Starting phenix.real_space_refine on Fri Jan 16 13:35:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxx_40860/01_2026/8sxx_40860_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxx_40860/01_2026/8sxx_40860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sxx_40860/01_2026/8sxx_40860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxx_40860/01_2026/8sxx_40860.map" model { file = "/net/cci-nas-00/data/ceres_data/8sxx_40860/01_2026/8sxx_40860_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxx_40860/01_2026/8sxx_40860_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 72 5.16 5 C 24321 2.51 5 N 6342 2.21 5 O 7181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s 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: 37940 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3185 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Chain: "B" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3081 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 11, 'TRANS': 372} Chain breaks: 2 Chain: "C" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3185 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Chain: "D" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3071 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 11, 'TRANS': 372} Chain breaks: 1 Chain: "E" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 388} Chain breaks: 1 Chain: "F" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3093 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 11, 'TRANS': 374} Chain breaks: 1 Chain: "G" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3119 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 379} Chain breaks: 2 Chain: "H" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3106 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 11, 'TRANS': 376} Chain breaks: 1 Chain: "I" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3139 Classifications: {'peptide': 393} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 382} Chain breaks: 3 Chain: "J" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3067 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 11, 'TRANS': 371} Chain breaks: 1 Chain: "K" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3078 Classifications: {'peptide': 384} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 372} Chain breaks: 1 Chain: "L" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3094 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 11, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.86, per 1000 atoms: 0.26 Number of scatterers: 37940 At special positions: 0 Unit cell: (102.486, 195.083, 190.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 24 15.00 O 7181 8.00 N 6342 7.00 C 24321 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 Atom "HETATM37891 O4D NAD K 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.5 seconds 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8596 Finding SS restraints... Secondary structure from input PDB file: 246 helices and 39 sheets defined 54.0% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.584A pdb=" N GLN A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 41 removed outlier: 4.133A pdb=" N VAL A 38 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY A 39 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A 41 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.506A pdb=" N VAL A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 65 removed outlier: 4.074A pdb=" N LEU A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 81 through 100 removed outlier: 3.677A pdb=" N LEU A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.558A pdb=" N GLU A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 124 removed outlier: 4.120A pdb=" N LEU A 124 " --> pdb=" O LYS A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 126 through 132 removed outlier: 4.333A pdb=" N GLN A 129 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.547A pdb=" N LYS A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP A 139 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA A 140 " --> pdb=" O LYS A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 140' Processing helix chain 'A' and resid 141 through 153 removed outlier: 3.695A pdb=" N GLU A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 4.194A pdb=" N TRP A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.778A pdb=" N ALA A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 277 through 296 removed outlier: 4.215A pdb=" N VAL A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 321 Processing helix chain 'A' and resid 336 through 345 Processing helix chain 'A' and resid 349 through 360 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 395 through 406 Processing helix chain 'B' and resid 11 through 24 removed outlier: 3.998A pdb=" N GLN B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.640A pdb=" N CYS B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 56 through 66 removed outlier: 3.663A pdb=" N LEU B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 82 through 100 Processing helix chain 'B' and resid 103 through 121 removed outlier: 3.817A pdb=" N GLU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 removed outlier: 3.504A pdb=" N GLN B 129 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 141 through 151 removed outlier: 4.225A pdb=" N GLU B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 148 " --> pdb=" O HIS B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 181 Processing helix chain 'B' and resid 197 through 202 Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.630A pdb=" N THR B 279 " --> pdb=" O TYR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 296 removed outlier: 3.658A pdb=" N MET B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 322 Processing helix chain 'B' and resid 336 through 345 removed outlier: 3.615A pdb=" N ILE B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 360 Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.872A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 24 removed outlier: 4.509A pdb=" N PHE C 15 " --> pdb=" O ASN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 removed outlier: 3.579A pdb=" N ALA C 36 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 38 " --> pdb=" O GLY C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.538A pdb=" N LEU C 60 " --> pdb=" O TYR C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 99 removed outlier: 3.905A pdb=" N LEU C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 122 removed outlier: 3.518A pdb=" N LYS C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 134 through 137 Processing helix chain 'C' and resid 138 through 151 removed outlier: 4.101A pdb=" N TYR C 143 " --> pdb=" O ASP C 139 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N HIS C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 178 removed outlier: 3.557A pdb=" N TRP C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.635A pdb=" N ALA C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 277 through 297 Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.683A pdb=" N ASN C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 349 through 360 Processing helix chain 'C' and resid 376 through 381 removed outlier: 4.003A pdb=" N PHE C 380 " --> pdb=" O TYR C 376 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL C 381 " --> pdb=" O PHE C 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 376 through 381' Processing helix chain 'C' and resid 395 through 407 removed outlier: 3.525A pdb=" N LEU C 399 " --> pdb=" O ILE C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 24 Processing helix chain 'D' and resid 44 through 55 Processing helix chain 'D' and resid 58 through 67 removed outlier: 4.575A pdb=" N ALA D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 78 Processing helix chain 'D' and resid 81 through 100 removed outlier: 4.027A pdb=" N ASP D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 4.833A pdb=" N LYS D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 132 removed outlier: 3.590A pdb=" N PHE D 130 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 131 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 141 through 154 removed outlier: 3.753A pdb=" N ASN D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.908A pdb=" N ASP D 202 " --> pdb=" O GLN D 199 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU D 203 " --> pdb=" O ASN D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 253 removed outlier: 3.684A pdb=" N TYR D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE D 253 " --> pdb=" O TYR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 282 through 296 removed outlier: 3.572A pdb=" N GLU D 286 " --> pdb=" O PHE D 282 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU D 293 " --> pdb=" O ARG D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 318 removed outlier: 3.839A pdb=" N ILE D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D 318 " --> pdb=" O ILE D 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 313 through 318' Processing helix chain 'D' and resid 319 through 322 removed outlier: 3.900A pdb=" N LEU D 322 " --> pdb=" O LEU D 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 319 through 322' Processing helix chain 'D' and resid 335 through 345 removed outlier: 3.644A pdb=" N ALA D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 361 Processing helix chain 'D' and resid 371 through 375 removed outlier: 4.053A pdb=" N LYS D 374 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.614A pdb=" N PHE D 380 " --> pdb=" O TYR D 376 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 24 Processing helix chain 'E' and resid 34 through 41 removed outlier: 3.637A pdb=" N SER E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLY E 39 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 58 through 68 removed outlier: 4.427A pdb=" N ALA E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 Processing helix chain 'E' and resid 81 through 100 Processing helix chain 'E' and resid 101 through 124 removed outlier: 3.816A pdb=" N GLU E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 132 removed outlier: 3.911A pdb=" N ARG E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 137 Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.592A pdb=" N TYR E 143 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N HIS E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS E 145 " --> pdb=" O PHE E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 180 Processing helix chain 'E' and resid 198 through 201 Processing helix chain 'E' and resid 244 through 250 removed outlier: 3.587A pdb=" N ALA E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 258 removed outlier: 3.510A pdb=" N ILE E 256 " --> pdb=" O TYR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 293 removed outlier: 3.868A pdb=" N GLU E 286 " --> pdb=" O PHE E 282 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N MET E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 322 Processing helix chain 'E' and resid 335 through 346 removed outlier: 4.424A pdb=" N THR E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS E 342 " --> pdb=" O GLU E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 361 removed outlier: 3.827A pdb=" N MET E 361 " --> pdb=" O THR E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 375 Processing helix chain 'E' and resid 376 through 384 removed outlier: 3.643A pdb=" N LEU E 384 " --> pdb=" O PHE E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 406 Processing helix chain 'F' and resid 11 through 25 removed outlier: 4.006A pdb=" N PHE F 15 " --> pdb=" O ASN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 37 removed outlier: 3.756A pdb=" N SER F 37 " --> pdb=" O ALA F 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 34 through 37' Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 56 through 66 removed outlier: 3.797A pdb=" N LEU F 60 " --> pdb=" O TYR F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 77 Processing helix chain 'F' and resid 82 through 100 removed outlier: 4.175A pdb=" N ASP F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 4.374A pdb=" N PHE F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 131 Processing helix chain 'F' and resid 134 through 140 removed outlier: 6.634A pdb=" N ASP F 139 " --> pdb=" O GLY F 136 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ALA F 140 " --> pdb=" O LYS F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 154 removed outlier: 3.673A pdb=" N LYS F 145 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER F 153 " --> pdb=" O SER F 149 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN F 154 " --> pdb=" O LYS F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 274 through 279 Processing helix chain 'F' and resid 282 through 295 removed outlier: 4.034A pdb=" N ILE F 295 " --> pdb=" O PHE F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 317 removed outlier: 3.699A pdb=" N ASN F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 322 Processing helix chain 'F' and resid 336 through 345 removed outlier: 3.618A pdb=" N LYS F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.808A pdb=" N THR F 357 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 383 Processing helix chain 'G' and resid 11 through 25 removed outlier: 3.569A pdb=" N PHE G 15 " --> pdb=" O ASN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 41 removed outlier: 4.411A pdb=" N GLY G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY G 41 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 56 removed outlier: 3.520A pdb=" N VAL G 48 " --> pdb=" O THR G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 65 removed outlier: 3.707A pdb=" N LEU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 78 Processing helix chain 'G' and resid 81 through 100 removed outlier: 3.934A pdb=" N LEU G 85 " --> pdb=" O ASN G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 107 removed outlier: 3.777A pdb=" N GLU G 106 " --> pdb=" O ASP G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 122 removed outlier: 3.639A pdb=" N ALA G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 131 removed outlier: 4.108A pdb=" N ARG G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 138 removed outlier: 3.549A pdb=" N LYS G 137 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS G 138 " --> pdb=" O GLN G 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 134 through 138' Processing helix chain 'G' and resid 142 through 155 removed outlier: 4.361A pdb=" N GLU G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 181 removed outlier: 3.859A pdb=" N TRP G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 201 removed outlier: 3.925A pdb=" N PHE G 201 " --> pdb=" O PRO G 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 201' Processing helix chain 'G' and resid 244 through 252 Processing helix chain 'G' and resid 252 through 259 removed outlier: 3.742A pdb=" N ILE G 256 " --> pdb=" O TYR G 252 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE G 257 " --> pdb=" O ILE G 253 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN G 258 " --> pdb=" O ASN G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 311 through 322 removed outlier: 3.765A pdb=" N ASN G 315 " --> pdb=" O ASP G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 345 Processing helix chain 'G' and resid 349 through 359 Processing helix chain 'G' and resid 376 through 384 Processing helix chain 'G' and resid 396 through 406 Processing helix chain 'H' and resid 11 through 25 removed outlier: 3.611A pdb=" N PHE H 15 " --> pdb=" O ASN H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 54 removed outlier: 3.686A pdb=" N VAL H 48 " --> pdb=" O THR H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 66 Processing helix chain 'H' and resid 71 through 78 Processing helix chain 'H' and resid 82 through 100 Processing helix chain 'H' and resid 102 through 122 removed outlier: 3.819A pdb=" N GLU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 122 " --> pdb=" O GLU H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 131 removed outlier: 3.627A pdb=" N PHE H 130 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG H 131 " --> pdb=" O GLU H 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 127 through 131' Processing helix chain 'H' and resid 138 through 140 No H-bonds generated for 'chain 'H' and resid 138 through 140' Processing helix chain 'H' and resid 141 through 154 Processing helix chain 'H' and resid 171 through 179 removed outlier: 3.831A pdb=" N ASP H 179 " --> pdb=" O TRP H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 203 removed outlier: 4.268A pdb=" N PHE H 201 " --> pdb=" O PRO H 198 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP H 202 " --> pdb=" O GLN H 199 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU H 203 " --> pdb=" O ASN H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 252 Processing helix chain 'H' and resid 282 through 296 removed outlier: 3.590A pdb=" N GLU H 286 " --> pdb=" O PHE H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 322 Processing helix chain 'H' and resid 336 through 345 Processing helix chain 'H' and resid 351 through 361 Processing helix chain 'H' and resid 376 through 384 removed outlier: 3.875A pdb=" N LEU H 384 " --> pdb=" O PHE H 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 23 removed outlier: 4.278A pdb=" N PHE I 15 " --> pdb=" O ASN I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 41 removed outlier: 3.613A pdb=" N SER I 37 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY I 39 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY I 41 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 56 removed outlier: 3.676A pdb=" N VAL I 48 " --> pdb=" O THR I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 66 removed outlier: 3.547A pdb=" N ILE I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 77 Processing helix chain 'I' and resid 81 through 100 removed outlier: 3.672A pdb=" N LYS I 91 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 122 removed outlier: 4.011A pdb=" N ALA I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 130 removed outlier: 3.833A pdb=" N PHE I 130 " --> pdb=" O GLY I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 140 removed outlier: 4.327A pdb=" N LYS I 137 " --> pdb=" O ASN I 134 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS I 138 " --> pdb=" O GLN I 135 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP I 139 " --> pdb=" O GLY I 136 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA I 140 " --> pdb=" O LYS I 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 134 through 140' Processing helix chain 'I' and resid 141 through 150 removed outlier: 3.632A pdb=" N GLU I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU I 147 " --> pdb=" O TYR I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 180 removed outlier: 3.596A pdb=" N ALA I 176 " --> pdb=" O ALA I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 201 Processing helix chain 'I' and resid 244 through 252 removed outlier: 3.907A pdb=" N ALA I 248 " --> pdb=" O SER I 244 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR I 252 " --> pdb=" O ALA I 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 258 removed outlier: 3.545A pdb=" N ILE I 256 " --> pdb=" O TYR I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 294 removed outlier: 3.812A pdb=" N GLY I 281 " --> pdb=" O SER I 277 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE I 282 " --> pdb=" O HIS I 278 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL I 283 " --> pdb=" O THR I 279 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR I 284 " --> pdb=" O ILE I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 297 No H-bonds generated for 'chain 'I' and resid 295 through 297' Processing helix chain 'I' and resid 311 through 321 Processing helix chain 'I' and resid 335 through 345 Processing helix chain 'I' and resid 351 through 360 Processing helix chain 'I' and resid 376 through 384 removed outlier: 3.502A pdb=" N LEU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 406 removed outlier: 3.745A pdb=" N VAL I 400 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU I 401 " --> pdb=" O ASP I 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 24 removed outlier: 3.817A pdb=" N SER J 17 " --> pdb=" O ASP J 13 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN J 24 " --> pdb=" O TYR J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 40 removed outlier: 3.798A pdb=" N VAL J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY J 39 " --> pdb=" O GLY J 35 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 34 through 40' Processing helix chain 'J' and resid 44 through 56 Processing helix chain 'J' and resid 56 through 66 Processing helix chain 'J' and resid 71 through 77 removed outlier: 3.624A pdb=" N SER J 75 " --> pdb=" O SER J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 100 Processing helix chain 'J' and resid 101 through 124 removed outlier: 3.925A pdb=" N LYS J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 112 " --> pdb=" O PHE J 108 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU J 124 " --> pdb=" O THR J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 removed outlier: 3.640A pdb=" N ARG J 131 " --> pdb=" O GLU J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 140 No H-bonds generated for 'chain 'J' and resid 138 through 140' Processing helix chain 'J' and resid 141 through 153 removed outlier: 3.908A pdb=" N SER J 149 " --> pdb=" O LYS J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 181 removed outlier: 4.468A pdb=" N ALA J 176 " --> pdb=" O ALA J 172 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA J 177 " --> pdb=" O LEU J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 203 removed outlier: 3.915A pdb=" N LEU J 203 " --> pdb=" O ASN J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 Processing helix chain 'J' and resid 281 through 295 removed outlier: 4.498A pdb=" N GLY J 285 " --> pdb=" O GLY J 281 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE J 295 " --> pdb=" O PHE J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 321 removed outlier: 4.137A pdb=" N LEU J 319 " --> pdb=" O ASN J 315 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA J 321 " --> pdb=" O ILE J 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 345 removed outlier: 3.525A pdb=" N ALA J 339 " --> pdb=" O GLU J 335 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS J 345 " --> pdb=" O THR J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 361 Processing helix chain 'J' and resid 372 through 375 Processing helix chain 'J' and resid 376 through 384 removed outlier: 4.008A pdb=" N LEU J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 22 Processing helix chain 'K' and resid 23 through 25 No H-bonds generated for 'chain 'K' and resid 23 through 25' Processing helix chain 'K' and resid 34 through 38 removed outlier: 3.639A pdb=" N VAL K 38 " --> pdb=" O GLY K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 56 Processing helix chain 'K' and resid 56 through 66 removed outlier: 4.212A pdb=" N LEU K 60 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY K 61 " --> pdb=" O PRO K 57 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA K 62 " --> pdb=" O GLU K 58 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU K 63 " --> pdb=" O LEU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 77 Processing helix chain 'K' and resid 81 through 100 Processing helix chain 'K' and resid 101 through 124 removed outlier: 3.540A pdb=" N ILE K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA K 122 " --> pdb=" O GLU K 118 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.758A pdb=" N ARG K 131 " --> pdb=" O GLU K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 140 removed outlier: 3.714A pdb=" N LYS K 138 " --> pdb=" O GLN K 135 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP K 139 " --> pdb=" O GLY K 136 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA K 140 " --> pdb=" O LYS K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 153 Processing helix chain 'K' and resid 171 through 179 removed outlier: 3.642A pdb=" N ASP K 179 " --> pdb=" O TRP K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 201 Processing helix chain 'K' and resid 244 through 252 removed outlier: 3.511A pdb=" N ALA K 248 " --> pdb=" O SER K 244 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 258 removed outlier: 4.096A pdb=" N ASN K 258 " --> pdb=" O ASN K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 286 removed outlier: 4.032A pdb=" N GLY K 281 " --> pdb=" O SER K 277 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL K 283 " --> pdb=" O THR K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 297 removed outlier: 3.600A pdb=" N ILE K 295 " --> pdb=" O PHE K 291 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS K 297 " --> pdb=" O GLU K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 324 removed outlier: 3.677A pdb=" N ASN K 315 " --> pdb=" O ASP K 311 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN K 324 " --> pdb=" O GLY K 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 344 Processing helix chain 'K' and resid 349 through 361 Processing helix chain 'K' and resid 372 through 375 Processing helix chain 'K' and resid 376 through 384 Processing helix chain 'L' and resid 11 through 24 removed outlier: 4.035A pdb=" N GLN L 24 " --> pdb=" O TYR L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 39 removed outlier: 3.905A pdb=" N GLY L 39 " --> pdb=" O GLY L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 56 removed outlier: 3.802A pdb=" N TYR L 56 " --> pdb=" O PHE L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 68 Processing helix chain 'L' and resid 71 through 77 Processing helix chain 'L' and resid 81 through 100 removed outlier: 4.137A pdb=" N ASP L 87 " --> pdb=" O GLU L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 105 Processing helix chain 'L' and resid 106 through 125 removed outlier: 4.258A pdb=" N LEU L 125 " --> pdb=" O LYS L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 4.395A pdb=" N GLN L 129 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 140 No H-bonds generated for 'chain 'L' and resid 138 through 140' Processing helix chain 'L' and resid 141 through 154 removed outlier: 3.807A pdb=" N GLU L 146 " --> pdb=" O LYS L 142 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE L 148 " --> pdb=" O HIS L 144 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER L 149 " --> pdb=" O LYS L 145 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU L 151 " --> pdb=" O LEU L 147 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE L 152 " --> pdb=" O ILE L 148 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER L 153 " --> pdb=" O SER L 149 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN L 154 " --> pdb=" O LYS L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 181 Processing helix chain 'L' and resid 198 through 202 removed outlier: 3.665A pdb=" N ASP L 202 " --> pdb=" O GLN L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 252 removed outlier: 4.239A pdb=" N ASP L 250 " --> pdb=" O SER L 246 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU L 251 " --> pdb=" O GLN L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 258 Processing helix chain 'L' and resid 282 through 287 removed outlier: 4.032A pdb=" N MET L 287 " --> pdb=" O TYR L 284 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 296 removed outlier: 3.638A pdb=" N SER L 296 " --> pdb=" O GLY L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 321 removed outlier: 3.629A pdb=" N GLY L 320 " --> pdb=" O ARG L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 324 No H-bonds generated for 'chain 'L' and resid 322 through 324' Processing helix chain 'L' and resid 336 through 345 removed outlier: 3.985A pdb=" N LYS L 345 " --> pdb=" O THR L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 349 through 361 removed outlier: 4.397A pdb=" N LEU L 358 " --> pdb=" O ALA L 354 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS L 359 " --> pdb=" O ILE L 355 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN L 360 " --> pdb=" O VAL L 356 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET L 361 " --> pdb=" O THR L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 371 through 375 removed outlier: 3.661A pdb=" N LYS L 374 " --> pdb=" O GLY L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 376 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 7.889A pdb=" N ILE A 331 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 164 removed outlier: 3.612A pdb=" N ILE A 164 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE A 185 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA4, first strand: chain 'A' and resid 204 through 206 removed outlier: 3.855A pdb=" N ALA A 204 " --> pdb=" O ARG L 206 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA L 204 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.586A pdb=" N TYR A 233 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 241 " --> pdb=" O TYR A 233 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.018A pdb=" N ILE B 331 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 30 Processing sheet with id=AA8, first strand: chain 'B' and resid 204 through 207 removed outlier: 4.303A pdb=" N ALA B 204 " --> pdb=" O ARG C 206 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 204 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=AB1, first strand: chain 'C' and resid 222 through 225 removed outlier: 4.067A pdb=" N THR C 166 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL C 28 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE C 165 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL C 30 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 301 " --> pdb=" O ASN C 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.588A pdb=" N ILE D 3 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 27 through 29 removed outlier: 6.435A pdb=" N ASN D 27 " --> pdb=" O ALA D 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 183 through 185 removed outlier: 3.894A pdb=" N ALA D 221 " --> pdb=" O GLN D 183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 188 through 189 removed outlier: 3.902A pdb=" N GLN D 195 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 204 through 207 Processing sheet with id=AB7, first strand: chain 'D' and resid 232 through 234 Processing sheet with id=AB8, first strand: chain 'D' and resid 329 through 332 Processing sheet with id=AB9, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.876A pdb=" N TYR E 4 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 302 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL E 330 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE E 304 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 29 through 32 Processing sheet with id=AC2, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.570A pdb=" N ASN F 8 " --> pdb=" O GLN F 5 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 222 through 225 removed outlier: 3.681A pdb=" N THR F 166 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN F 27 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N PHE F 303 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY F 29 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASN F 305 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU F 31 " --> pdb=" O ASN F 305 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR F 300 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N VAL F 330 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU F 302 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TYR F 332 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE F 304 " --> pdb=" O TYR F 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 206 through 207 removed outlier: 4.268A pdb=" N ARG F 206 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA G 204 " --> pdb=" O ARG F 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 222 through 225 removed outlier: 6.664A pdb=" N ILE G 164 " --> pdb=" O TYR G 224 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL G 28 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE G 165 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL G 30 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN G 305 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR G 300 " --> pdb=" O HIS G 328 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL G 330 " --> pdb=" O THR G 300 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU G 302 " --> pdb=" O VAL G 330 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N TYR G 332 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE G 304 " --> pdb=" O TYR G 332 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL G 329 " --> pdb=" O THR G 367 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL G 369 " --> pdb=" O VAL G 329 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE G 331 " --> pdb=" O VAL G 369 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 188 through 189 removed outlier: 3.728A pdb=" N GLN G 195 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 222 through 225 removed outlier: 5.460A pdb=" N LEU H 31 " --> pdb=" O ASN H 305 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL H 330 " --> pdb=" O LEU H 302 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 204 through 207 removed outlier: 3.983A pdb=" N ALA H 204 " --> pdb=" O ARG I 206 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG I 206 " --> pdb=" O ALA H 204 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA I 204 " --> pdb=" O ARG H 206 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 27 through 28 removed outlier: 7.021A pdb=" N ASN I 27 " --> pdb=" O ALA I 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 163 through 166 removed outlier: 5.874A pdb=" N PHE I 185 " --> pdb=" O LEU I 223 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS I 225 " --> pdb=" O PHE I 185 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 188 through 189 removed outlier: 3.664A pdb=" N SER I 189 " --> pdb=" O GLN I 195 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN I 195 " --> pdb=" O SER I 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 329 through 332 removed outlier: 6.487A pdb=" N VAL I 329 " --> pdb=" O THR I 367 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL I 369 " --> pdb=" O VAL I 329 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE I 331 " --> pdb=" O VAL I 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'J' and resid 222 through 225 removed outlier: 3.613A pdb=" N ILE J 164 " --> pdb=" O TYR J 222 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR J 224 " --> pdb=" O ILE J 164 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR J 166 " --> pdb=" O TYR J 224 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU J 32 " --> pdb=" O PHE J 165 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASN J 305 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU J 31 " --> pdb=" O ASN J 305 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 205 through 207 removed outlier: 3.575A pdb=" N ARG J 206 " --> pdb=" O ALA K 204 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA K 204 " --> pdb=" O ARG J 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 329 through 331 removed outlier: 3.994A pdb=" N THR J 367 " --> pdb=" O VAL J 329 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE J 331 " --> pdb=" O THR J 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'K' and resid 8 through 9 removed outlier: 4.094A pdb=" N THR K 367 " --> pdb=" O VAL K 329 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL K 369 " --> pdb=" O ILE K 331 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.140A pdb=" N VAL K 30 " --> pdb=" O PHE K 165 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR K 166 " --> pdb=" O TYR K 224 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 188 through 189 Processing sheet with id=AE1, first strand: chain 'L' and resid 8 through 10 removed outlier: 3.692A pdb=" N ASN L 8 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE L 3 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL L 329 " --> pdb=" O THR L 367 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU L 302 " --> pdb=" O HIS L 328 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL L 330 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE L 304 " --> pdb=" O VAL L 330 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY L 29 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL L 30 " --> pdb=" O PHE L 165 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 184 through 185 Processing sheet with id=AE3, first strand: chain 'L' and resid 188 through 189 1434 hydrogen bonds defined for protein. 4014 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.13 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6293 1.31 - 1.44: 11125 1.44 - 1.56: 21227 1.56 - 1.69: 115 1.69 - 1.82: 108 Bond restraints: 38868 Sorted by residual: bond pdb=" C2D NAD J 501 " pdb=" C3D NAD J 501 " ideal model delta sigma weight residual 1.531 1.286 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C2D NAD D 501 " pdb=" C3D NAD D 501 " ideal model delta sigma weight residual 1.531 1.287 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C2D NAD F 501 " pdb=" C3D NAD F 501 " ideal model delta sigma weight residual 1.531 1.287 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C2D NAD A 501 " pdb=" C3D NAD A 501 " ideal model delta sigma weight residual 1.531 1.287 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C2D NAD K 501 " pdb=" C3D NAD K 501 " ideal model delta sigma weight residual 1.531 1.288 0.243 2.00e-02 2.50e+03 1.48e+02 ... (remaining 38863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 52408 4.33 - 8.65: 142 8.65 - 12.98: 38 12.98 - 17.30: 10 17.30 - 21.63: 24 Bond angle restraints: 52622 Sorted by residual: angle pdb=" N1N NAD E 501 " pdb=" C1D NAD E 501 " pdb=" O4D NAD E 501 " ideal model delta sigma weight residual 110.88 89.25 21.63 3.00e+00 1.11e-01 5.20e+01 angle pdb=" N1N NAD L 501 " pdb=" C1D NAD L 501 " pdb=" O4D NAD L 501 " ideal model delta sigma weight residual 110.88 89.33 21.55 3.00e+00 1.11e-01 5.16e+01 angle pdb=" N1N NAD B 501 " pdb=" C1D NAD B 501 " pdb=" O4D NAD B 501 " ideal model delta sigma weight residual 110.88 89.77 21.11 3.00e+00 1.11e-01 4.95e+01 angle pdb=" N1N NAD J 501 " pdb=" C1D NAD J 501 " pdb=" O4D NAD J 501 " ideal model delta sigma weight residual 110.88 89.88 21.00 3.00e+00 1.11e-01 4.90e+01 angle pdb=" C2D NAD D 501 " pdb=" C1D NAD D 501 " pdb=" N1N NAD D 501 " ideal model delta sigma weight residual 110.95 131.82 -20.87 3.00e+00 1.11e-01 4.84e+01 ... (remaining 52617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 22420 35.61 - 71.22: 497 71.22 - 106.83: 73 106.83 - 142.44: 45 142.44 - 178.05: 61 Dihedral angle restraints: 23096 sinusoidal: 9578 harmonic: 13518 Sorted by residual: dihedral pdb=" CA TYR F 263 " pdb=" C TYR F 263 " pdb=" N ARG F 264 " pdb=" CA ARG F 264 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA GLY B 228 " pdb=" C GLY B 228 " pdb=" N SER B 229 " pdb=" CA SER B 229 " ideal model delta harmonic sigma weight residual 180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" O3B NAD J 501 " pdb=" C3B NAD J 501 " pdb=" C4B NAD J 501 " pdb=" O4B NAD J 501 " ideal model delta sinusoidal sigma weight residual -86.01 92.04 -178.05 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 23093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.090: 5575 1.090 - 2.180: 0 2.180 - 3.269: 0 3.269 - 4.359: 0 4.359 - 5.449: 35 Chirality restraints: 5610 Sorted by residual: chirality pdb=" C4D NAD F 501 " pdb=" C3D NAD F 501 " pdb=" C5D NAD F 501 " pdb=" O4D NAD F 501 " both_signs ideal model delta sigma weight residual False -2.48 2.97 -5.45 2.00e-01 2.50e+01 7.42e+02 chirality pdb=" C4D NAD G 501 " pdb=" C3D NAD G 501 " pdb=" C5D NAD G 501 " pdb=" O4D NAD G 501 " both_signs ideal model delta sigma weight residual False -2.48 2.95 -5.43 2.00e-01 2.50e+01 7.36e+02 chirality pdb=" C4D NAD E 501 " pdb=" C3D NAD E 501 " pdb=" C5D NAD E 501 " pdb=" O4D NAD E 501 " both_signs ideal model delta sigma weight residual False -2.48 2.95 -5.42 2.00e-01 2.50e+01 7.35e+02 ... (remaining 5607 not shown) Planarity restraints: 6748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR K 270 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.94e+00 pdb=" N PRO K 271 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO K 271 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO K 271 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 161 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO L 162 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO L 162 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 162 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 145 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C LYS D 145 " 0.027 2.00e-02 2.50e+03 pdb=" O LYS D 145 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU D 146 " -0.009 2.00e-02 2.50e+03 ... (remaining 6745 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 281 2.48 - 3.08: 27576 3.08 - 3.69: 54308 3.69 - 4.29: 77311 4.29 - 4.90: 126118 Nonbonded interactions: 285594 Sorted by model distance: nonbonded pdb=" O ASP I 87 " pdb=" OG1 THR I 90 " model vdw 1.874 3.040 nonbonded pdb=" OG1 THR K 120 " pdb=" OH TYR K 270 " model vdw 1.911 3.040 nonbonded pdb=" O TYR J 270 " pdb=" O2D NAD J 501 " model vdw 1.933 3.040 nonbonded pdb=" OG SER F 37 " pdb=" OD2 ASP F 170 " model vdw 1.958 3.040 nonbonded pdb=" O TYR F 276 " pdb=" OG1 THR F 279 " model vdw 1.966 3.040 ... (remaining 285589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 208 or resid 218 through 229 or resid 231 throug \ h 348 or resid 350 through 387 or resid 501)) selection = (chain 'B' and (resid 2 through 348 or resid 350 through 387 or resid 501)) selection = (chain 'C' and (resid 2 through 208 or resid 218 through 229 or resid 231 throug \ h 348 or resid 350 through 387 or resid 501)) selection = (chain 'D' and (resid 2 through 208 or resid 218 through 229 or resid 231 throug \ h 348 or resid 350 through 387 or resid 501)) selection = (chain 'E' and (resid 2 through 208 or resid 218 through 229 or resid 231 throug \ h 348 or resid 350 through 387 or resid 501)) selection = (chain 'F' and (resid 2 through 208 or resid 218 through 229 or resid 231 throug \ h 348 or resid 350 through 387 or resid 501)) selection = (chain 'G' and (resid 2 through 208 or resid 218 through 229 or resid 231 throug \ h 348 or resid 350 through 387 or resid 501)) selection = (chain 'H' and (resid 2 through 208 or resid 218 through 229 or resid 231 throug \ h 348 or resid 350 through 387 or resid 501)) selection = (chain 'I' and (resid 2 through 208 or resid 218 through 229 or resid 231 throug \ h 387 or resid 501)) selection = (chain 'J' and (resid 2 through 208 or resid 218 through 229 or resid 231 throug \ h 348 or resid 350 through 387 or resid 501)) selection = (chain 'K' and (resid 2 through 208 or resid 218 through 229 or resid 231 throug \ h 348 or resid 350 through 387 or resid 501)) selection = (chain 'L' and (resid 2 through 208 or resid 218 through 229 or resid 231 throug \ h 348 or resid 350 through 387 or resid 501)) } 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 group one per residue 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: 32.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.540 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 34.410 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3652 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 : 0.009 0.245 38874 Z= 0.443 Angle : 0.810 21.629 52622 Z= 0.339 Chirality : 0.416 5.449 5610 Planarity : 0.003 0.070 6748 Dihedral : 20.243 178.048 14500 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: -0.92 (0.13), residues: 4618 helix: 0.44 (0.12), residues: 2081 sheet: -0.13 (0.35), residues: 276 loop : -1.71 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 316 TYR 0.014 0.001 TYR E 252 PHE 0.019 0.001 PHE G 188 TRP 0.010 0.001 TRP J 232 HIS 0.006 0.001 HIS L 278 Details of bonding type rmsd covalent geometry : bond 0.00887 (38868) covalent geometry : angle 0.81009 (52622) hydrogen bonds : bond 0.17187 ( 1434) hydrogen bonds : angle 6.34179 ( 4014) Misc. bond : bond 0.00175 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.3911 (mp0) cc_final: 0.2228 (tp30) REVERT: F 45 MET cc_start: 0.4054 (mmt) cc_final: 0.3636 (mmt) REVERT: F 81 ASN cc_start: 0.5398 (t0) cc_final: 0.5063 (t0) REVERT: J 97 LYS cc_start: 0.7832 (tttm) cc_final: 0.6772 (pptt) REVERT: J 125 LEU cc_start: 0.3721 (mt) cc_final: 0.3306 (tt) REVERT: K 45 MET cc_start: 0.1458 (mmm) cc_final: 0.1217 (mmt) REVERT: K 359 LYS cc_start: 0.3853 (tmtt) cc_final: 0.3012 (mmmt) REVERT: L 263 TYR cc_start: 0.2826 (t80) cc_final: 0.1997 (t80) outliers start: 0 outliers final: 0 residues processed: 679 average time/residue: 0.2343 time to fit residues: 258.6215 Evaluate side-chains 327 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.0670 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 6.9990 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS B 18 HIS B 154 ASN C 135 GLN C 247 GLN D 278 HIS ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 GLN F 18 HIS F 27 ASN F 144 HIS ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS G 315 ASN ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN H 258 ASN I 200 ASN I 266 GLN ** J 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN ** K 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 HIS ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5476 r_free = 0.5476 target = 0.231707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.204141 restraints weight = 106591.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5176 r_free = 0.5176 target = 0.207312 restraints weight = 74748.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5215 r_free = 0.5215 target = 0.209529 restraints weight = 54611.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5219 r_free = 0.5219 target = 0.209927 restraints weight = 46088.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5221 r_free = 0.5221 target = 0.210197 restraints weight = 39912.915| |-----------------------------------------------------------------------------| r_work (final): 0.5210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4370 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 38874 Z= 0.196 Angle : 0.754 14.297 52622 Z= 0.376 Chirality : 0.047 0.717 5610 Planarity : 0.005 0.078 6748 Dihedral : 14.151 87.895 5734 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.66 % Allowed : 9.02 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: -1.20 (0.12), residues: 4618 helix: 0.01 (0.11), residues: 2156 sheet: -0.51 (0.33), residues: 280 loop : -1.65 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 155 TYR 0.038 0.002 TYR G 263 PHE 0.027 0.003 PHE F 327 TRP 0.034 0.002 TRP G 232 HIS 0.020 0.002 HIS K 227 Details of bonding type rmsd covalent geometry : bond 0.00437 (38868) covalent geometry : angle 0.75409 (52622) hydrogen bonds : bond 0.04357 ( 1434) hydrogen bonds : angle 5.27662 ( 4014) Misc. bond : bond 0.00683 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 371 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7223 (pm20) cc_final: 0.6939 (mp0) REVERT: B 174 GLU cc_start: 0.4710 (mp0) cc_final: 0.3426 (tp30) REVERT: B 358 LEU cc_start: 0.5918 (mt) cc_final: 0.5688 (tp) REVERT: C 45 MET cc_start: 0.6304 (tpt) cc_final: 0.5057 (tpp) REVERT: C 380 PHE cc_start: 0.3184 (t80) cc_final: 0.2822 (t80) REVERT: E 88 GLU cc_start: 0.6616 (mm-30) cc_final: 0.5796 (mm-30) REVERT: F 361 MET cc_start: 0.2878 (ttm) cc_final: 0.2538 (tpt) REVERT: F 377 PHE cc_start: 0.4907 (OUTLIER) cc_final: 0.4592 (t80) REVERT: H 63 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6633 (mm) REVERT: H 254 ASN cc_start: 0.3900 (m-40) cc_final: 0.3617 (m110) REVERT: J 97 LYS cc_start: 0.7984 (tttm) cc_final: 0.6769 (pptt) REVERT: J 125 LEU cc_start: 0.3822 (mt) cc_final: 0.3276 (tt) REVERT: J 263 TYR cc_start: 0.3116 (t80) cc_final: 0.2503 (t80) REVERT: K 255 ASP cc_start: 0.6217 (t0) cc_final: 0.5413 (m-30) REVERT: K 359 LYS cc_start: 0.3995 (tmtt) cc_final: 0.3254 (mttt) REVERT: L 263 TYR cc_start: 0.2676 (t80) cc_final: 0.1663 (t80) outliers start: 66 outliers final: 33 residues processed: 414 average time/residue: 0.2189 time to fit residues: 151.9713 Evaluate side-chains 333 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 278 HIS Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 98 THR Chi-restraints excluded: chain J residue 143 TYR Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 267 HIS Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 182 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 106 optimal weight: 10.0000 chunk 348 optimal weight: 30.0000 chunk 269 optimal weight: 7.9990 chunk 421 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 242 optimal weight: 0.0970 chunk 103 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 31 optimal weight: 0.0770 chunk 264 optimal weight: 20.0000 overall best weight: 2.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS B 254 ASN D 18 HIS D 195 GLN D 278 HIS ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN J 218 HIS J 220 HIS ** J 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5545 r_free = 0.5545 target = 0.233437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5285 r_free = 0.5285 target = 0.210656 restraints weight = 108565.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5271 r_free = 0.5271 target = 0.211627 restraints weight = 85947.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5278 r_free = 0.5278 target = 0.212337 restraints weight = 73331.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5288 r_free = 0.5288 target = 0.212897 restraints weight = 64382.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.213102 restraints weight = 60846.081| |-----------------------------------------------------------------------------| r_work (final): 0.5308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4304 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38874 Z= 0.142 Angle : 0.620 14.667 52622 Z= 0.315 Chirality : 0.043 0.624 5610 Planarity : 0.004 0.080 6748 Dihedral : 12.322 89.491 5734 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.73 % Allowed : 11.35 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: -1.12 (0.12), residues: 4618 helix: 0.11 (0.11), residues: 2162 sheet: -0.34 (0.34), residues: 271 loop : -1.67 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 131 TYR 0.032 0.002 TYR L 116 PHE 0.025 0.002 PHE A 108 TRP 0.018 0.001 TRP G 232 HIS 0.021 0.001 HIS D 278 Details of bonding type rmsd covalent geometry : bond 0.00317 (38868) covalent geometry : angle 0.62031 (52622) hydrogen bonds : bond 0.03740 ( 1434) hydrogen bonds : angle 4.96638 ( 4014) Misc. bond : bond 0.00539 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 327 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.6532 (pm20) cc_final: 0.6139 (pm20) REVERT: A 264 ARG cc_start: 0.5036 (tpp-160) cc_final: 0.3259 (ptt90) REVERT: B 174 GLU cc_start: 0.4157 (mp0) cc_final: 0.3418 (tp30) REVERT: B 268 LEU cc_start: 0.5685 (OUTLIER) cc_final: 0.5153 (pp) REVERT: B 358 LEU cc_start: 0.5543 (mt) cc_final: 0.5340 (mt) REVERT: C 45 MET cc_start: 0.6124 (tpt) cc_final: 0.4873 (tpp) REVERT: C 380 PHE cc_start: 0.3026 (t80) cc_final: 0.2656 (t80) REVERT: E 267 HIS cc_start: 0.5168 (OUTLIER) cc_final: 0.4383 (t70) REVERT: F 194 ARG cc_start: 0.2516 (mtp85) cc_final: 0.0290 (ptp-170) REVERT: F 377 PHE cc_start: 0.5228 (OUTLIER) cc_final: 0.4834 (t80) REVERT: H 63 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6364 (mm) REVERT: H 254 ASN cc_start: 0.3751 (m-40) cc_final: 0.3399 (m110) REVERT: H 282 PHE cc_start: -0.0971 (OUTLIER) cc_final: -0.1334 (m-10) REVERT: J 97 LYS cc_start: 0.7992 (tttm) cc_final: 0.6946 (pttp) REVERT: J 125 LEU cc_start: 0.3953 (mt) cc_final: 0.3219 (tt) REVERT: J 263 TYR cc_start: 0.3109 (t80) cc_final: 0.2493 (t80) REVERT: K 255 ASP cc_start: 0.6069 (t0) cc_final: 0.5314 (m-30) REVERT: K 359 LYS cc_start: 0.3950 (tmtt) cc_final: 0.3177 (mttt) REVERT: L 10 LEU cc_start: 0.4255 (OUTLIER) cc_final: 0.3810 (tt) REVERT: L 263 TYR cc_start: 0.2958 (t80) cc_final: 0.1893 (t80) outliers start: 69 outliers final: 37 residues processed: 376 average time/residue: 0.2154 time to fit residues: 137.9071 Evaluate side-chains 336 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 293 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 278 HIS Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 98 THR Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 143 TYR Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 278 HIS Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 267 HIS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 368 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 200 optimal weight: 0.9980 chunk 363 optimal weight: 20.0000 chunk 438 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 226 optimal weight: 6.9990 chunk 429 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN B 18 HIS B 134 ASN B 135 GLN D 235 ASN ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 HIS G 241 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN H 267 HIS K 218 HIS ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN L 218 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5437 r_free = 0.5437 target = 0.226788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.196862 restraints weight = 106928.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.5147 r_free = 0.5147 target = 0.200911 restraints weight = 73726.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.202855 restraints weight = 57203.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.202843 restraints weight = 43955.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.202915 restraints weight = 40558.212| |-----------------------------------------------------------------------------| r_work (final): 0.5141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4618 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 38874 Z= 0.186 Angle : 0.690 14.608 52622 Z= 0.355 Chirality : 0.045 0.625 5610 Planarity : 0.004 0.084 6748 Dihedral : 11.360 89.222 5734 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.38 % Favored : 92.59 % Rotamer: Outliers : 2.64 % Allowed : 13.74 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.12), residues: 4618 helix: -0.04 (0.11), residues: 2155 sheet: -0.67 (0.34), residues: 292 loop : -1.78 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 194 TYR 0.037 0.002 TYR L 116 PHE 0.032 0.002 PHE H 291 TRP 0.036 0.002 TRP A 232 HIS 0.018 0.002 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00420 (38868) covalent geometry : angle 0.69037 (52622) hydrogen bonds : bond 0.03901 ( 1434) hydrogen bonds : angle 5.04146 ( 4014) Misc. bond : bond 0.00520 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 324 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ARG cc_start: 0.5083 (tpp-160) cc_final: 0.2796 (ptt90) REVERT: B 51 SER cc_start: 0.8353 (m) cc_final: 0.8140 (p) REVERT: B 169 TYR cc_start: 0.5826 (OUTLIER) cc_final: 0.5075 (m-80) REVERT: B 174 GLU cc_start: 0.4835 (mp0) cc_final: 0.4379 (mm-30) REVERT: B 183 GLN cc_start: 0.5352 (OUTLIER) cc_final: 0.4357 (mm110) REVERT: B 358 LEU cc_start: 0.5721 (mt) cc_final: 0.5416 (mt) REVERT: C 45 MET cc_start: 0.6274 (tpt) cc_final: 0.5795 (tpt) REVERT: C 227 HIS cc_start: 0.0812 (OUTLIER) cc_final: -0.0221 (m-70) REVERT: C 380 PHE cc_start: 0.3273 (t80) cc_final: 0.2944 (t80) REVERT: F 194 ARG cc_start: 0.2879 (mtp85) cc_final: 0.0716 (mtp85) REVERT: F 377 PHE cc_start: 0.5169 (OUTLIER) cc_final: 0.4527 (t80) REVERT: G 231 THR cc_start: 0.7320 (p) cc_final: 0.6972 (t) REVERT: G 312 TYR cc_start: 0.5487 (m-10) cc_final: 0.5282 (m-10) REVERT: H 63 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6725 (mm) REVERT: H 254 ASN cc_start: 0.4319 (m-40) cc_final: 0.3950 (m-40) REVERT: H 282 PHE cc_start: -0.0113 (OUTLIER) cc_final: -0.0693 (m-10) REVERT: J 97 LYS cc_start: 0.8098 (tttm) cc_final: 0.6951 (pttp) REVERT: J 263 TYR cc_start: 0.3005 (t80) cc_final: 0.2336 (t80) REVERT: K 23 CYS cc_start: 0.4872 (m) cc_final: 0.4417 (p) REVERT: K 255 ASP cc_start: 0.6366 (t0) cc_final: 0.5530 (m-30) REVERT: K 359 LYS cc_start: 0.3924 (tmtt) cc_final: 0.3260 (mttt) REVERT: L 263 TYR cc_start: 0.2938 (t80) cc_final: 0.1788 (t80) outliers start: 105 outliers final: 59 residues processed: 402 average time/residue: 0.2154 time to fit residues: 146.8436 Evaluate side-chains 351 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 286 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 278 HIS Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 309 PHE Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 361 MET Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 270 TYR Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain J residue 278 HIS Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 166 THR Chi-restraints excluded: chain K residue 267 HIS Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain L residue 239 THR Chi-restraints excluded: chain L residue 368 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 122 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 368 optimal weight: 5.9990 chunk 455 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 335 optimal weight: 10.0000 chunk 235 optimal weight: 30.0000 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 267 HIS ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS E 383 HIS G 27 ASN G 200 ASN G 299 GLN G 313 HIS H 18 HIS ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 HIS ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN L 313 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5376 r_free = 0.5376 target = 0.221670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.191434 restraints weight = 109418.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.195527 restraints weight = 76961.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5066 r_free = 0.5066 target = 0.196212 restraints weight = 57529.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.197044 restraints weight = 48800.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.5083 r_free = 0.5083 target = 0.197541 restraints weight = 44079.338| |-----------------------------------------------------------------------------| r_work (final): 0.5075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4749 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 38874 Z= 0.245 Angle : 0.758 15.124 52622 Z= 0.389 Chirality : 0.047 0.638 5610 Planarity : 0.005 0.090 6748 Dihedral : 11.218 87.893 5734 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.27 % Allowed : 16.08 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: -1.66 (0.12), residues: 4618 helix: -0.35 (0.11), residues: 2163 sheet: -0.84 (0.32), residues: 299 loop : -1.92 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 99 TYR 0.035 0.003 TYR E 252 PHE 0.044 0.003 PHE J 291 TRP 0.032 0.002 TRP A 232 HIS 0.035 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00533 (38868) covalent geometry : angle 0.75778 (52622) hydrogen bonds : bond 0.04287 ( 1434) hydrogen bonds : angle 5.29004 ( 4014) Misc. bond : bond 0.00466 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 308 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ARG cc_start: 0.5062 (tpp-160) cc_final: 0.2497 (ptt90) REVERT: B 51 SER cc_start: 0.8479 (m) cc_final: 0.8273 (p) REVERT: B 169 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.4905 (m-80) REVERT: B 174 GLU cc_start: 0.4960 (mp0) cc_final: 0.4452 (mm-30) REVERT: B 183 GLN cc_start: 0.5465 (OUTLIER) cc_final: 0.3817 (mm110) REVERT: B 358 LEU cc_start: 0.5842 (mt) cc_final: 0.5540 (mt) REVERT: C 45 MET cc_start: 0.6538 (tpt) cc_final: 0.6098 (tpt) REVERT: C 227 HIS cc_start: 0.1022 (OUTLIER) cc_final: -0.0011 (m-70) REVERT: D 386 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6553 (t80) REVERT: F 178 GLU cc_start: 0.4103 (OUTLIER) cc_final: 0.3866 (tt0) REVERT: F 194 ARG cc_start: 0.3120 (mtp85) cc_final: 0.0304 (ptp90) REVERT: F 377 PHE cc_start: 0.5206 (OUTLIER) cc_final: 0.4528 (t80) REVERT: G 231 THR cc_start: 0.7453 (p) cc_final: 0.7041 (t) REVERT: H 63 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6932 (mm) REVERT: H 98 THR cc_start: 0.4785 (m) cc_final: 0.4541 (p) REVERT: H 254 ASN cc_start: 0.3923 (m-40) cc_final: 0.3608 (m-40) REVERT: I 93 LEU cc_start: 0.7498 (tt) cc_final: 0.7261 (mm) REVERT: J 182 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6676 (mm) REVERT: J 263 TYR cc_start: 0.2921 (t80) cc_final: 0.2457 (t80) REVERT: K 23 CYS cc_start: 0.5413 (m) cc_final: 0.5012 (p) REVERT: K 232 TRP cc_start: 0.6385 (m-10) cc_final: 0.5854 (m-10) REVERT: K 255 ASP cc_start: 0.6472 (t0) cc_final: 0.5582 (m-30) REVERT: K 290 ARG cc_start: 0.6051 (tpt170) cc_final: 0.5800 (tmt-80) REVERT: L 263 TYR cc_start: 0.3012 (t80) cc_final: 0.1783 (t80) outliers start: 130 outliers final: 79 residues processed: 408 average time/residue: 0.2161 time to fit residues: 149.6243 Evaluate side-chains 370 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 283 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 386 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 278 HIS Chi-restraints excluded: chain F residue 377 PHE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 299 GLN Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 361 MET Chi-restraints excluded: chain I residue 254 ASN Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 270 TYR Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain I residue 305 ASN Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 250 ASP Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain K residue 267 HIS Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain L residue 239 THR Chi-restraints excluded: chain L residue 313 HIS Chi-restraints excluded: chain L residue 368 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 112 optimal weight: 10.0000 chunk 419 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 292 optimal weight: 0.6980 chunk 272 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 401 optimal weight: 3.9990 chunk 262 optimal weight: 8.9990 chunk 188 optimal weight: 40.0000 chunk 396 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 ASN E 72 GLN ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN I 200 ASN J 78 ASN K 144 HIS ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5389 r_free = 0.5389 target = 0.222979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.194619 restraints weight = 109674.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.196023 restraints weight = 87913.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5070 r_free = 0.5070 target = 0.197839 restraints weight = 66018.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5080 r_free = 0.5080 target = 0.198593 restraints weight = 53978.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5082 r_free = 0.5082 target = 0.198570 restraints weight = 49926.126| |-----------------------------------------------------------------------------| r_work (final): 0.5081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4703 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 38874 Z= 0.160 Angle : 0.656 14.633 52622 Z= 0.335 Chirality : 0.044 0.620 5610 Planarity : 0.004 0.089 6748 Dihedral : 10.843 88.607 5734 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.81 % Allowed : 17.99 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: -1.45 (0.12), residues: 4618 helix: -0.14 (0.11), residues: 2153 sheet: -0.86 (0.32), residues: 293 loop : -1.82 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 194 TYR 0.032 0.002 TYR B 332 PHE 0.031 0.002 PHE A 377 TRP 0.039 0.002 TRP G 232 HIS 0.026 0.002 HIS L 313 Details of bonding type rmsd covalent geometry : bond 0.00362 (38868) covalent geometry : angle 0.65572 (52622) hydrogen bonds : bond 0.03708 ( 1434) hydrogen bonds : angle 5.01332 ( 4014) Misc. bond : bond 0.00498 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 307 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ARG cc_start: 0.5157 (tpp-160) cc_final: 0.2431 (ptt90) REVERT: B 169 TYR cc_start: 0.5860 (OUTLIER) cc_final: 0.4846 (m-80) REVERT: B 174 GLU cc_start: 0.4884 (mp0) cc_final: 0.4462 (mm-30) REVERT: B 358 LEU cc_start: 0.5789 (mt) cc_final: 0.5566 (mt) REVERT: C 45 MET cc_start: 0.6729 (tpt) cc_final: 0.6520 (tpt) REVERT: C 227 HIS cc_start: 0.0920 (OUTLIER) cc_final: -0.0058 (m-70) REVERT: D 386 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6629 (t80) REVERT: E 222 TYR cc_start: -0.0688 (OUTLIER) cc_final: -0.2818 (m-80) REVERT: F 178 GLU cc_start: 0.4170 (OUTLIER) cc_final: 0.3954 (tt0) REVERT: F 194 ARG cc_start: 0.2922 (mtp85) cc_final: 0.0085 (ptp90) REVERT: G 231 THR cc_start: 0.7246 (p) cc_final: 0.6801 (t) REVERT: H 63 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6912 (mm) REVERT: H 254 ASN cc_start: 0.4049 (m-40) cc_final: 0.3691 (m-40) REVERT: I 93 LEU cc_start: 0.7369 (tt) cc_final: 0.7147 (mm) REVERT: I 116 TYR cc_start: 0.3235 (OUTLIER) cc_final: 0.2448 (m-80) REVERT: J 97 LYS cc_start: 0.8089 (tttm) cc_final: 0.7023 (pttp) REVERT: J 185 PHE cc_start: 0.6155 (OUTLIER) cc_final: 0.4634 (t80) REVERT: J 263 TYR cc_start: 0.2969 (t80) cc_final: 0.2208 (t80) REVERT: J 345 LYS cc_start: 0.6184 (pttm) cc_final: 0.5933 (pttp) REVERT: K 23 CYS cc_start: 0.5559 (m) cc_final: 0.5126 (p) REVERT: K 232 TRP cc_start: 0.6167 (m-10) cc_final: 0.5692 (m-10) REVERT: K 255 ASP cc_start: 0.6423 (t0) cc_final: 0.5494 (m-30) REVERT: K 264 ARG cc_start: 0.4567 (tpm170) cc_final: 0.4260 (tpm170) REVERT: K 359 LYS cc_start: 0.3903 (tmtt) cc_final: 0.3206 (mttt) REVERT: L 258 ASN cc_start: 0.7042 (m110) cc_final: 0.5818 (m-40) REVERT: L 263 TYR cc_start: 0.3121 (t80) cc_final: 0.1925 (t80) outliers start: 112 outliers final: 79 residues processed: 395 average time/residue: 0.2121 time to fit residues: 142.7105 Evaluate side-chains 368 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 281 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 386 TYR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 222 TYR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 278 HIS Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 263 TYR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 309 PHE Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 361 MET Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 116 TYR Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 250 ASP Chi-restraints excluded: chain J residue 278 HIS Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 256 ILE Chi-restraints excluded: chain K residue 260 ASP Chi-restraints excluded: chain K residue 267 HIS Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain L residue 218 HIS Chi-restraints excluded: chain L residue 239 THR Chi-restraints excluded: chain L residue 278 HIS Chi-restraints excluded: chain L residue 368 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 453 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 400 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 chunk 405 optimal weight: 0.0770 chunk 452 optimal weight: 0.8980 chunk 425 optimal weight: 0.0060 chunk 449 optimal weight: 6.9990 chunk 211 optimal weight: 0.3980 chunk 440 optimal weight: 3.9990 chunk 460 optimal weight: 6.9990 overall best weight: 0.8756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 HIS D 305 ASN G 299 GLN H 168 ASN H 195 GLN ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5425 r_free = 0.5425 target = 0.226756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.197455 restraints weight = 110016.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5149 r_free = 0.5149 target = 0.201715 restraints weight = 77256.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.202553 restraints weight = 57654.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.203297 restraints weight = 48965.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5162 r_free = 0.5162 target = 0.204114 restraints weight = 43854.420| |-----------------------------------------------------------------------------| r_work (final): 0.5165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4558 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 38874 Z= 0.110 Angle : 0.591 15.295 52622 Z= 0.299 Chirality : 0.042 0.570 5610 Planarity : 0.004 0.086 6748 Dihedral : 10.314 89.067 5734 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.46 % Favored : 94.52 % Rotamer: Outliers : 2.51 % Allowed : 18.61 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: -1.06 (0.13), residues: 4618 helix: 0.19 (0.11), residues: 2141 sheet: -0.73 (0.33), residues: 289 loop : -1.62 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 131 TYR 0.038 0.001 TYR D 332 PHE 0.026 0.001 PHE F 15 TRP 0.037 0.001 TRP A 232 HIS 0.061 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00238 (38868) covalent geometry : angle 0.59136 (52622) hydrogen bonds : bond 0.03168 ( 1434) hydrogen bonds : angle 4.66221 ( 4014) Misc. bond : bond 0.00519 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 310 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ARG cc_start: 0.4995 (tpp-160) cc_final: 0.2329 (ptt90) REVERT: B 93 LEU cc_start: 0.5069 (OUTLIER) cc_final: 0.4862 (tt) REVERT: B 116 TYR cc_start: 0.6335 (m-80) cc_final: 0.5997 (m-80) REVERT: B 174 GLU cc_start: 0.4548 (mp0) cc_final: 0.4332 (mm-30) REVERT: B 183 GLN cc_start: 0.5338 (OUTLIER) cc_final: 0.3430 (mm110) REVERT: C 45 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.6161 (tpt) REVERT: C 227 HIS cc_start: 0.0389 (OUTLIER) cc_final: -0.0452 (m-70) REVERT: D 332 TYR cc_start: 0.5055 (m-80) cc_final: 0.4444 (m-80) REVERT: E 222 TYR cc_start: -0.0761 (OUTLIER) cc_final: -0.2750 (m-80) REVERT: F 194 ARG cc_start: 0.3035 (mtp85) cc_final: 0.0029 (ptt-90) REVERT: H 63 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6760 (mm) REVERT: H 254 ASN cc_start: 0.3988 (m-40) cc_final: 0.3651 (m-40) REVERT: J 97 LYS cc_start: 0.8035 (tttm) cc_final: 0.7012 (pttp) REVERT: J 263 TYR cc_start: 0.2793 (t80) cc_final: 0.2155 (t80) REVERT: J 300 THR cc_start: 0.4156 (OUTLIER) cc_final: 0.3912 (p) REVERT: J 345 LYS cc_start: 0.5900 (pttm) cc_final: 0.5533 (pttp) REVERT: K 23 CYS cc_start: 0.5373 (m) cc_final: 0.5019 (p) REVERT: K 255 ASP cc_start: 0.6333 (t0) cc_final: 0.5345 (m-30) REVERT: K 264 ARG cc_start: 0.4377 (tpm170) cc_final: 0.4048 (tpm170) REVERT: L 263 TYR cc_start: 0.3244 (t80) cc_final: 0.2037 (t80) outliers start: 100 outliers final: 67 residues processed: 385 average time/residue: 0.2140 time to fit residues: 139.2411 Evaluate side-chains 351 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 277 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 222 TYR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 278 HIS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 267 HIS Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 309 PHE Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 250 ASP Chi-restraints excluded: chain J residue 278 HIS Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 260 ASP Chi-restraints excluded: chain K residue 267 HIS Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 218 HIS Chi-restraints excluded: chain L residue 239 THR Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 278 HIS Chi-restraints excluded: chain L residue 368 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 436 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 451 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 376 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 345 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5415 r_free = 0.5415 target = 0.223496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.192744 restraints weight = 107987.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.5087 r_free = 0.5087 target = 0.195758 restraints weight = 72155.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.197483 restraints weight = 54949.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.199236 restraints weight = 46111.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.199936 restraints weight = 40783.207| |-----------------------------------------------------------------------------| r_work (final): 0.5129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4696 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 38874 Z= 0.178 Angle : 0.671 15.834 52622 Z= 0.342 Chirality : 0.044 0.595 5610 Planarity : 0.004 0.093 6748 Dihedral : 10.390 89.126 5734 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.47 % Favored : 92.51 % Rotamer: Outliers : 2.84 % Allowed : 18.94 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: -1.25 (0.12), residues: 4618 helix: 0.07 (0.11), residues: 2143 sheet: -1.00 (0.32), residues: 299 loop : -1.72 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 194 TYR 0.047 0.002 TYR D 332 PHE 0.034 0.002 PHE A 377 TRP 0.037 0.002 TRP G 232 HIS 0.015 0.001 HIS L 278 Details of bonding type rmsd covalent geometry : bond 0.00401 (38868) covalent geometry : angle 0.67147 (52622) hydrogen bonds : bond 0.03649 ( 1434) hydrogen bonds : angle 4.89752 ( 4014) Misc. bond : bond 0.00466 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 289 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ARG cc_start: 0.5131 (tpp-160) cc_final: 0.2401 (ptt90) REVERT: B 169 TYR cc_start: 0.5801 (OUTLIER) cc_final: 0.4889 (m-80) REVERT: B 174 GLU cc_start: 0.4963 (mp0) cc_final: 0.4471 (mm-30) REVERT: B 183 GLN cc_start: 0.5427 (OUTLIER) cc_final: 0.3698 (mm110) REVERT: C 45 MET cc_start: 0.6600 (OUTLIER) cc_final: 0.6205 (tpt) REVERT: C 227 HIS cc_start: 0.0866 (OUTLIER) cc_final: -0.0073 (m-70) REVERT: D 386 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.5443 (t80) REVERT: E 222 TYR cc_start: -0.0539 (OUTLIER) cc_final: -0.2591 (m-80) REVERT: F 194 ARG cc_start: 0.3104 (mtp85) cc_final: 0.0274 (ptp90) REVERT: G 231 THR cc_start: 0.7149 (p) cc_final: 0.6731 (t) REVERT: H 63 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6691 (mm) REVERT: I 116 TYR cc_start: 0.3704 (OUTLIER) cc_final: 0.2761 (m-80) REVERT: J 97 LYS cc_start: 0.8104 (tttm) cc_final: 0.7078 (pttp) REVERT: J 263 TYR cc_start: 0.2956 (t80) cc_final: 0.2226 (t80) REVERT: J 300 THR cc_start: 0.4598 (OUTLIER) cc_final: 0.4275 (p) REVERT: J 345 LYS cc_start: 0.5765 (pttm) cc_final: 0.5440 (pttp) REVERT: K 23 CYS cc_start: 0.5514 (m) cc_final: 0.5163 (p) REVERT: K 232 TRP cc_start: 0.6270 (m-10) cc_final: 0.5668 (m-10) REVERT: K 255 ASP cc_start: 0.6426 (t0) cc_final: 0.5447 (m-30) REVERT: K 264 ARG cc_start: 0.4673 (tpt170) cc_final: 0.4320 (tpm170) REVERT: L 263 TYR cc_start: 0.3354 (t80) cc_final: 0.2964 (t80) outliers start: 113 outliers final: 79 residues processed: 373 average time/residue: 0.2098 time to fit residues: 132.9802 Evaluate side-chains 361 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 273 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 386 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 222 TYR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 278 HIS Chi-restraints excluded: chain F residue 288 PHE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 263 TYR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 267 HIS Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 309 PHE Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 116 TYR Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 224 TYR Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 250 ASP Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain K residue 18 HIS Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 260 ASP Chi-restraints excluded: chain K residue 267 HIS Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain L residue 218 HIS Chi-restraints excluded: chain L residue 239 THR Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 278 HIS Chi-restraints excluded: chain L residue 368 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 324 optimal weight: 6.9990 chunk 402 optimal weight: 8.9990 chunk 115 optimal weight: 50.0000 chunk 124 optimal weight: 8.9990 chunk 396 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 412 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 239 optimal weight: 0.0050 chunk 59 optimal weight: 9.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 HIS ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5496 r_free = 0.5496 target = 0.227431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5225 r_free = 0.5225 target = 0.204733 restraints weight = 110752.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5213 r_free = 0.5213 target = 0.205296 restraints weight = 89409.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5213 r_free = 0.5213 target = 0.205356 restraints weight = 76941.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.5218 r_free = 0.5218 target = 0.205704 restraints weight = 73894.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5221 r_free = 0.5221 target = 0.205848 restraints weight = 71008.203| |-----------------------------------------------------------------------------| r_work (final): 0.5248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4542 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38874 Z= 0.127 Angle : 0.614 15.334 52622 Z= 0.310 Chirality : 0.042 0.571 5610 Planarity : 0.004 0.091 6748 Dihedral : 10.130 89.165 5734 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.04 % Favored : 93.94 % Rotamer: Outliers : 2.36 % Allowed : 19.59 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.10 (0.12), residues: 4618 helix: 0.22 (0.11), residues: 2128 sheet: -0.94 (0.32), residues: 297 loop : -1.65 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 16 TYR 0.045 0.002 TYR D 332 PHE 0.022 0.001 PHE L 188 TRP 0.033 0.001 TRP A 232 HIS 0.027 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00283 (38868) covalent geometry : angle 0.61446 (52622) hydrogen bonds : bond 0.03239 ( 1434) hydrogen bonds : angle 4.71775 ( 4014) Misc. bond : bond 0.00497 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 290 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ARG cc_start: 0.5364 (tpp-160) cc_final: 0.2715 (ptt90) REVERT: B 174 GLU cc_start: 0.4446 (mp0) cc_final: 0.4233 (mm-30) REVERT: B 183 GLN cc_start: 0.5472 (OUTLIER) cc_final: 0.3859 (mm110) REVERT: C 227 HIS cc_start: 0.1136 (OUTLIER) cc_final: 0.0123 (m-70) REVERT: D 173 LEU cc_start: 0.4506 (OUTLIER) cc_final: 0.4243 (tp) REVERT: D 386 TYR cc_start: 0.6272 (OUTLIER) cc_final: 0.5099 (t80) REVERT: E 91 LYS cc_start: 0.7043 (mttm) cc_final: 0.6409 (mttm) REVERT: E 222 TYR cc_start: -0.0400 (OUTLIER) cc_final: -0.2429 (m-80) REVERT: F 194 ARG cc_start: 0.3085 (mtp85) cc_final: 0.1921 (mtm180) REVERT: H 63 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6592 (mm) REVERT: I 107 GLU cc_start: 0.2456 (OUTLIER) cc_final: 0.1884 (tt0) REVERT: I 116 TYR cc_start: 0.3821 (OUTLIER) cc_final: 0.2741 (m-80) REVERT: J 97 LYS cc_start: 0.7981 (tttm) cc_final: 0.7194 (pttp) REVERT: J 263 TYR cc_start: 0.2989 (t80) cc_final: 0.2556 (t80) REVERT: J 300 THR cc_start: 0.4343 (OUTLIER) cc_final: 0.4127 (p) REVERT: K 23 CYS cc_start: 0.5654 (m) cc_final: 0.5270 (p) REVERT: K 232 TRP cc_start: 0.5897 (m-10) cc_final: 0.5285 (m-10) REVERT: K 255 ASP cc_start: 0.6223 (t0) cc_final: 0.5285 (m-30) REVERT: L 263 TYR cc_start: 0.3633 (t80) cc_final: 0.3259 (t80) outliers start: 94 outliers final: 75 residues processed: 360 average time/residue: 0.2148 time to fit residues: 130.7664 Evaluate side-chains 365 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 281 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 386 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 222 TYR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 278 HIS Chi-restraints excluded: chain F residue 288 PHE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 263 TYR Chi-restraints excluded: chain H residue 267 HIS Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 284 TYR Chi-restraints excluded: chain H residue 309 PHE Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 361 MET Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 116 TYR Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain J residue 143 TYR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 250 ASP Chi-restraints excluded: chain J residue 278 HIS Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 256 ILE Chi-restraints excluded: chain K residue 260 ASP Chi-restraints excluded: chain K residue 267 HIS Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain L residue 218 HIS Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 278 HIS Chi-restraints excluded: chain L residue 368 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 59 optimal weight: 6.9990 chunk 276 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 333 optimal weight: 5.9990 chunk 324 optimal weight: 0.0370 chunk 305 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 250 optimal weight: 0.0270 chunk 237 optimal weight: 10.0000 chunk 171 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 overall best weight: 1.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS B 328 HIS ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN F 315 ASN I 254 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5501 r_free = 0.5501 target = 0.227872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5227 r_free = 0.5227 target = 0.204649 restraints weight = 109347.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.206033 restraints weight = 87144.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5221 r_free = 0.5221 target = 0.205976 restraints weight = 70434.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.206325 restraints weight = 71552.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5231 r_free = 0.5231 target = 0.206551 restraints weight = 65936.162| |-----------------------------------------------------------------------------| r_work (final): 0.5260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4499 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38874 Z= 0.119 Angle : 0.607 15.315 52622 Z= 0.304 Chirality : 0.042 0.540 5610 Planarity : 0.004 0.091 6748 Dihedral : 9.902 88.266 5734 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.63 % Favored : 93.35 % Rotamer: Outliers : 2.21 % Allowed : 19.99 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4618 helix: 0.30 (0.11), residues: 2133 sheet: -0.88 (0.32), residues: 304 loop : -1.63 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 131 TYR 0.044 0.001 TYR E 284 PHE 0.036 0.001 PHE A 377 TRP 0.032 0.001 TRP A 232 HIS 0.013 0.001 HIS L 278 Details of bonding type rmsd covalent geometry : bond 0.00267 (38868) covalent geometry : angle 0.60702 (52622) hydrogen bonds : bond 0.03100 ( 1434) hydrogen bonds : angle 4.61775 ( 4014) Misc. bond : bond 0.00493 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 290 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ARG cc_start: 0.5333 (tpp-160) cc_final: 0.2701 (ptt90) REVERT: B 183 GLN cc_start: 0.5477 (OUTLIER) cc_final: 0.3729 (mm110) REVERT: B 197 TYR cc_start: 0.3899 (m-80) cc_final: 0.3170 (m-80) REVERT: D 173 LEU cc_start: 0.4170 (OUTLIER) cc_final: 0.3820 (tp) REVERT: D 386 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.5128 (t80) REVERT: E 222 TYR cc_start: -0.0388 (OUTLIER) cc_final: -0.2361 (m-80) REVERT: F 194 ARG cc_start: 0.3057 (mtp85) cc_final: 0.1779 (mtm180) REVERT: H 63 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6508 (mm) REVERT: H 254 ASN cc_start: 0.3865 (m-40) cc_final: 0.3553 (m-40) REVERT: I 107 GLU cc_start: 0.2524 (OUTLIER) cc_final: 0.2086 (tt0) REVERT: J 97 LYS cc_start: 0.7966 (tttm) cc_final: 0.7198 (pttp) REVERT: J 263 TYR cc_start: 0.2905 (t80) cc_final: 0.2556 (t80) REVERT: J 300 THR cc_start: 0.4530 (OUTLIER) cc_final: 0.4312 (p) REVERT: K 23 CYS cc_start: 0.5613 (m) cc_final: 0.5243 (p) REVERT: K 232 TRP cc_start: 0.5830 (m-10) cc_final: 0.5229 (m-10) REVERT: K 255 ASP cc_start: 0.6138 (t0) cc_final: 0.5201 (m-30) REVERT: K 264 ARG cc_start: 0.4581 (tpm170) cc_final: 0.4162 (tpp-160) REVERT: L 263 TYR cc_start: 0.3697 (t80) cc_final: 0.3289 (t80) REVERT: L 368 VAL cc_start: 0.7541 (OUTLIER) cc_final: 0.7275 (p) outliers start: 88 outliers final: 74 residues processed: 353 average time/residue: 0.2163 time to fit residues: 129.4035 Evaluate side-chains 351 residues out of total 3981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 269 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 143 TYR Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 267 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 386 TYR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 222 TYR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 278 HIS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 263 TYR Chi-restraints excluded: chain H residue 267 HIS Chi-restraints excluded: chain H residue 284 TYR Chi-restraints excluded: chain H residue 309 PHE Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 361 MET Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain J residue 143 TYR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 224 TYR Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 250 ASP Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 256 ILE Chi-restraints excluded: chain K residue 260 ASP Chi-restraints excluded: chain K residue 267 HIS Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain L residue 218 HIS Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 278 HIS Chi-restraints excluded: chain L residue 368 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 248 optimal weight: 8.9990 chunk 362 optimal weight: 6.9990 chunk 440 optimal weight: 0.0770 chunk 226 optimal weight: 0.0470 chunk 211 optimal weight: 0.8980 chunk 392 optimal weight: 0.0870 chunk 328 optimal weight: 0.0970 chunk 197 optimal weight: 7.9990 chunk 232 optimal weight: 40.0000 chunk 304 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 overall best weight: 0.2412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN E 135 GLN E 183 GLN ** E 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 ASN F 383 HIS H 254 ASN J 247 GLN L 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5531 r_free = 0.5531 target = 0.231130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5278 r_free = 0.5278 target = 0.208830 restraints weight = 109523.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5275 r_free = 0.5275 target = 0.210483 restraints weight = 85552.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5278 r_free = 0.5278 target = 0.210747 restraints weight = 71877.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5288 r_free = 0.5288 target = 0.211474 restraints weight = 63853.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.211728 restraints weight = 59919.438| |-----------------------------------------------------------------------------| r_work (final): 0.5322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4315 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 38874 Z= 0.104 Angle : 0.600 22.088 52622 Z= 0.297 Chirality : 0.041 0.507 5610 Planarity : 0.004 0.090 6748 Dihedral : 9.661 88.967 5734 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.92 % Favored : 95.06 % Rotamer: Outliers : 1.68 % Allowed : 20.67 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.80 (0.13), residues: 4618 helix: 0.46 (0.11), residues: 2129 sheet: -0.65 (0.32), residues: 303 loop : -1.52 (0.14), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 316 TYR 0.049 0.001 TYR E 284 PHE 0.022 0.001 PHE G 188 TRP 0.033 0.002 TRP G 232 HIS 0.015 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00221 (38868) covalent geometry : angle 0.60030 (52622) hydrogen bonds : bond 0.02974 ( 1434) hydrogen bonds : angle 4.46800 ( 4014) Misc. bond : bond 0.00518 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7810.52 seconds wall clock time: 135 minutes 46.16 seconds (8146.16 seconds total)