pdb=" O MET B 29 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE B 31 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL B 101 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE B 33 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N CYS B 42 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ALA F 195 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY F 191 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN F 205 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR F 193 " --> pdb=" O GLU F 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU F 203 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA F 195 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN F 201 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE F 131 " --> pdb=" O PRO F 208 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY F 315 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 60 through 63 removed outlier: 5.507A pdb=" N LEU F 79 " --> pdb=" O PHE F 102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE F 102 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU F 100 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN F 27 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL F 97 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N MET F 29 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS F 99 " --> pdb=" O MET F 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE F 31 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL F 101 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE F 33 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS F 42 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA I 195 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY I 191 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN I 205 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR I 193 " --> pdb=" O GLU I 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU I 203 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA I 195 " --> pdb=" O GLN I 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN I 201 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE I 131 " --> pdb=" O PRO I 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 60 through 63 removed outlier: 5.507A pdb=" N LEU F 79 " --> pdb=" O PHE F 102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE F 102 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU F 100 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN F 27 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL F 97 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N MET F 29 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS F 99 " --> pdb=" O MET F 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE F 31 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL F 101 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE F 33 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS F 42 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA I 195 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY I 191 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN I 205 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR I 193 " --> pdb=" O GLU I 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU I 203 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA I 195 " --> pdb=" O GLN I 201 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN I 201 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE I 131 " --> pdb=" O PRO I 208 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY I 315 " --> pdb=" O ILE I 325 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 60 through 63 removed outlier: 5.506A pdb=" N LEU I 79 " --> pdb=" O PHE I 102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE I 102 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU I 100 " --> pdb=" O PRO I 81 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN I 27 " --> pdb=" O LYS I 95 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL I 97 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET I 29 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS I 99 " --> pdb=" O MET I 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE I 31 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL I 101 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE I 33 " --> pdb=" O VAL I 101 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS I 42 " --> pdb=" O ALA M 195 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA M 195 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY M 191 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN M 205 " --> pdb=" O GLY M 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR M 193 " --> pdb=" O GLU M 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU M 203 " --> pdb=" O THR M 193 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA M 195 " --> pdb=" O GLN M 201 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLN M 201 " --> pdb=" O ALA M 195 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE M 131 " --> pdb=" O PRO M 208 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 60 through 63 removed outlier: 5.506A pdb=" N LEU I 79 " --> pdb=" O PHE I 102 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE I 102 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU I 100 " --> pdb=" O PRO I 81 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN I 27 " --> pdb=" O LYS I 95 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL I 97 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET I 29 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS I 99 " --> pdb=" O MET I 29 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE I 31 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL I 101 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE I 33 " --> pdb=" O VAL I 101 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS I 42 " --> pdb=" O ALA M 195 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA M 195 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY M 191 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN M 205 " --> pdb=" O GLY M 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR M 193 " --> pdb=" O GLU M 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU M 203 " --> pdb=" O THR M 193 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA M 195 " --> pdb=" O GLN M 201 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLN M 201 " --> pdb=" O ALA M 195 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE M 131 " --> pdb=" O PRO M 208 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY M 315 " --> pdb=" O ILE M 325 " (cutoff:3.500A) 2322 hydrogen bonds defined for protein. 6498 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: 11.40 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 7285 1.29 - 1.43: 12931 1.43 - 1.56: 24949 1.56 - 1.70: 0 1.70 - 1.83: 475 Bond restraints: 45640 Sorted by residual: bond pdb=" C ILE H 13 " pdb=" O ILE H 13 " ideal model delta sigma weight residual 1.236 1.161 0.076 1.11e-02 8.12e+03 4.68e+01 bond pdb=" C ILE A 13 " pdb=" O ILE A 13 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.11e-02 8.12e+03 4.61e+01 bond pdb=" C ILE J 13 " pdb=" O ILE J 13 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.11e-02 8.12e+03 4.59e+01 bond pdb=" C ILE F 13 " pdb=" O ILE F 13 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.11e-02 8.12e+03 4.57e+01 bond pdb=" C ILE I 13 " pdb=" O ILE I 13 " ideal model delta sigma weight residual 1.236 1.162 0.075 1.11e-02 8.12e+03 4.56e+01 ... (remaining 45635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 43969 1.29 - 2.58: 15782 2.58 - 3.87: 1755 3.87 - 5.16: 224 5.16 - 6.44: 40 Bond angle restraints: 61770 Sorted by residual: angle pdb=" CA GLY J 12 " pdb=" C GLY J 12 " pdb=" O GLY J 12 " ideal model delta sigma weight residual 121.05 115.74 5.31 1.03e+00 9.43e-01 2.66e+01 angle pdb=" CA GLY M 12 " pdb=" C GLY M 12 " pdb=" O GLY M 12 " ideal model delta sigma weight residual 121.05 115.76 5.29 1.03e+00 9.43e-01 2.64e+01 angle pdb=" CA GLY H 12 " pdb=" C GLY H 12 " pdb=" O GLY H 12 " ideal model delta sigma weight residual 121.05 115.76 5.29 1.03e+00 9.43e-01 2.63e+01 angle pdb=" CA GLY L 12 " pdb=" C GLY L 12 " pdb=" O GLY L 12 " ideal model delta sigma weight residual 121.05 115.79 5.26 1.03e+00 9.43e-01 2.61e+01 angle pdb=" CA GLY I 12 " pdb=" C GLY I 12 " pdb=" O GLY I 12 " ideal model delta sigma weight residual 121.05 115.80 5.25 1.03e+00 9.43e-01 2.60e+01 ... (remaining 61765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 24404 17.24 - 34.47: 1982 34.47 - 51.71: 329 51.71 - 68.95: 105 68.95 - 86.18: 75 Dihedral angle restraints: 26895 sinusoidal: 10945 harmonic: 15950 Sorted by residual: dihedral pdb=" CA VAL C 114 " pdb=" C VAL C 114 " pdb=" N HIS C 115 " pdb=" CA HIS C 115 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA VAL E 114 " pdb=" C VAL E 114 " pdb=" N HIS E 115 " pdb=" CA HIS E 115 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA VAL G 114 " pdb=" C VAL G 114 " pdb=" N HIS G 115 " pdb=" CA HIS G 115 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 26892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2648 0.039 - 0.078: 1896 0.078 - 0.117: 1237 0.117 - 0.156: 443 0.156 - 0.195: 131 Chirality restraints: 6355 Sorted by residual: chirality pdb=" CA VAL C 232 " pdb=" N VAL C 232 " pdb=" C VAL C 232 " pdb=" CB VAL C 232 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CA ARG I 181 " pdb=" N ARG I 181 " pdb=" C ARG I 181 " pdb=" CB ARG I 181 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA VAL K 232 " pdb=" N VAL K 232 " pdb=" C VAL K 232 " pdb=" CB VAL K 232 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 6352 not shown) Planarity restraints: 8075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 32 " 0.029 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP F 32 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP F 32 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP F 32 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP F 32 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP F 32 " 0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP F 32 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 32 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 32 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP F 32 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 32 " -0.029 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP M 32 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP M 32 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP M 32 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP M 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP M 32 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP M 32 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 32 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 32 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP M 32 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 32 " -0.029 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP B 32 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 32 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 32 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP B 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 32 " -0.020 2.00e-02 2.50e+03 pdb=" CE3 TRP B 32 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 32 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 32 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP B 32 " -0.016 2.00e-02 2.50e+03 ... (remaining 8072 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 853 2.59 - 3.17: 40757 3.17 - 3.75: 83761 3.75 - 4.32: 122175 4.32 - 4.90: 184797 Nonbonded interactions: 432343 Sorted by model distance: nonbonded pdb=" OE1 GLU F 203 " pdb="MN MN F 401 " model vdw 2.013 2.320 nonbonded pdb=" OE1 GLU H 203 " pdb="MN MN H 401 " model vdw 2.019 2.320 nonbonded pdb=" OE2 GLU J 338 " pdb="MN MN J 402 " model vdw 2.067 2.320 nonbonded pdb=" OE1 GLU Q 203 " pdb="MN MN Q 401 " model vdw 2.072 2.320 nonbonded pdb=" OE1 GLU J 203 " pdb="MN MN J 401 " model vdw 2.079 2.320 ... (remaining 432338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = (chain 'C' and resid 2 through 501) selection = chain 'E' selection = chain 'G' selection = chain 'K' selection = chain 'N' } 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: 13.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 43.350 Find NCS groups from input model: 1.120 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.076 45640 Z= 0.869 Angle : 1.212 6.444 61770 Z= 0.894 Chirality : 0.069 0.195 6355 Planarity : 0.006 0.026 8075 Dihedral : 14.041 86.184 16725 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.11), residues: 5510 helix: 0.95 (0.10), residues: 2265 sheet: -0.47 (0.19), residues: 660 loop : 0.06 (0.12), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG B 45 TYR 0.044 0.006 TYR M 30 PHE 0.031 0.005 PHE A 89 TRP 0.042 0.007 TRP A 32 HIS 0.015 0.003 HIS Q 217 Details of bonding type rmsd covalent geometry : bond 0.01191 (45640) covalent geometry : angle 1.21200 (61770) hydrogen bonds : bond 0.16560 ( 2106) hydrogen bonds : angle 6.70432 ( 6498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 774 time to evaluate : 2.142 Fit side-chains REVERT: E 19 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8300 (ptmt) REVERT: E 25 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7423 (ttt90) REVERT: E 80 PHE cc_start: 0.8127 (m-80) cc_final: 0.7726 (m-80) REVERT: E 119 GLU cc_start: 0.8126 (tt0) cc_final: 0.7222 (pp20) REVERT: E 220 LYS cc_start: 0.8434 (mttt) cc_final: 0.7459 (mtpt) REVERT: E 361 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7825 (mm-40) REVERT: C 19 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8154 (ptmt) REVERT: C 25 ARG cc_start: 0.7766 (ttp80) cc_final: 0.7416 (ttt90) REVERT: C 44 MET cc_start: 0.7460 (mmp) cc_final: 0.7211 (mmm) REVERT: C 220 LYS cc_start: 0.8466 (mttt) cc_final: 0.7622 (mtpt) REVERT: C 324 GLU cc_start: 0.7679 (mp0) cc_final: 0.7401 (mp0) REVERT: C 333 GLU cc_start: 0.7955 (pt0) cc_final: 0.6798 (tp30) REVERT: G 19 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8124 (ptmt) REVERT: G 25 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7380 (ttt90) REVERT: G 44 MET cc_start: 0.7486 (mmp) cc_final: 0.7240 (mmm) REVERT: G 220 LYS cc_start: 0.8374 (mttt) cc_final: 0.7781 (mtpt) REVERT: K 19 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8156 (ptmt) REVERT: K 25 ARG cc_start: 0.7831 (ttp80) cc_final: 0.7522 (ttt90) REVERT: K 44 MET cc_start: 0.7453 (mmp) cc_final: 0.7226 (mmm) REVERT: K 80 PHE cc_start: 0.7991 (m-80) cc_final: 0.7592 (m-80) REVERT: K 180 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8320 (mtmt) REVERT: K 220 LYS cc_start: 0.8349 (mttt) cc_final: 0.7759 (mtpt) REVERT: K 324 GLU cc_start: 0.7698 (mp0) cc_final: 0.7403 (mp0) REVERT: K 333 GLU cc_start: 0.7866 (pt0) cc_final: 0.6789 (tp30) REVERT: K 361 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7401 (mm110) REVERT: N 19 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8164 (ptmt) REVERT: N 25 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7472 (ttt90) REVERT: N 44 MET cc_start: 0.7501 (mmp) cc_final: 0.7269 (mmm) REVERT: N 220 LYS cc_start: 0.8329 (mttt) cc_final: 0.7753 (mtpt) REVERT: N 223 MET cc_start: 0.8270 (tpp) cc_final: 0.7992 (tpp) REVERT: A 18 MET cc_start: 0.8672 (mmm) cc_final: 0.8448 (mmm) REVERT: A 29 MET cc_start: 0.8616 (ttm) cc_final: 0.8392 (ttp) REVERT: A 77 MET cc_start: 0.8465 (mmm) cc_final: 0.8224 (mmm) REVERT: A 110 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8244 (mp0) REVERT: A 118 LYS cc_start: 0.7831 (tttp) cc_final: 0.7169 (tptp) REVERT: A 268 LYS cc_start: 0.8059 (ptmm) cc_final: 0.7850 (ptpp) REVERT: J 55 GLU cc_start: 0.7823 (mp0) cc_final: 0.7549 (mp0) REVERT: J 84 MET cc_start: 0.8714 (ttp) cc_final: 0.8357 (ttp) REVERT: J 118 LYS cc_start: 0.7840 (tttp) cc_final: 0.7221 (tptp) REVERT: J 268 LYS cc_start: 0.8146 (ptmm) cc_final: 0.7849 (ptpp) REVERT: J 272 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8121 (mt-10) REVERT: L 38 GLU cc_start: 0.8289 (pt0) cc_final: 0.7196 (tm-30) REVERT: L 55 GLU cc_start: 0.7808 (mp0) cc_final: 0.7290 (mp0) REVERT: L 106 ARG cc_start: 0.8348 (mmm160) cc_final: 0.8139 (mmm160) REVERT: L 107 LYS cc_start: 0.8604 (mttt) cc_final: 0.7965 (mmtm) REVERT: L 118 LYS cc_start: 0.7792 (tttp) cc_final: 0.7158 (tptp) REVERT: L 268 LYS cc_start: 0.8128 (ptmm) cc_final: 0.7874 (ptpp) REVERT: Q 15 GLN cc_start: 0.7400 (mt0) cc_final: 0.6818 (mm-40) REVERT: Q 29 MET cc_start: 0.8596 (ttm) cc_final: 0.8369 (ttm) REVERT: Q 55 GLU cc_start: 0.7858 (mp0) cc_final: 0.7619 (mp0) REVERT: Q 57 LEU cc_start: 0.8746 (mt) cc_final: 0.8538 (mm) REVERT: Q 107 LYS cc_start: 0.8554 (mttt) cc_final: 0.7875 (mmtm) REVERT: Q 118 LYS cc_start: 0.7767 (tttp) cc_final: 0.7110 (tptp) REVERT: Q 133 MET cc_start: 0.8339 (mtp) cc_final: 0.8088 (mtp) REVERT: Q 268 LYS cc_start: 0.8068 (ptmm) cc_final: 0.7743 (ptpp) REVERT: H 15 GLN cc_start: 0.7394 (mt0) cc_final: 0.6834 (mm-40) REVERT: H 29 MET cc_start: 0.8605 (ttm) cc_final: 0.8388 (ttm) REVERT: H 57 LEU cc_start: 0.8767 (mt) cc_final: 0.8541 (mm) REVERT: H 107 LYS cc_start: 0.8585 (mttt) cc_final: 0.7913 (mmtm) REVERT: H 118 LYS cc_start: 0.7733 (tttp) cc_final: 0.7075 (tptp) REVERT: H 133 MET cc_start: 0.8346 (mtp) cc_final: 0.8118 (mtp) REVERT: H 268 LYS cc_start: 0.8091 (ptmm) cc_final: 0.7768 (ptpp) REVERT: D 55 GLU cc_start: 0.7812 (mp0) cc_final: 0.7386 (mp0) REVERT: D 107 LYS cc_start: 0.8602 (mttt) cc_final: 0.7977 (mmtm) REVERT: D 118 LYS cc_start: 0.7748 (tttp) cc_final: 0.7113 (tptp) REVERT: D 121 MET cc_start: 0.8365 (mmt) cc_final: 0.7994 (mmt) REVERT: D 133 MET cc_start: 0.8371 (mtp) cc_final: 0.8108 (mtp) REVERT: D 267 LEU cc_start: 0.8373 (tp) cc_final: 0.8157 (tp) REVERT: D 268 LYS cc_start: 0.8101 (ptmm) cc_final: 0.7856 (ptpp) REVERT: B 8 HIS cc_start: 0.8161 (m170) cc_final: 0.7949 (m-70) REVERT: B 55 GLU cc_start: 0.7824 (mp0) cc_final: 0.7400 (mp0) REVERT: B 107 LYS cc_start: 0.8571 (mttt) cc_final: 0.7923 (mmtm) REVERT: B 118 LYS cc_start: 0.7744 (tttp) cc_final: 0.7114 (tptp) REVERT: B 121 MET cc_start: 0.8371 (mmt) cc_final: 0.8013 (mmt) REVERT: B 133 MET cc_start: 0.8387 (mtp) cc_final: 0.8102 (mtp) REVERT: B 267 LEU cc_start: 0.8331 (tp) cc_final: 0.8108 (tp) REVERT: B 268 LYS cc_start: 0.8134 (ptmm) cc_final: 0.7880 (ptpp) REVERT: F 18 MET cc_start: 0.8676 (mmm) cc_final: 0.8467 (mmm) REVERT: F 29 MET cc_start: 0.8628 (ttm) cc_final: 0.8418 (ttp) REVERT: F 77 MET cc_start: 0.8466 (mmm) cc_final: 0.8166 (mmm) REVERT: F 110 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8245 (mp0) REVERT: F 118 LYS cc_start: 0.7868 (tttp) cc_final: 0.7199 (tptp) REVERT: F 268 LYS cc_start: 0.8039 (ptmm) cc_final: 0.7825 (ptpp) REVERT: I 55 GLU cc_start: 0.7755 (mp0) cc_final: 0.7479 (mp0) REVERT: I 84 MET cc_start: 0.8701 (ttp) cc_final: 0.8340 (ttp) REVERT: I 118 LYS cc_start: 0.7846 (tttp) cc_final: 0.7225 (tptp) REVERT: I 267 LEU cc_start: 0.8394 (tp) cc_final: 0.8186 (tp) REVERT: I 268 LYS cc_start: 0.8172 (ptmm) cc_final: 0.7908 (ptpp) REVERT: M 38 GLU cc_start: 0.8285 (pt0) cc_final: 0.7212 (tm-30) REVERT: M 55 GLU cc_start: 0.7795 (mp0) cc_final: 0.7288 (mp0) REVERT: M 107 LYS cc_start: 0.8580 (mttt) cc_final: 0.7947 (mmtm) REVERT: M 118 LYS cc_start: 0.7799 (tttp) cc_final: 0.7186 (tptp) REVERT: M 268 LYS cc_start: 0.8108 (ptmm) cc_final: 0.7856 (ptpp) REVERT: M 322 SER cc_start: 0.8206 (m) cc_final: 0.7840 (p) outliers start: 0 outliers final: 2 residues processed: 774 average time/residue: 0.9607 time to fit residues: 883.3636 Evaluate side-chains 641 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 639 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain H residue 126 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 523 optimal weight: 0.7980 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 0.2980 chunk 223 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 175 ASN E 316 GLN C 156 HIS C 293 GLN C 361 GLN G 156 HIS G 175 ASN G 308 ASN K 175 ASN K 308 ASN N 204 ASN N 293 GLN A 8 HIS A 27 GLN A 127 GLN A 205 GLN A 304 HIS J 27 GLN J 127 GLN J 304 HIS L 8 HIS L 27 GLN L 127 GLN L 304 HIS Q 8 HIS Q 27 GLN Q 127 GLN Q 205 GLN Q 255 ASN Q 304 HIS H 8 HIS H 27 GLN H 127 GLN H 205 GLN H 255 ASN H 304 HIS D 8 HIS D 27 GLN D 127 GLN D 205 GLN D 304 HIS B 27 GLN B 127 GLN B 205 GLN B 304 HIS F 8 HIS F 27 GLN F 127 GLN F 205 GLN F 304 HIS I 8 HIS I 27 GLN I 127 GLN I 304 HIS M 8 HIS M 27 GLN M 127 GLN ** M 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.196669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156325 restraints weight = 34704.216| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.03 r_work: 0.3784 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 45640 Z= 0.142 Angle : 0.552 5.641 61770 Z= 0.298 Chirality : 0.042 0.164 6355 Planarity : 0.004 0.051 8075 Dihedral : 4.193 18.552 6139 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.11 % Allowed : 5.85 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.11), residues: 5510 helix: 1.69 (0.11), residues: 2250 sheet: -0.69 (0.18), residues: 670 loop : 0.23 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 114 TYR 0.016 0.002 TYR E 97 PHE 0.021 0.002 PHE A 147 TRP 0.014 0.002 TRP Q 32 HIS 0.011 0.002 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00299 (45640) covalent geometry : angle 0.55242 (61770) hydrogen bonds : bond 0.04996 ( 2106) hydrogen bonds : angle 5.14741 ( 6498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 659 time to evaluate : 1.146 Fit side-chains REVERT: E 19 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8369 (pttp) REVERT: E 220 LYS cc_start: 0.8689 (mttt) cc_final: 0.8458 (mtpt) REVERT: C 220 LYS cc_start: 0.8721 (mttt) cc_final: 0.8501 (mtpt) REVERT: G 19 LYS cc_start: 0.8648 (mtmt) cc_final: 0.8418 (ptmt) REVERT: G 220 LYS cc_start: 0.8658 (mttt) cc_final: 0.8399 (mtpt) REVERT: G 223 MET cc_start: 0.8621 (mmm) cc_final: 0.8018 (tpp) REVERT: K 35 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: K 80 PHE cc_start: 0.7443 (m-80) cc_final: 0.7070 (m-80) REVERT: K 220 LYS cc_start: 0.8662 (mttt) cc_final: 0.8422 (mtpt) REVERT: N 19 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8350 (ptmt) REVERT: N 44 MET cc_start: 0.7865 (mmp) cc_final: 0.7616 (mmm) REVERT: N 80 PHE cc_start: 0.7412 (m-80) cc_final: 0.7078 (m-80) REVERT: N 166 GLU cc_start: 0.7426 (mp0) cc_final: 0.7192 (mp0) REVERT: N 170 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8012 (tppt) REVERT: N 220 LYS cc_start: 0.8660 (mttt) cc_final: 0.8388 (mtpt) REVERT: A 29 MET cc_start: 0.8882 (ttm) cc_final: 0.8592 (ttp) REVERT: A 118 LYS cc_start: 0.8069 (tttp) cc_final: 0.7846 (tptp) REVERT: J 84 MET cc_start: 0.8902 (ttp) cc_final: 0.8558 (ttp) REVERT: L 38 GLU cc_start: 0.7872 (pt0) cc_final: 0.7643 (tm-30) REVERT: L 106 ARG cc_start: 0.8296 (mmm160) cc_final: 0.8047 (mmm160) REVERT: Q 110 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: Q 118 LYS cc_start: 0.7959 (tttp) cc_final: 0.7727 (tptp) REVERT: Q 133 MET cc_start: 0.8243 (mtp) cc_final: 0.7992 (mtp) REVERT: H 110 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: H 118 LYS cc_start: 0.7977 (tttp) cc_final: 0.7701 (tptp) REVERT: D 107 LYS cc_start: 0.8722 (mttt) cc_final: 0.8464 (mmtm) REVERT: D 110 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: D 133 MET cc_start: 0.8412 (mtp) cc_final: 0.8134 (mtp) REVERT: B 110 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: B 133 MET cc_start: 0.8401 (mtp) cc_final: 0.8120 (mtp) REVERT: F 29 MET cc_start: 0.8883 (ttm) cc_final: 0.8603 (ttp) REVERT: F 118 LYS cc_start: 0.8084 (tttp) cc_final: 0.7872 (tptp) REVERT: I 84 MET cc_start: 0.8902 (ttp) cc_final: 0.8632 (ttp) REVERT: M 118 LYS cc_start: 0.8013 (tttp) cc_final: 0.7812 (tptp) outliers start: 52 outliers final: 23 residues processed: 677 average time/residue: 0.8277 time to fit residues: 661.6185 Evaluate side-chains 633 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 604 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 255 ARG Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 303 ASP Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain N residue 255 ARG Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain M residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 252 optimal weight: 0.6980 chunk 532 optimal weight: 0.6980 chunk 476 optimal weight: 4.9990 chunk 410 optimal weight: 0.4980 chunk 370 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 520 optimal weight: 0.0470 chunk 458 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 451 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 361 GLN C 204 ASN C 293 GLN C 361 GLN G 361 GLN K 361 GLN N 293 GLN A 8 HIS A 201 GLN A 205 GLN J 8 HIS J 201 GLN L 8 HIS L 127 GLN L 201 GLN Q 8 HIS Q 201 GLN Q 205 GLN H 8 HIS H 201 GLN H 205 GLN D 8 HIS D 127 GLN D 201 GLN D 205 GLN B 8 HIS B 127 GLN B 201 GLN B 205 GLN F 8 HIS F 201 GLN F 205 GLN I 8 HIS I 201 GLN I 205 GLN M 8 HIS M 127 GLN M 201 GLN M 304 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.197745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.156964 restraints weight = 34674.029| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 0.90 r_work: 0.3799 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 45640 Z= 0.116 Angle : 0.501 5.845 61770 Z= 0.269 Chirality : 0.040 0.163 6355 Planarity : 0.003 0.047 8075 Dihedral : 3.978 17.295 6135 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.11 % Allowed : 7.34 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.14 (0.11), residues: 5510 helix: 1.87 (0.11), residues: 2275 sheet: -0.69 (0.18), residues: 710 loop : 0.28 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 25 TYR 0.013 0.001 TYR G 97 PHE 0.020 0.001 PHE G 80 TRP 0.012 0.001 TRP Q 32 HIS 0.007 0.001 HIS M 145 Details of bonding type rmsd covalent geometry : bond 0.00241 (45640) covalent geometry : angle 0.50095 (61770) hydrogen bonds : bond 0.04450 ( 2106) hydrogen bonds : angle 4.91451 ( 6498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 648 time to evaluate : 1.068 Fit side-chains REVERT: E 19 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8426 (ptmt) REVERT: E 80 PHE cc_start: 0.7468 (m-80) cc_final: 0.7125 (m-80) REVERT: E 220 LYS cc_start: 0.8608 (mttt) cc_final: 0.8385 (mtpt) REVERT: C 306 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7757 (mm-30) REVERT: G 19 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8362 (ptmt) REVERT: G 220 LYS cc_start: 0.8598 (mttt) cc_final: 0.8362 (mtpt) REVERT: G 223 MET cc_start: 0.8566 (mmm) cc_final: 0.7971 (tpp) REVERT: K 35 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: K 80 PHE cc_start: 0.7421 (m-80) cc_final: 0.7027 (m-80) REVERT: N 19 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8370 (ptmt) REVERT: N 80 PHE cc_start: 0.7314 (m-80) cc_final: 0.6861 (m-80) REVERT: N 220 LYS cc_start: 0.8627 (mttt) cc_final: 0.8368 (mtpt) REVERT: A 29 MET cc_start: 0.8873 (ttm) cc_final: 0.8576 (ttp) REVERT: A 118 LYS cc_start: 0.7959 (tttp) cc_final: 0.7569 (pptt) REVERT: J 84 MET cc_start: 0.8886 (ttp) cc_final: 0.8578 (ttp) REVERT: L 38 GLU cc_start: 0.7819 (pt0) cc_final: 0.7609 (tm-30) REVERT: L 106 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7944 (mmm160) REVERT: Q 110 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: Q 133 MET cc_start: 0.8237 (mtp) cc_final: 0.7949 (mtp) REVERT: H 110 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: H 118 LYS cc_start: 0.7912 (tttp) cc_final: 0.7676 (tptp) REVERT: D 107 LYS cc_start: 0.8701 (mttt) cc_final: 0.8450 (mmtm) REVERT: D 121 MET cc_start: 0.8463 (mmt) cc_final: 0.8009 (mmt) REVERT: D 133 MET cc_start: 0.8369 (mtp) cc_final: 0.8074 (mtp) REVERT: B 121 MET cc_start: 0.8453 (mmt) cc_final: 0.8001 (mmt) REVERT: B 133 MET cc_start: 0.8373 (mtp) cc_final: 0.8075 (mtt) REVERT: F 29 MET cc_start: 0.8862 (ttm) cc_final: 0.8567 (ttp) REVERT: I 84 MET cc_start: 0.8870 (ttp) cc_final: 0.8553 (ttp) outliers start: 52 outliers final: 20 residues processed: 664 average time/residue: 0.7057 time to fit residues: 556.7179 Evaluate side-chains 642 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 618 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 255 ARG Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 149 LYS Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 255 ARG Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain M residue 75 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 282 optimal weight: 0.0970 chunk 350 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 392 optimal weight: 0.7980 chunk 507 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 323 optimal weight: 3.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 316 GLN E 361 GLN C 204 ASN C 293 GLN C 308 ASN C 361 GLN G 361 GLN K 91 HIS N 293 GLN A 8 HIS A 205 GLN J 8 HIS J 127 GLN J 205 GLN L 8 HIS L 127 GLN L 205 GLN L 331 GLN Q 8 HIS Q 205 GLN Q 331 GLN H 8 HIS H 205 GLN H 331 GLN D 8 HIS D 127 GLN D 205 GLN D 331 GLN B 8 HIS B 127 GLN B 205 GLN B 331 GLN F 8 HIS F 205 GLN I 8 HIS I 205 GLN M 8 HIS M 127 GLN M 205 GLN M 331 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.193592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.152739 restraints weight = 34211.552| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 0.97 r_work: 0.3711 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 45640 Z= 0.224 Angle : 0.632 7.092 61770 Z= 0.343 Chirality : 0.046 0.207 6355 Planarity : 0.005 0.051 8075 Dihedral : 4.461 21.459 6135 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.33 % Allowed : 8.24 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.11), residues: 5510 helix: 1.34 (0.10), residues: 2280 sheet: -0.96 (0.18), residues: 700 loop : 0.13 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 181 TYR 0.024 0.002 TYR H 78 PHE 0.024 0.003 PHE A 223 TRP 0.017 0.002 TRP H 32 HIS 0.012 0.002 HIS F 145 Details of bonding type rmsd covalent geometry : bond 0.00489 (45640) covalent geometry : angle 0.63202 (61770) hydrogen bonds : bond 0.05652 ( 2106) hydrogen bonds : angle 5.38079 ( 6498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 634 time to evaluate : 1.008 Fit side-chains REVERT: E 80 PHE cc_start: 0.7680 (m-80) cc_final: 0.7290 (m-80) REVERT: E 220 LYS cc_start: 0.8731 (mttt) cc_final: 0.8429 (mtpt) REVERT: C 306 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: G 19 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8286 (pttp) REVERT: G 166 GLU cc_start: 0.7493 (mp0) cc_final: 0.7290 (mp0) REVERT: G 203 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7196 (p0) REVERT: G 220 LYS cc_start: 0.8721 (mttt) cc_final: 0.8472 (mtpt) REVERT: K 35 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: K 80 PHE cc_start: 0.7556 (m-80) cc_final: 0.7178 (m-80) REVERT: N 19 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8386 (ptmt) REVERT: N 44 MET cc_start: 0.7752 (mmm) cc_final: 0.7536 (mmm) REVERT: N 80 PHE cc_start: 0.7534 (m-80) cc_final: 0.7066 (m-80) REVERT: N 166 GLU cc_start: 0.7498 (mp0) cc_final: 0.7233 (mp0) REVERT: N 220 LYS cc_start: 0.8685 (mttt) cc_final: 0.8407 (mtpt) REVERT: A 29 MET cc_start: 0.8898 (ttm) cc_final: 0.8599 (ttp) REVERT: A 118 LYS cc_start: 0.8127 (tttp) cc_final: 0.7889 (tptp) REVERT: J 84 MET cc_start: 0.8882 (ttp) cc_final: 0.8577 (ttp) REVERT: J 110 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: Q 15 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7875 (mt0) REVERT: Q 110 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: Q 214 MET cc_start: 0.8909 (tpt) cc_final: 0.8707 (tpt) REVERT: H 15 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: H 55 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: H 110 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: H 118 LYS cc_start: 0.8066 (tttp) cc_final: 0.7781 (tptp) REVERT: D 107 LYS cc_start: 0.8687 (mttt) cc_final: 0.8460 (mmtm) REVERT: F 29 MET cc_start: 0.8907 (ttm) cc_final: 0.8615 (ttp) REVERT: F 110 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: I 84 MET cc_start: 0.8870 (ttp) cc_final: 0.8568 (ttp) REVERT: I 110 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: I 123 MET cc_start: 0.8074 (mtp) cc_final: 0.7785 (mtp) outliers start: 62 outliers final: 30 residues processed: 659 average time/residue: 0.5955 time to fit residues: 466.1324 Evaluate side-chains 649 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 608 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 255 ARG Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 149 LYS Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 303 ASP Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 255 ARG Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 319 MET Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 268 LYS Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain M residue 75 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 186 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 278 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 240 optimal weight: 0.0970 chunk 383 optimal weight: 0.5980 chunk 275 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 316 GLN E 361 GLN C 204 ASN C 293 GLN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 ASN G 308 ASN G 361 GLN K 361 GLN N 293 GLN A 8 HIS A 15 GLN A 205 GLN J 8 HIS J 127 GLN J 205 GLN L 8 HIS L 127 GLN Q 8 HIS Q 205 GLN Q 331 GLN H 8 HIS H 205 GLN H 331 GLN D 8 HIS D 127 GLN D 331 GLN B 8 HIS B 127 GLN B 331 GLN F 8 HIS F 15 GLN F 205 GLN I 8 HIS M 8 HIS M 127 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.196790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.156620 restraints weight = 34429.817| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 0.99 r_work: 0.3806 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 45640 Z= 0.119 Angle : 0.510 7.468 61770 Z= 0.273 Chirality : 0.040 0.168 6355 Planarity : 0.004 0.051 8075 Dihedral : 4.075 18.451 6135 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.24 % Allowed : 8.89 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.01 (0.11), residues: 5510 helix: 1.76 (0.11), residues: 2275 sheet: -0.86 (0.18), residues: 710 loop : 0.24 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 13 TYR 0.012 0.001 TYR E 97 PHE 0.018 0.001 PHE C 80 TRP 0.013 0.001 TRP H 32 HIS 0.006 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00248 (45640) covalent geometry : angle 0.50973 (61770) hydrogen bonds : bond 0.04427 ( 2106) hydrogen bonds : angle 4.97880 ( 6498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 631 time to evaluate : 0.984 Fit side-chains REVERT: E 19 LYS cc_start: 0.8847 (mttt) cc_final: 0.8298 (ptmt) REVERT: E 80 PHE cc_start: 0.7448 (m-80) cc_final: 0.7093 (m-80) REVERT: E 272 CYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6447 (t) REVERT: E 306 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: C 272 CYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6520 (t) REVERT: C 306 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: G 19 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8282 (pttp) REVERT: G 220 LYS cc_start: 0.8618 (mttt) cc_final: 0.8387 (mtpt) REVERT: G 223 MET cc_start: 0.8612 (mmm) cc_final: 0.7994 (tpp) REVERT: G 255 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7925 (mmt90) REVERT: K 35 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: K 272 CYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6414 (t) REVERT: N 19 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8358 (ptmt) REVERT: N 80 PHE cc_start: 0.7338 (m-80) cc_final: 0.6907 (m-80) REVERT: N 220 LYS cc_start: 0.8646 (mttt) cc_final: 0.8370 (mtpt) REVERT: N 272 CYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6477 (t) REVERT: N 306 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7678 (mm-30) REVERT: A 29 MET cc_start: 0.8854 (ttm) cc_final: 0.8545 (ttp) REVERT: A 118 LYS cc_start: 0.8022 (tttp) cc_final: 0.7806 (tptp) REVERT: J 84 MET cc_start: 0.8870 (ttp) cc_final: 0.8559 (ttp) REVERT: J 268 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7982 (ptpp) REVERT: L 133 MET cc_start: 0.8261 (mtp) cc_final: 0.8040 (mtp) REVERT: Q 110 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: H 55 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: H 110 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: H 118 LYS cc_start: 0.7961 (tttp) cc_final: 0.7695 (tptp) REVERT: D 107 LYS cc_start: 0.8708 (mttt) cc_final: 0.8471 (mmtm) REVERT: D 133 MET cc_start: 0.8371 (mtp) cc_final: 0.7999 (mtt) REVERT: B 133 MET cc_start: 0.8370 (mtp) cc_final: 0.7999 (mtt) REVERT: F 29 MET cc_start: 0.8857 (ttm) cc_final: 0.8548 (ttp) REVERT: I 84 MET cc_start: 0.8852 (ttp) cc_final: 0.8536 (ttp) REVERT: I 123 MET cc_start: 0.8018 (mtp) cc_final: 0.7700 (mtp) outliers start: 58 outliers final: 27 residues processed: 653 average time/residue: 0.5846 time to fit residues: 454.5325 Evaluate side-chains 650 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 610 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 255 ARG Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 149 LYS Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 255 ARG Chi-restraints excluded: chain N residue 272 CYS Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 306 GLU Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 268 LYS Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain M residue 75 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 376 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 537 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 chunk 543 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 430 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 316 GLN E 361 GLN C 204 ASN C 293 GLN C 361 GLN G 204 ASN G 308 ASN N 293 GLN A 8 HIS A 15 GLN A 205 GLN J 8 HIS J 127 GLN J 205 GLN L 8 HIS L 127 GLN L 205 GLN Q 8 HIS Q 205 GLN Q 331 GLN H 8 HIS H 205 GLN H 331 GLN D 8 HIS D 127 GLN D 205 GLN D 331 GLN B 8 HIS B 127 GLN B 205 GLN B 331 GLN F 8 HIS F 15 GLN F 205 GLN I 8 HIS I 205 GLN M 8 HIS M 127 GLN M 205 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.194963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.154820 restraints weight = 34176.922| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 0.96 r_work: 0.3757 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 45640 Z= 0.157 Angle : 0.557 8.652 61770 Z= 0.299 Chirality : 0.042 0.174 6355 Planarity : 0.004 0.051 8075 Dihedral : 4.231 19.937 6135 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.31 % Allowed : 9.27 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.11), residues: 5510 helix: 1.60 (0.10), residues: 2280 sheet: -0.96 (0.18), residues: 710 loop : 0.22 (0.13), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 25 TYR 0.018 0.002 TYR E 97 PHE 0.019 0.002 PHE A 223 TRP 0.016 0.002 TRP H 32 HIS 0.008 0.001 HIS F 145 Details of bonding type rmsd covalent geometry : bond 0.00338 (45640) covalent geometry : angle 0.55663 (61770) hydrogen bonds : bond 0.04932 ( 2106) hydrogen bonds : angle 5.14569 ( 6498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 618 time to evaluate : 0.953 Fit side-chains REVERT: E 19 LYS cc_start: 0.8851 (mttt) cc_final: 0.8154 (pttp) REVERT: E 80 PHE cc_start: 0.7484 (m-80) cc_final: 0.7139 (m-80) REVERT: E 306 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7853 (mm-30) REVERT: C 272 CYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6506 (t) REVERT: C 306 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7786 (mm-30) REVERT: G 19 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8276 (pttp) REVERT: G 220 LYS cc_start: 0.8674 (mttt) cc_final: 0.8426 (mtpt) REVERT: G 255 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7924 (mmt90) REVERT: K 35 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: K 170 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7388 (ttpt) REVERT: K 272 CYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6425 (t) REVERT: N 19 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8383 (ptmt) REVERT: N 80 PHE cc_start: 0.7457 (m-80) cc_final: 0.6999 (m-80) REVERT: N 220 LYS cc_start: 0.8650 (mttt) cc_final: 0.8365 (mtpt) REVERT: N 272 CYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6505 (t) REVERT: N 306 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: A 29 MET cc_start: 0.8859 (ttm) cc_final: 0.8551 (ttp) REVERT: A 118 LYS cc_start: 0.8062 (tttp) cc_final: 0.7829 (tptp) REVERT: J 84 MET cc_start: 0.8869 (ttp) cc_final: 0.8573 (ttp) REVERT: L 110 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: Q 110 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: Q 214 MET cc_start: 0.8874 (tpt) cc_final: 0.8664 (tpt) REVERT: H 55 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: H 110 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: H 118 LYS cc_start: 0.7990 (tttp) cc_final: 0.7735 (tptp) REVERT: D 107 LYS cc_start: 0.8694 (mttt) cc_final: 0.8450 (mmtm) REVERT: D 133 MET cc_start: 0.8395 (mtp) cc_final: 0.8042 (mtt) REVERT: B 133 MET cc_start: 0.8391 (mtp) cc_final: 0.8042 (mtt) REVERT: F 29 MET cc_start: 0.8869 (ttm) cc_final: 0.8565 (ttp) REVERT: F 110 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: I 123 MET cc_start: 0.8047 (mtp) cc_final: 0.7729 (mtp) REVERT: M 133 MET cc_start: 0.8324 (mtp) cc_final: 0.7866 (mtt) outliers start: 61 outliers final: 37 residues processed: 645 average time/residue: 0.5841 time to fit residues: 448.5447 Evaluate side-chains 654 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 603 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 255 ARG Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 149 LYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 303 ASP Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 255 ARG Chi-restraints excluded: chain N residue 272 CYS Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 306 GLU Chi-restraints excluded: chain N residue 319 MET Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 268 LYS Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 268 LYS Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 75 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 295 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 544 optimal weight: 10.0000 chunk 401 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 362 optimal weight: 2.9990 chunk 443 optimal weight: 0.9990 chunk 347 optimal weight: 0.8980 chunk 409 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 316 GLN E 356 GLN E 361 GLN C 204 ASN C 356 GLN C 361 GLN G 204 ASN G 308 ASN G 361 GLN K 356 GLN N 293 GLN N 356 GLN A 8 HIS A 15 GLN A 205 GLN J 8 HIS J 127 GLN L 8 HIS L 127 GLN L 205 GLN Q 8 HIS Q 331 GLN H 8 HIS H 15 GLN H 331 GLN D 8 HIS D 127 GLN D 331 GLN B 8 HIS B 127 GLN B 331 GLN F 8 HIS F 15 GLN F 205 GLN I 8 HIS M 8 HIS M 127 GLN M 205 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.194851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.154297 restraints weight = 34152.931| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 0.97 r_work: 0.3762 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 45640 Z= 0.161 Angle : 0.564 8.124 61770 Z= 0.303 Chirality : 0.042 0.175 6355 Planarity : 0.004 0.052 8075 Dihedral : 4.260 20.107 6135 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.39 % Allowed : 9.51 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.11), residues: 5510 helix: 1.55 (0.10), residues: 2275 sheet: -0.98 (0.18), residues: 710 loop : 0.20 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 25 TYR 0.017 0.002 TYR E 97 PHE 0.019 0.002 PHE A 223 TRP 0.016 0.002 TRP Q 32 HIS 0.008 0.001 HIS F 145 Details of bonding type rmsd covalent geometry : bond 0.00347 (45640) covalent geometry : angle 0.56385 (61770) hydrogen bonds : bond 0.04949 ( 2106) hydrogen bonds : angle 5.16989 ( 6498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 616 time to evaluate : 0.978 Fit side-chains REVERT: E 19 LYS cc_start: 0.8850 (mttt) cc_final: 0.8152 (pttp) REVERT: E 80 PHE cc_start: 0.7483 (m-80) cc_final: 0.7125 (m-80) REVERT: E 223 MET cc_start: 0.8568 (mmm) cc_final: 0.8171 (tpp) REVERT: E 255 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7903 (mmt90) REVERT: E 292 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: E 306 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7850 (mm-30) REVERT: C 306 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7774 (mm-30) REVERT: G 19 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8274 (pttp) REVERT: G 220 LYS cc_start: 0.8670 (mttt) cc_final: 0.8433 (mtpt) REVERT: G 255 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7919 (mmt90) REVERT: K 35 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: K 170 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7382 (ttpt) REVERT: N 19 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8323 (ptmt) REVERT: N 80 PHE cc_start: 0.7477 (m-80) cc_final: 0.7024 (m-80) REVERT: N 166 GLU cc_start: 0.7412 (mp0) cc_final: 0.7207 (mp0) REVERT: N 220 LYS cc_start: 0.8639 (mttt) cc_final: 0.8359 (mtpt) REVERT: N 272 CYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6460 (t) REVERT: N 306 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7664 (mm-30) REVERT: A 118 LYS cc_start: 0.8076 (tttp) cc_final: 0.7831 (tptp) REVERT: J 84 MET cc_start: 0.8863 (ttp) cc_final: 0.8587 (ttp) REVERT: L 110 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: Q 110 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: Q 214 MET cc_start: 0.8879 (tpt) cc_final: 0.8661 (tpt) REVERT: H 55 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: H 110 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: H 118 LYS cc_start: 0.8038 (tttp) cc_final: 0.7759 (tptp) REVERT: D 107 LYS cc_start: 0.8692 (mttt) cc_final: 0.8445 (mmtm) REVERT: D 133 MET cc_start: 0.8404 (mtp) cc_final: 0.8053 (mtt) REVERT: B 133 MET cc_start: 0.8398 (mtp) cc_final: 0.8047 (mtt) REVERT: F 29 MET cc_start: 0.8865 (ttm) cc_final: 0.8562 (ttp) REVERT: F 110 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: I 123 MET cc_start: 0.8034 (mtp) cc_final: 0.7722 (mtp) REVERT: M 110 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7647 (mp0) outliers start: 65 outliers final: 37 residues processed: 645 average time/residue: 0.5858 time to fit residues: 449.0056 Evaluate side-chains 660 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 608 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 255 ARG Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 149 LYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 255 ARG Chi-restraints excluded: chain N residue 272 CYS Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 306 GLU Chi-restraints excluded: chain N residue 319 MET Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 268 LYS Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 268 LYS Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 110 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 448 optimal weight: 0.8980 chunk 471 optimal weight: 0.5980 chunk 326 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 258 optimal weight: 2.9990 chunk 475 optimal weight: 0.6980 chunk 445 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 347 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 316 GLN E 361 GLN C 204 ASN C 361 GLN G 204 ASN G 308 ASN N 293 GLN A 8 HIS A 15 GLN A 205 GLN J 8 HIS J 127 GLN L 8 HIS L 127 GLN Q 8 HIS Q 15 GLN Q 331 GLN H 8 HIS H 15 GLN H 331 GLN D 8 HIS D 127 GLN D 331 GLN B 8 HIS B 127 GLN F 8 HIS F 15 GLN F 205 GLN I 8 HIS I 205 GLN M 8 HIS M 127 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.195069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.154512 restraints weight = 34305.059| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 0.99 r_work: 0.3780 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 45640 Z= 0.153 Angle : 0.555 9.393 61770 Z= 0.298 Chirality : 0.042 0.173 6355 Planarity : 0.004 0.052 8075 Dihedral : 4.238 19.822 6135 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.16 % Allowed : 10.04 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.11), residues: 5510 helix: 1.57 (0.10), residues: 2275 sheet: -0.98 (0.18), residues: 710 loop : 0.21 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 25 TYR 0.016 0.002 TYR E 97 PHE 0.018 0.002 PHE A 223 TRP 0.016 0.002 TRP Q 32 HIS 0.007 0.001 HIS F 145 Details of bonding type rmsd covalent geometry : bond 0.00329 (45640) covalent geometry : angle 0.55543 (61770) hydrogen bonds : bond 0.04866 ( 2106) hydrogen bonds : angle 5.14347 ( 6498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 617 time to evaluate : 0.936 Fit side-chains REVERT: E 19 LYS cc_start: 0.8859 (mttt) cc_final: 0.8146 (pttp) REVERT: E 80 PHE cc_start: 0.7476 (m-80) cc_final: 0.7102 (m-80) REVERT: E 255 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7938 (mmt90) REVERT: E 292 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: E 306 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: C 306 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: G 19 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8330 (ptmt) REVERT: G 220 LYS cc_start: 0.8680 (mttt) cc_final: 0.8441 (mtpt) REVERT: G 255 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7960 (mmt90) REVERT: K 35 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: K 170 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7371 (ttpt) REVERT: N 80 PHE cc_start: 0.7454 (m-80) cc_final: 0.7021 (m-80) REVERT: N 220 LYS cc_start: 0.8651 (mttt) cc_final: 0.8367 (mtpt) REVERT: N 272 CYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6468 (t) REVERT: N 306 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7641 (mm-30) REVERT: A 29 MET cc_start: 0.8859 (ttm) cc_final: 0.8549 (ttp) REVERT: A 118 LYS cc_start: 0.8069 (tttp) cc_final: 0.7848 (tptp) REVERT: J 84 MET cc_start: 0.8867 (ttp) cc_final: 0.8586 (ttp) REVERT: L 110 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: Q 110 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: H 55 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: H 110 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: H 118 LYS cc_start: 0.8010 (tttp) cc_final: 0.7754 (tptp) REVERT: D 107 LYS cc_start: 0.8682 (mttt) cc_final: 0.8453 (mmtm) REVERT: D 133 MET cc_start: 0.8394 (mtp) cc_final: 0.8036 (mtt) REVERT: B 133 MET cc_start: 0.8385 (mtp) cc_final: 0.8014 (mtt) REVERT: F 29 MET cc_start: 0.8867 (ttm) cc_final: 0.8558 (ttp) REVERT: F 110 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: I 123 MET cc_start: 0.8024 (mtp) cc_final: 0.7722 (mtp) outliers start: 54 outliers final: 36 residues processed: 642 average time/residue: 0.5809 time to fit residues: 443.5838 Evaluate side-chains 640 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 590 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 255 ARG Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 149 LYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 249 LEU Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 303 ASP Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 255 ARG Chi-restraints excluded: chain N residue 272 CYS Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 306 GLU Chi-restraints excluded: chain N residue 319 MET Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 268 LYS Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 268 LYS Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 75 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 8 optimal weight: 3.9990 chunk 522 optimal weight: 0.5980 chunk 479 optimal weight: 3.9990 chunk 434 optimal weight: 2.9990 chunk 204 optimal weight: 0.0970 chunk 375 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 344 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 546 optimal weight: 5.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 361 GLN C 204 ASN C 361 GLN G 204 ASN G 308 ASN K 361 GLN N 293 GLN A 8 HIS A 15 GLN A 205 GLN J 8 HIS J 127 GLN J 205 GLN L 8 HIS L 127 GLN Q 8 HIS Q 331 GLN H 8 HIS H 205 GLN H 331 GLN D 8 HIS D 127 GLN D 205 GLN B 8 HIS F 8 HIS F 15 GLN F 205 GLN I 8 HIS I 205 GLN M 8 HIS M 127 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.195952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.155636 restraints weight = 34168.114| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 0.97 r_work: 0.3773 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 45640 Z= 0.134 Angle : 0.537 9.923 61770 Z= 0.286 Chirality : 0.041 0.171 6355 Planarity : 0.004 0.053 8075 Dihedral : 4.143 19.047 6135 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.33 % Allowed : 10.11 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.11), residues: 5510 helix: 1.68 (0.11), residues: 2275 sheet: -0.95 (0.18), residues: 710 loop : 0.25 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 25 TYR 0.015 0.001 TYR E 97 PHE 0.018 0.002 PHE K 80 TRP 0.015 0.002 TRP H 32 HIS 0.006 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00285 (45640) covalent geometry : angle 0.53745 (61770) hydrogen bonds : bond 0.04609 ( 2106) hydrogen bonds : angle 5.04842 ( 6498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 600 time to evaluate : 0.957 Fit side-chains REVERT: E 19 LYS cc_start: 0.8862 (mttt) cc_final: 0.8140 (pttp) REVERT: E 80 PHE cc_start: 0.7443 (m-80) cc_final: 0.7053 (m-80) REVERT: E 255 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7909 (mmt90) REVERT: E 292 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: E 306 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: C 306 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7777 (mm-30) REVERT: G 19 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8327 (ptmt) REVERT: G 220 LYS cc_start: 0.8654 (mttt) cc_final: 0.8414 (mtpt) REVERT: G 255 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7926 (mmt90) REVERT: K 35 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: K 170 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7398 (ttpt) REVERT: N 80 PHE cc_start: 0.7438 (m-80) cc_final: 0.6984 (m-80) REVERT: N 255 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7661 (mmt90) REVERT: N 272 CYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6451 (t) REVERT: N 306 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7669 (mm-30) REVERT: A 29 MET cc_start: 0.8856 (ttm) cc_final: 0.8545 (ttp) REVERT: A 118 LYS cc_start: 0.8040 (tttp) cc_final: 0.7800 (tptp) REVERT: J 84 MET cc_start: 0.8867 (ttp) cc_final: 0.8602 (ttp) REVERT: J 123 MET cc_start: 0.8021 (mtp) cc_final: 0.7689 (mtp) REVERT: Q 110 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: H 55 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: H 110 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: H 118 LYS cc_start: 0.8030 (tttp) cc_final: 0.7777 (tptp) REVERT: D 107 LYS cc_start: 0.8688 (mttt) cc_final: 0.8453 (mmtm) REVERT: D 133 MET cc_start: 0.8377 (mtp) cc_final: 0.8014 (mtt) REVERT: B 133 MET cc_start: 0.8387 (mtp) cc_final: 0.8032 (mtt) REVERT: F 29 MET cc_start: 0.8861 (ttm) cc_final: 0.8550 (ttp) REVERT: F 110 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: I 123 MET cc_start: 0.8011 (mtp) cc_final: 0.7716 (mtp) outliers start: 62 outliers final: 35 residues processed: 627 average time/residue: 0.5710 time to fit residues: 427.2274 Evaluate side-chains 641 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 592 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 255 ARG Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 149 LYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 303 ASP Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 255 ARG Chi-restraints excluded: chain N residue 272 CYS Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 306 GLU Chi-restraints excluded: chain N residue 319 MET Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 268 LYS Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 66 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 384 optimal weight: 4.9990 chunk 288 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 338 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 476 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 355 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 316 GLN E 361 GLN C 204 ASN C 361 GLN G 204 ASN G 308 ASN G 356 GLN K 361 GLN N 293 GLN A 8 HIS A 15 GLN A 205 GLN J 8 HIS J 127 GLN L 8 HIS L 127 GLN Q 8 HIS Q 205 GLN Q 331 GLN H 8 HIS H 205 GLN H 331 GLN D 8 HIS B 8 HIS F 8 HIS F 15 GLN F 205 GLN I 8 HIS I 127 GLN M 8 HIS M 127 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.195437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.155452 restraints weight = 34332.316| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 0.97 r_work: 0.3790 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 45640 Z= 0.143 Angle : 0.553 10.666 61770 Z= 0.294 Chirality : 0.042 0.171 6355 Planarity : 0.004 0.051 8075 Dihedral : 4.183 19.308 6135 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.18 % Allowed : 10.41 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.11), residues: 5510 helix: 1.63 (0.10), residues: 2275 sheet: -0.98 (0.18), residues: 710 loop : 0.24 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 25 TYR 0.016 0.002 TYR E 97 PHE 0.018 0.002 PHE A 223 TRP 0.015 0.002 TRP H 32 HIS 0.006 0.001 HIS F 145 Details of bonding type rmsd covalent geometry : bond 0.00306 (45640) covalent geometry : angle 0.55263 (61770) hydrogen bonds : bond 0.04733 ( 2106) hydrogen bonds : angle 5.09784 ( 6498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11020 Ramachandran restraints generated. 5510 Oldfield, 0 Emsley, 5510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 597 time to evaluate : 0.930 Fit side-chains REVERT: E 19 LYS cc_start: 0.8864 (mttt) cc_final: 0.8138 (pttp) REVERT: E 80 PHE cc_start: 0.7438 (m-80) cc_final: 0.7048 (m-80) REVERT: E 255 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7957 (mmt90) REVERT: E 292 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: E 306 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7828 (mm-30) REVERT: C 306 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: G 19 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8319 (ptmt) REVERT: G 80 PHE cc_start: 0.7537 (m-80) cc_final: 0.7159 (m-80) REVERT: G 220 LYS cc_start: 0.8658 (mttt) cc_final: 0.8405 (mtpt) REVERT: K 35 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: K 170 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7384 (ttpt) REVERT: N 80 PHE cc_start: 0.7427 (m-80) cc_final: 0.6985 (m-80) REVERT: N 255 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7709 (mmt90) REVERT: N 272 CYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6473 (t) REVERT: N 306 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7635 (mm-30) REVERT: A 29 MET cc_start: 0.8851 (ttm) cc_final: 0.8544 (ttp) REVERT: A 118 LYS cc_start: 0.8041 (tttp) cc_final: 0.7800 (tptp) REVERT: J 84 MET cc_start: 0.8871 (ttp) cc_final: 0.8604 (ttp) REVERT: J 123 MET cc_start: 0.8021 (mtp) cc_final: 0.7681 (mtp) REVERT: L 110 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: Q 110 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: H 55 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: H 110 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: H 118 LYS cc_start: 0.7986 (tttp) cc_final: 0.7732 (tptp) REVERT: D 107 LYS cc_start: 0.8687 (mttt) cc_final: 0.8449 (mmtm) REVERT: D 133 MET cc_start: 0.8376 (mtp) cc_final: 0.8009 (mtt) REVERT: B 133 MET cc_start: 0.8370 (mtp) cc_final: 0.8002 (mtt) REVERT: F 29 MET cc_start: 0.8855 (ttm) cc_final: 0.8547 (ttp) REVERT: F 110 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: I 123 MET cc_start: 0.8012 (mtp) cc_final: 0.7716 (mtp) outliers start: 55 outliers final: 37 residues processed: 620 average time/residue: 0.5761 time to fit residues: 425.2934 Evaluate side-chains 642 residues out of total 4670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 591 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 255 ARG Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 277 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 149 LYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 303 ASP Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 255 ARG Chi-restraints excluded: chain N residue 272 CYS Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 306 GLU Chi-restraints excluded: chain N residue 319 MET Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 268 LYS Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 268 LYS Chi-restraints excluded: chain H residue 15 GLN Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 374 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 347 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 253 optimal weight: 0.1980 chunk 401 optimal weight: 4.9990 chunk 506 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 359 optimal weight: 0.9980 chunk 464 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 316 GLN E 361 GLN C 204 ASN C 361 GLN G 204 ASN G 308 ASN K 361 GLN N 293 GLN A 8 HIS A 15 GLN J 8 HIS J 127 GLN L 8 HIS L 127 GLN Q 8 HIS Q 205 GLN Q 331 GLN H 8 HIS H 331 GLN D 8 HIS B 8 HIS F 8 HIS F 15 GLN I 8 HIS M 8 HIS M 127 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.195441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154211 restraints weight = 34142.511| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 0.89 r_work: 0.3765 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 45640 Z= 0.148 Angle : 0.561 10.756 61770 Z= 0.298 Chirality : 0.042 0.172 6355 Planarity : 0.004 0.054 8075 Dihedral : 4.202 19.477 6135 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.11 % Allowed : 10.36 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.11), residues: 5510 helix: 1.62 (0.10), residues: 2275 sheet: -1.00 (0.18), residues: 710 loop : 0.23 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 25 TYR 0.016 0.002 TYR E 97 PHE 0.018 0.002 PHE K 248 TRP 0.016 0.002 TRP H 32 HIS 0.006 0.001 HIS F 145 Details of bonding type rmsd covalent geometry : bond 0.00316 (45640) covalent geometry : angle 0.56068 (61770) hydrogen bonds : bond 0.04781 ( 2106) hydrogen bonds : angle 5.11210 ( 6498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16086.18 seconds wall clock time: 272 minutes 50.81 seconds (16370.81 seconds total)