Starting phenix.real_space_refine on Mon Dec 22 20:12:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6evx_3962/12_2025/6evx_3962.cif Found real_map, /net/cci-nas-00/data/ceres_data/6evx_3962/12_2025/6evx_3962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6evx_3962/12_2025/6evx_3962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6evx_3962/12_2025/6evx_3962.map" model { file = "/net/cci-nas-00/data/ceres_data/6evx_3962/12_2025/6evx_3962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6evx_3962/12_2025/6evx_3962.cif" } resolution = 4.2 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= 0.010 sd= 0.040 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 6 5.21 5 S 276 5.16 5 C 25674 2.51 5 N 6978 2.21 5 O 7926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40896 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' MG': 1, 'GTP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GDP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GDP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GDP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' MG': 1, 'GTP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' MG': 1, 'GTP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, E, J, K, L, D, F, G, H, I Time building chain proxies: 7.48, per 1000 atoms: 0.18 Number of scatterers: 40896 At special positions: 0 Unit cell: (119.54, 173.75, 212.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 276 16.00 P 36 15.00 Mg 6 11.99 O 7926 8.00 N 6978 7.00 C 25674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 2.0 seconds 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9576 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 42 sheets defined 46.9% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'F' and resid 10 through 27 removed outlier: 3.668A pdb=" N GLN F 15 " --> pdb=" O GLN F 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY F 17 " --> pdb=" O GLY F 13 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.573A pdb=" N GLN F 43 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 44 " --> pdb=" O ASP F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 49 removed outlier: 3.655A pdb=" N VAL F 49 " --> pdb=" O ARG F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 46 through 49' Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 78 removed outlier: 3.760A pdb=" N ARG F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER F 78 " --> pdb=" O ASP F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 113 removed outlier: 3.528A pdb=" N VAL F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 127 removed outlier: 3.837A pdb=" N ASP F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER F 126 " --> pdb=" O LYS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 removed outlier: 4.199A pdb=" N GLY F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS F 154 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.637A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL F 193 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN F 195 " --> pdb=" O GLN F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 removed outlier: 3.631A pdb=" N ASP F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS F 211 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 237 removed outlier: 4.643A pdb=" N HIS F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 256 Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.654A pdb=" N GLN F 291 " --> pdb=" O PRO F 287 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN F 292 " --> pdb=" O GLU F 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET F 293 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 337 removed outlier: 4.321A pdb=" N GLN F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 390 removed outlier: 3.808A pdb=" N ILE F 381 " --> pdb=" O LEU F 377 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 390 " --> pdb=" O THR F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 401 removed outlier: 4.434A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 427 removed outlier: 3.873A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET F 415 " --> pdb=" O ALA F 411 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU F 421 " --> pdb=" O ASP F 417 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.559A pdb=" N ILE A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.693A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.895A pdb=" N LEU A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.523A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.326A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.511A pdb=" N ARG A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.556A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.750A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.662A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.559A pdb=" N ALA A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 removed outlier: 3.893A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.552A pdb=" N HIS A 309 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.526A pdb=" N ALA A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.820A pdb=" N LEU A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 437 removed outlier: 3.518A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 27 removed outlier: 3.667A pdb=" N GLN G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY G 17 " --> pdb=" O GLY G 13 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.572A pdb=" N GLN G 43 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 44 " --> pdb=" O ASP G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 49 removed outlier: 3.655A pdb=" N VAL G 49 " --> pdb=" O ARG G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 46 through 49' Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 78 removed outlier: 3.759A pdb=" N ARG G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER G 78 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.528A pdb=" N VAL G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 127 removed outlier: 3.838A pdb=" N ASP G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER G 126 " --> pdb=" O LYS G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 159 removed outlier: 4.199A pdb=" N GLY G 148 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS G 154 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU G 157 " --> pdb=" O SER G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 196 removed outlier: 3.637A pdb=" N SER G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 193 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU G 194 " --> pdb=" O HIS G 190 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN G 195 " --> pdb=" O GLN G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 214 removed outlier: 3.630A pdb=" N ASP G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 237 removed outlier: 4.643A pdb=" N HIS G 227 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR G 237 " --> pdb=" O MET G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 256 Processing helix chain 'G' and resid 285 through 294 removed outlier: 3.655A pdb=" N GLN G 291 " --> pdb=" O PRO G 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN G 292 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET G 293 " --> pdb=" O LEU G 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE G 294 " --> pdb=" O THR G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 337 removed outlier: 4.321A pdb=" N GLN G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN G 337 " --> pdb=" O VAL G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 390 removed outlier: 3.808A pdb=" N ILE G 381 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG G 390 " --> pdb=" O THR G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 401 removed outlier: 4.435A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 427 removed outlier: 3.873A pdb=" N PHE G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET G 415 " --> pdb=" O ALA G 411 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU G 421 " --> pdb=" O ASP G 417 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP G 427 " --> pdb=" O GLN G 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 27 removed outlier: 3.667A pdb=" N GLN D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.573A pdb=" N GLN D 43 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 44 " --> pdb=" O ASP D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 49 removed outlier: 3.655A pdb=" N VAL D 49 " --> pdb=" O ARG D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 49' Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 72 through 78 removed outlier: 3.759A pdb=" N ARG D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.528A pdb=" N VAL D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 127 removed outlier: 3.837A pdb=" N ASP D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 removed outlier: 4.199A pdb=" N GLY D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.636A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN D 195 " --> pdb=" O GLN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 removed outlier: 3.630A pdb=" N ASP D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 237 removed outlier: 4.643A pdb=" N HIS D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.655A pdb=" N GLN D 291 " --> pdb=" O PRO D 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 292 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 337 removed outlier: 4.321A pdb=" N GLN D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN D 337 " --> pdb=" O VAL D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.807A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 390 " --> pdb=" O THR D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 removed outlier: 4.434A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 427 removed outlier: 3.873A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 27 removed outlier: 3.667A pdb=" N GLN I 15 " --> pdb=" O GLN I 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY I 17 " --> pdb=" O GLY I 13 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.573A pdb=" N GLN I 43 " --> pdb=" O SER I 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU I 44 " --> pdb=" O ASP I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 49 removed outlier: 3.656A pdb=" N VAL I 49 " --> pdb=" O ARG I 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 46 through 49' Processing helix chain 'I' and resid 55 through 57 No H-bonds generated for 'chain 'I' and resid 55 through 57' Processing helix chain 'I' and resid 72 through 78 removed outlier: 3.760A pdb=" N ARG I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER I 78 " --> pdb=" O ASP I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 113 removed outlier: 3.528A pdb=" N VAL I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 127 removed outlier: 3.837A pdb=" N ASP I 118 " --> pdb=" O ASP I 114 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL I 119 " --> pdb=" O SER I 115 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 159 removed outlier: 4.200A pdb=" N GLY I 148 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS I 154 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU I 157 " --> pdb=" O SER I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.636A pdb=" N SER I 188 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL I 193 " --> pdb=" O VAL I 189 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN I 195 " --> pdb=" O GLN I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 removed outlier: 3.631A pdb=" N ASP I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS I 211 " --> pdb=" O LEU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 237 removed outlier: 4.643A pdb=" N HIS I 227 " --> pdb=" O GLY I 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU I 228 " --> pdb=" O ASP I 224 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 285 through 294 removed outlier: 3.655A pdb=" N GLN I 291 " --> pdb=" O PRO I 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET I 293 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE I 294 " --> pdb=" O THR I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 337 removed outlier: 4.321A pdb=" N GLN I 329 " --> pdb=" O GLU I 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN I 334 " --> pdb=" O MET I 330 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN I 337 " --> pdb=" O VAL I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 390 removed outlier: 3.807A pdb=" N ILE I 381 " --> pdb=" O LEU I 377 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG I 390 " --> pdb=" O THR I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 401 removed outlier: 4.433A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 427 removed outlier: 3.873A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET I 415 " --> pdb=" O ALA I 411 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU I 421 " --> pdb=" O ASP I 417 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 removed outlier: 3.667A pdb=" N GLN B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.572A pdb=" N GLN B 43 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 44 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.655A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 72 through 78 removed outlier: 3.760A pdb=" N ARG B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.528A pdb=" N VAL B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.837A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 4.199A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.636A pdb=" N SER B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.629A pdb=" N ASP B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 4.643A pdb=" N HIS B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.654A pdb=" N GLN B 291 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 337 removed outlier: 4.320A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.808A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 4.433A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.873A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 27 removed outlier: 3.667A pdb=" N GLN H 15 " --> pdb=" O GLN H 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY H 17 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.574A pdb=" N GLN H 43 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU H 44 " --> pdb=" O ASP H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 49 removed outlier: 3.654A pdb=" N VAL H 49 " --> pdb=" O ARG H 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 46 through 49' Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 78 removed outlier: 3.759A pdb=" N ARG H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 removed outlier: 3.528A pdb=" N VAL H 113 " --> pdb=" O GLY H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 127 removed outlier: 3.837A pdb=" N ASP H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER H 126 " --> pdb=" O LYS H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 159 removed outlier: 4.199A pdb=" N GLY H 148 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS H 154 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 196 removed outlier: 3.636A pdb=" N SER H 188 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL H 193 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN H 195 " --> pdb=" O GLN H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 removed outlier: 3.630A pdb=" N ASP H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS H 211 " --> pdb=" O LEU H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 237 removed outlier: 4.643A pdb=" N HIS H 227 " --> pdb=" O GLY H 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL H 229 " --> pdb=" O LEU H 225 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'H' and resid 285 through 294 removed outlier: 3.655A pdb=" N GLN H 291 " --> pdb=" O PRO H 287 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN H 292 " --> pdb=" O GLU H 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET H 293 " --> pdb=" O LEU H 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE H 294 " --> pdb=" O THR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 337 removed outlier: 4.321A pdb=" N GLN H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN H 337 " --> pdb=" O VAL H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 390 removed outlier: 3.807A pdb=" N ILE H 381 " --> pdb=" O LEU H 377 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG H 390 " --> pdb=" O THR H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 401 removed outlier: 4.434A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 427 removed outlier: 3.873A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET H 415 " --> pdb=" O ALA H 411 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU H 421 " --> pdb=" O ASP H 417 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP H 427 " --> pdb=" O GLN H 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 removed outlier: 3.559A pdb=" N ILE E 16 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 removed outlier: 3.693A pdb=" N GLU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.895A pdb=" N LEU E 119 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.523A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.327A pdb=" N ILE E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 removed outlier: 3.511A pdb=" N ARG E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 239 removed outlier: 3.556A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 244 removed outlier: 3.751A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 259 removed outlier: 3.662A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 297 removed outlier: 3.559A pdb=" N ALA E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS E 295 " --> pdb=" O ILE E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 301 removed outlier: 3.893A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 298 through 301' Processing helix chain 'E' and resid 306 through 310 removed outlier: 3.553A pdb=" N HIS E 309 " --> pdb=" O ASP E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.526A pdb=" N ALA E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.820A pdb=" N LEU E 397 " --> pdb=" O HIS E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 416 through 437 removed outlier: 3.518A pdb=" N GLU E 423 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 28 removed outlier: 3.559A pdb=" N ILE J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU J 23 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS J 28 " --> pdb=" O TYR J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 80 removed outlier: 3.693A pdb=" N GLU J 77 " --> pdb=" O THR J 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 Processing helix chain 'J' and resid 114 through 128 removed outlier: 3.895A pdb=" N LEU J 119 " --> pdb=" O ILE J 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP J 120 " --> pdb=" O ASP J 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG J 121 " --> pdb=" O LEU J 117 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 161 removed outlier: 4.523A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU J 155 " --> pdb=" O SER J 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER J 158 " --> pdb=" O MET J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 removed outlier: 4.327A pdb=" N ILE J 188 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR J 190 " --> pdb=" O ASN J 186 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 216 removed outlier: 3.511A pdb=" N ARG J 214 " --> pdb=" O TYR J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 239 removed outlier: 3.555A pdb=" N ARG J 229 " --> pdb=" O THR J 225 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE J 231 " --> pdb=" O LEU J 227 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN J 233 " --> pdb=" O ARG J 229 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 244 removed outlier: 3.750A pdb=" N ARG J 243 " --> pdb=" O THR J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 259 removed outlier: 3.662A pdb=" N PHE J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 297 removed outlier: 3.558A pdb=" N ALA J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS J 295 " --> pdb=" O ILE J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 301 removed outlier: 3.894A pdb=" N GLN J 301 " --> pdb=" O PRO J 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 298 through 301' Processing helix chain 'J' and resid 306 through 310 removed outlier: 3.552A pdb=" N HIS J 309 " --> pdb=" O ASP J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 337 removed outlier: 3.526A pdb=" N ALA J 333 " --> pdb=" O ASN J 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR J 334 " --> pdb=" O ALA J 330 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE J 335 " --> pdb=" O ALA J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 401 removed outlier: 3.820A pdb=" N LEU J 397 " --> pdb=" O HIS J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 410 Processing helix chain 'J' and resid 416 through 437 removed outlier: 3.519A pdb=" N GLU J 423 " --> pdb=" O SER J 419 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR J 432 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.560A pdb=" N ILE C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 removed outlier: 3.693A pdb=" N GLU C 77 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.895A pdb=" N LEU C 119 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.523A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 4.327A pdb=" N ILE C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 removed outlier: 3.511A pdb=" N ARG C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.556A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.750A pdb=" N ARG C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.662A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 removed outlier: 3.558A pdb=" N ALA C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 301 removed outlier: 3.893A pdb=" N GLN C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.552A pdb=" N HIS C 309 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 337 removed outlier: 3.526A pdb=" N ALA C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.819A pdb=" N LEU C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 437 removed outlier: 3.517A pdb=" N GLU C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 28 removed outlier: 3.560A pdb=" N ILE L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU L 23 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 80 removed outlier: 3.693A pdb=" N GLU L 77 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 108 Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.895A pdb=" N LEU L 119 " --> pdb=" O ILE L 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG L 121 " --> pdb=" O LEU L 117 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 161 removed outlier: 4.523A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU L 155 " --> pdb=" O SER L 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 removed outlier: 4.326A pdb=" N ILE L 188 " --> pdb=" O PRO L 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR L 190 " --> pdb=" O ASN L 186 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR L 193 " --> pdb=" O LEU L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 216 removed outlier: 3.512A pdb=" N ARG L 214 " --> pdb=" O TYR L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 239 removed outlier: 3.556A pdb=" N ARG L 229 " --> pdb=" O THR L 225 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE L 231 " --> pdb=" O LEU L 227 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN L 233 " --> pdb=" O ARG L 229 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 244 removed outlier: 3.751A pdb=" N ARG L 243 " --> pdb=" O THR L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 259 removed outlier: 3.662A pdb=" N PHE L 255 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 297 removed outlier: 3.558A pdb=" N ALA L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 301 removed outlier: 3.893A pdb=" N GLN L 301 " --> pdb=" O PRO L 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 298 through 301' Processing helix chain 'L' and resid 306 through 310 removed outlier: 3.552A pdb=" N HIS L 309 " --> pdb=" O ASP L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 337 removed outlier: 3.526A pdb=" N ALA L 333 " --> pdb=" O ASN L 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR L 334 " --> pdb=" O ALA L 330 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE L 335 " --> pdb=" O ALA L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 401 removed outlier: 3.820A pdb=" N LEU L 397 " --> pdb=" O HIS L 393 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 Processing helix chain 'L' and resid 416 through 437 removed outlier: 3.518A pdb=" N GLU L 423 " --> pdb=" O SER L 419 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR L 432 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU L 433 " --> pdb=" O GLU L 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 28 removed outlier: 3.559A pdb=" N ILE K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU K 23 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS K 28 " --> pdb=" O TYR K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 80 removed outlier: 3.692A pdb=" N GLU K 77 " --> pdb=" O THR K 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 108 Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.895A pdb=" N LEU K 119 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP K 120 " --> pdb=" O ASP K 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG K 121 " --> pdb=" O LEU K 117 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 161 removed outlier: 4.523A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER K 158 " --> pdb=" O MET K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 removed outlier: 4.326A pdb=" N ILE K 188 " --> pdb=" O PRO K 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR K 190 " --> pdb=" O ASN K 186 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 216 removed outlier: 3.511A pdb=" N ARG K 214 " --> pdb=" O TYR K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 239 removed outlier: 3.555A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE K 231 " --> pdb=" O LEU K 227 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 244 removed outlier: 3.751A pdb=" N ARG K 243 " --> pdb=" O THR K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 259 removed outlier: 3.663A pdb=" N PHE K 255 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 289 through 297 removed outlier: 3.559A pdb=" N ALA K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS K 295 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 301 removed outlier: 3.893A pdb=" N GLN K 301 " --> pdb=" O PRO K 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 298 through 301' Processing helix chain 'K' and resid 306 through 310 removed outlier: 3.553A pdb=" N HIS K 309 " --> pdb=" O ASP K 306 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 337 removed outlier: 3.527A pdb=" N ALA K 333 " --> pdb=" O ASN K 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR K 334 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 401 removed outlier: 3.820A pdb=" N LEU K 397 " --> pdb=" O HIS K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 416 through 437 removed outlier: 3.519A pdb=" N GLU K 423 " --> pdb=" O SER K 419 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR K 432 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU K 433 " --> pdb=" O GLU K 429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.013A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR F 166 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA F 271 " --> pdb=" O ALA F 365 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER F 364 " --> pdb=" O PHE F 317 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE F 317 " --> pdb=" O SER F 364 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR F 366 " --> pdb=" O ALA F 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA F 315 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE F 368 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL F 313 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN F 370 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 93 removed outlier: 8.071A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 5 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 168 through 172 removed outlier: 6.040A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 273 removed outlier: 4.031A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LYS A 352 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN A 356 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR A 319 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 90 through 92 removed outlier: 8.012A pdb=" N VAL G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU G 65 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN G 131 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ASN G 165 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE G 133 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE G 167 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU G 135 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR G 166 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE G 265 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N SER G 371 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA G 271 " --> pdb=" O ALA G 365 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER G 364 " --> pdb=" O PHE G 317 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE G 317 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR G 366 " --> pdb=" O ALA G 315 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA G 315 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE G 368 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL G 313 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASN G 370 " --> pdb=" O LEU G 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 51 through 53 Processing sheet with id=AB1, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.013A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR D 166 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA D 271 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER D 364 " --> pdb=" O PHE D 317 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE D 317 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR D 366 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA D 315 " --> pdb=" O THR D 366 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE D 368 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL D 313 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN D 370 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AB4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.013A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ASN I 165 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE I 133 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR I 166 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA I 271 " --> pdb=" O ALA I 365 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER I 364 " --> pdb=" O PHE I 317 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE I 317 " --> pdb=" O SER I 364 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR I 366 " --> pdb=" O ALA I 315 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA I 315 " --> pdb=" O THR I 366 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE I 368 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL I 313 " --> pdb=" O ILE I 368 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASN I 370 " --> pdb=" O LEU I 311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.013A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 166 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B 271 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER B 364 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE B 317 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR B 366 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA B 315 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE B 368 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL B 313 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AC1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AC2, first strand: chain 'H' and resid 90 through 92 removed outlier: 8.012A pdb=" N VAL H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU H 65 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLN H 131 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ASN H 165 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE H 133 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE H 167 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU H 135 " --> pdb=" O PHE H 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR H 166 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA H 271 " --> pdb=" O ALA H 365 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER H 364 " --> pdb=" O PHE H 317 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE H 317 " --> pdb=" O SER H 364 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR H 366 " --> pdb=" O ALA H 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA H 315 " --> pdb=" O THR H 366 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE H 368 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL H 313 " --> pdb=" O ILE H 368 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN H 370 " --> pdb=" O LEU H 311 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 51 through 53 Processing sheet with id=AC4, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'E' and resid 92 through 93 removed outlier: 8.071A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE E 5 " --> pdb=" O GLY E 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 168 through 172 removed outlier: 6.040A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 269 through 273 removed outlier: 4.031A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LYS E 352 " --> pdb=" O MET E 313 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N CYS E 315 " --> pdb=" O LYS E 352 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY E 354 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU E 317 " --> pdb=" O GLY E 354 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN E 356 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR E 319 " --> pdb=" O ASN E 356 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 92 through 93 removed outlier: 8.071A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU J 3 " --> pdb=" O LEU J 132 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY J 134 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE J 5 " --> pdb=" O GLY J 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AD2, first strand: chain 'J' and resid 168 through 172 removed outlier: 6.041A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 269 through 273 removed outlier: 4.031A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LYS J 352 " --> pdb=" O MET J 313 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N CYS J 315 " --> pdb=" O LYS J 352 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY J 354 " --> pdb=" O CYS J 315 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU J 317 " --> pdb=" O GLY J 354 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN J 356 " --> pdb=" O LEU J 317 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR J 319 " --> pdb=" O ASN J 356 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 92 through 93 removed outlier: 8.071A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 5 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 168 through 172 removed outlier: 6.041A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 269 through 273 removed outlier: 4.030A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LYS C 352 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N CYS C 315 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY C 354 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 317 " --> pdb=" O GLY C 354 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN C 356 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR C 319 " --> pdb=" O ASN C 356 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 92 through 93 removed outlier: 8.070A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU L 3 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY L 134 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE L 5 " --> pdb=" O GLY L 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AE1, first strand: chain 'L' and resid 168 through 172 removed outlier: 6.040A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'L' and resid 269 through 273 removed outlier: 4.032A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LYS L 352 " --> pdb=" O MET L 313 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N CYS L 315 " --> pdb=" O LYS L 352 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N GLY L 354 " --> pdb=" O CYS L 315 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU L 317 " --> pdb=" O GLY L 354 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN L 356 " --> pdb=" O LEU L 317 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR L 319 " --> pdb=" O ASN L 356 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 92 through 93 removed outlier: 8.070A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU K 3 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY K 134 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE K 5 " --> pdb=" O GLY K 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AE5, first strand: chain 'K' and resid 168 through 172 removed outlier: 6.041A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 269 through 273 removed outlier: 4.031A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LYS K 352 " --> pdb=" O MET K 313 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N CYS K 315 " --> pdb=" O LYS K 352 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N GLY K 354 " --> pdb=" O CYS K 315 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU K 317 " --> pdb=" O GLY K 354 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASN K 356 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR K 319 " --> pdb=" O ASN K 356 " (cutoff:3.500A) 1368 hydrogen bonds defined for protein. 4032 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: 9.10 Time building geometry restraints manager: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13569 1.34 - 1.46: 8550 1.46 - 1.57: 19222 1.57 - 1.69: 47 1.69 - 1.81: 432 Bond restraints: 41820 Sorted by residual: bond pdb=" C5 GDP D 501 " pdb=" C4 GDP D 501 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C5 GDP G 502 " pdb=" C4 GDP G 502 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C5 GDP F 501 " pdb=" C4 GDP F 501 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C5 GDP H 502 " pdb=" C4 GDP H 502 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.27e+01 ... (remaining 41815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 55952 2.45 - 4.91: 670 4.91 - 7.36: 120 7.36 - 9.82: 54 9.82 - 12.27: 24 Bond angle restraints: 56820 Sorted by residual: angle pdb=" C THR D 285 " pdb=" N VAL D 286 " pdb=" CA VAL D 286 " ideal model delta sigma weight residual 120.24 123.44 -3.20 6.30e-01 2.52e+00 2.58e+01 angle pdb=" C THR F 285 " pdb=" N VAL F 286 " pdb=" CA VAL F 286 " ideal model delta sigma weight residual 120.24 123.37 -3.13 6.30e-01 2.52e+00 2.47e+01 angle pdb=" C THR G 285 " pdb=" N VAL G 286 " pdb=" CA VAL G 286 " ideal model delta sigma weight residual 120.24 123.37 -3.13 6.30e-01 2.52e+00 2.47e+01 angle pdb=" C THR I 285 " pdb=" N VAL I 286 " pdb=" CA VAL I 286 " ideal model delta sigma weight residual 120.24 123.36 -3.12 6.30e-01 2.52e+00 2.45e+01 angle pdb=" C THR B 285 " pdb=" N VAL B 286 " pdb=" CA VAL B 286 " ideal model delta sigma weight residual 120.24 123.34 -3.10 6.30e-01 2.52e+00 2.42e+01 ... (remaining 56815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 24616 33.81 - 67.63: 180 67.63 - 101.44: 28 101.44 - 135.25: 9 135.25 - 169.06: 19 Dihedral angle restraints: 24852 sinusoidal: 9924 harmonic: 14928 Sorted by residual: dihedral pdb=" C5' GTP J 501 " pdb=" O5' GTP J 501 " pdb=" PA GTP J 501 " pdb=" O3A GTP J 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.67 -169.06 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP E 502 " pdb=" O5' GTP E 502 " pdb=" PA GTP E 502 " pdb=" O3A GTP E 502 " ideal model delta sinusoidal sigma weight residual 69.27 -121.71 -169.02 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.71 -169.02 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 24849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4083 0.045 - 0.091: 1658 0.091 - 0.136: 403 0.136 - 0.182: 46 0.182 - 0.227: 26 Chirality restraints: 6216 Sorted by residual: chirality pdb=" C2' GTP C 502 " pdb=" C1' GTP C 502 " pdb=" C3' GTP C 502 " pdb=" O2' GTP C 502 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C2' GTP J 501 " pdb=" C1' GTP J 501 " pdb=" C3' GTP J 501 " pdb=" O2' GTP J 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C2' GTP K 501 " pdb=" C1' GTP K 501 " pdb=" C3' GTP K 501 " pdb=" O2' GTP K 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 6213 not shown) Planarity restraints: 7398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GDP F 501 " 0.056 2.00e-02 2.50e+03 2.37e-02 1.69e+01 pdb=" N9 GDP F 501 " -0.010 2.00e-02 2.50e+03 pdb=" C8 GDP F 501 " -0.008 2.00e-02 2.50e+03 pdb=" N7 GDP F 501 " -0.012 2.00e-02 2.50e+03 pdb=" C5 GDP F 501 " -0.019 2.00e-02 2.50e+03 pdb=" C6 GDP F 501 " 0.011 2.00e-02 2.50e+03 pdb=" O6 GDP F 501 " 0.022 2.00e-02 2.50e+03 pdb=" N1 GDP F 501 " 0.023 2.00e-02 2.50e+03 pdb=" C2 GDP F 501 " -0.002 2.00e-02 2.50e+03 pdb=" N2 GDP F 501 " -0.001 2.00e-02 2.50e+03 pdb=" N3 GDP F 501 " -0.030 2.00e-02 2.50e+03 pdb=" C4 GDP F 501 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP H 502 " 0.045 2.00e-02 2.50e+03 2.12e-02 1.34e+01 pdb=" N9 GDP H 502 " -0.007 2.00e-02 2.50e+03 pdb=" C8 GDP H 502 " 0.003 2.00e-02 2.50e+03 pdb=" N7 GDP H 502 " -0.006 2.00e-02 2.50e+03 pdb=" C5 GDP H 502 " -0.021 2.00e-02 2.50e+03 pdb=" C6 GDP H 502 " 0.002 2.00e-02 2.50e+03 pdb=" O6 GDP H 502 " 0.025 2.00e-02 2.50e+03 pdb=" N1 GDP H 502 " 0.011 2.00e-02 2.50e+03 pdb=" C2 GDP H 502 " -0.005 2.00e-02 2.50e+03 pdb=" N2 GDP H 502 " 0.014 2.00e-02 2.50e+03 pdb=" N3 GDP H 502 " -0.030 2.00e-02 2.50e+03 pdb=" C4 GDP H 502 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP I 502 " -0.043 2.00e-02 2.50e+03 1.94e-02 1.13e+01 pdb=" N9 GDP I 502 " 0.005 2.00e-02 2.50e+03 pdb=" C8 GDP I 502 " 0.003 2.00e-02 2.50e+03 pdb=" N7 GDP I 502 " 0.013 2.00e-02 2.50e+03 pdb=" C5 GDP I 502 " 0.020 2.00e-02 2.50e+03 pdb=" C6 GDP I 502 " -0.000 2.00e-02 2.50e+03 pdb=" O6 GDP I 502 " -0.033 2.00e-02 2.50e+03 pdb=" N1 GDP I 502 " -0.005 2.00e-02 2.50e+03 pdb=" C2 GDP I 502 " 0.005 2.00e-02 2.50e+03 pdb=" N2 GDP I 502 " -0.006 2.00e-02 2.50e+03 pdb=" N3 GDP I 502 " 0.020 2.00e-02 2.50e+03 pdb=" C4 GDP I 502 " 0.022 2.00e-02 2.50e+03 ... (remaining 7395 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 18 2.32 - 2.96: 17665 2.96 - 3.61: 57708 3.61 - 4.25: 93896 4.25 - 4.90: 154518 Nonbonded interactions: 323805 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.671 2.170 nonbonded pdb=" O1G GTP C 502 " pdb="MG MG C 503 " model vdw 1.671 2.170 nonbonded pdb=" O1G GTP L 501 " pdb="MG MG L 502 " model vdw 1.671 2.170 nonbonded pdb=" O1G GTP J 501 " pdb="MG MG J 502 " model vdw 1.671 2.170 nonbonded pdb=" O1G GTP E 502 " pdb="MG MG E 503 " model vdw 1.672 2.170 ... (remaining 323800 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 441) selection = (chain 'C' and resid 1 through 441) selection = (chain 'E' and resid 1 through 441) selection = (chain 'J' and resid 1 through 441) selection = (chain 'K' and resid 1 through 441) selection = (chain 'L' and resid 1 through 441) } ncs_group { reference = (chain 'B' and resid 1 through 429) selection = (chain 'D' and resid 1 through 429) selection = (chain 'F' and resid 1 through 429) selection = (chain 'G' and resid 1 through 429) selection = (chain 'H' and resid 1 through 429) selection = (chain 'I' and resid 1 through 429) } 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 37.160 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.005 0.115 41820 Z= 0.236 Angle : 0.789 12.270 56820 Z= 0.400 Chirality : 0.051 0.227 6216 Planarity : 0.006 0.062 7398 Dihedral : 11.490 169.063 15276 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.77 (0.08), residues: 5130 helix: -4.02 (0.05), residues: 2088 sheet: -1.33 (0.18), residues: 780 loop : -2.85 (0.10), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 318 TYR 0.018 0.002 TYR K 224 PHE 0.012 0.002 PHE B 92 TRP 0.013 0.002 TRP D 101 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00492 (41820) covalent geometry : angle 0.78860 (56820) hydrogen bonds : bond 0.31767 ( 1368) hydrogen bonds : angle 9.91774 ( 4032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1778 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1778 time to evaluate : 1.593 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: 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: F 21 TRP cc_start: 0.8964 (m100) cc_final: 0.8655 (m100) REVERT: F 59 TYR cc_start: 0.8924 (m-80) cc_final: 0.8632 (m-80) REVERT: F 65 LEU cc_start: 0.8665 (mp) cc_final: 0.8428 (mp) REVERT: F 95 SER cc_start: 0.9065 (m) cc_final: 0.8755 (t) REVERT: F 125 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7941 (mt-10) REVERT: F 162 ARG cc_start: 0.8354 (mmt-90) cc_final: 0.8039 (mmp80) REVERT: F 164 MET cc_start: 0.9118 (tpt) cc_final: 0.8633 (mmm) REVERT: F 205 GLU cc_start: 0.8900 (tp30) cc_final: 0.8645 (mm-30) REVERT: F 233 MET cc_start: 0.8730 (mtp) cc_final: 0.8455 (mtm) REVERT: F 264 HIS cc_start: 0.8044 (p-80) cc_final: 0.7223 (p-80) REVERT: F 288 GLU cc_start: 0.6311 (tm-30) cc_final: 0.5840 (tm-30) REVERT: F 300 MET cc_start: 0.7739 (mtt) cc_final: 0.7126 (mtm) REVERT: F 303 CYS cc_start: 0.7382 (p) cc_final: 0.6654 (p) REVERT: F 322 SER cc_start: 0.8668 (m) cc_final: 0.8386 (t) REVERT: F 334 GLN cc_start: 0.8849 (tt0) cc_final: 0.8623 (tm-30) REVERT: F 340 TYR cc_start: 0.7798 (m-80) cc_final: 0.7565 (m-10) REVERT: F 367 PHE cc_start: 0.8636 (t80) cc_final: 0.8028 (t80) REVERT: A 2 ARG cc_start: 0.8070 (mpp-170) cc_final: 0.7515 (ptp90) REVERT: A 24 TYR cc_start: 0.8677 (m-80) cc_final: 0.8303 (m-80) REVERT: A 31 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8239 (mm-40) REVERT: A 33 ASP cc_start: 0.8444 (m-30) cc_final: 0.7512 (p0) REVERT: A 50 ASN cc_start: 0.8405 (t0) cc_final: 0.7765 (t0) REVERT: A 56 THR cc_start: 0.7959 (p) cc_final: 0.7648 (t) REVERT: A 85 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8386 (mm110) REVERT: A 90 GLU cc_start: 0.7788 (mm-30) cc_final: 0.6896 (tp30) REVERT: A 93 ILE cc_start: 0.8904 (mt) cc_final: 0.8693 (mm) REVERT: A 97 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6827 (tt0) REVERT: A 120 ASP cc_start: 0.8041 (t70) cc_final: 0.7627 (t0) REVERT: A 151 SER cc_start: 0.8970 (m) cc_final: 0.8452 (p) REVERT: A 154 MET cc_start: 0.9037 (mmm) cc_final: 0.8602 (mmm) REVERT: A 172 TYR cc_start: 0.8099 (t80) cc_final: 0.7886 (t80) REVERT: A 188 ILE cc_start: 0.8710 (mm) cc_final: 0.8403 (mt) REVERT: A 210 TYR cc_start: 0.8929 (m-80) cc_final: 0.8586 (m-10) REVERT: A 233 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8291 (mm-40) REVERT: A 252 LEU cc_start: 0.8962 (mp) cc_final: 0.8697 (mt) REVERT: A 258 ASN cc_start: 0.8902 (m110) cc_final: 0.8670 (t0) REVERT: A 295 CYS cc_start: 0.8463 (m) cc_final: 0.8112 (m) REVERT: A 308 ARG cc_start: 0.8761 (mtm180) cc_final: 0.8448 (ptp-110) REVERT: A 368 LEU cc_start: 0.9035 (mp) cc_final: 0.8629 (pp) REVERT: A 378 LEU cc_start: 0.8085 (mt) cc_final: 0.7583 (mm) REVERT: A 388 TRP cc_start: 0.8860 (m100) cc_final: 0.8617 (m100) REVERT: A 425 MET cc_start: 0.8319 (tpp) cc_final: 0.8105 (tpp) REVERT: A 435 VAL cc_start: 0.8255 (t) cc_final: 0.7990 (t) REVERT: G 4 ILE cc_start: 0.9553 (mt) cc_final: 0.9343 (mm) REVERT: G 26 ASP cc_start: 0.9016 (m-30) cc_final: 0.8747 (t70) REVERT: G 101 TRP cc_start: 0.9198 (t60) cc_final: 0.8727 (t60) REVERT: G 147 MET cc_start: 0.8954 (tpt) cc_final: 0.8658 (tpp) REVERT: G 184 ASN cc_start: 0.8456 (m-40) cc_final: 0.7856 (t0) REVERT: G 245 GLN cc_start: 0.8275 (mt0) cc_final: 0.7993 (mm110) REVERT: G 264 HIS cc_start: 0.7639 (p-80) cc_final: 0.7224 (p-80) REVERT: G 300 MET cc_start: 0.7873 (mtt) cc_final: 0.6921 (mtm) REVERT: G 324 LYS cc_start: 0.8455 (tttm) cc_final: 0.8103 (ttmm) REVERT: G 388 MET cc_start: 0.8316 (mtp) cc_final: 0.7826 (mmp) REVERT: D 6 HIS cc_start: 0.8231 (t70) cc_final: 0.7852 (t70) REVERT: D 26 ASP cc_start: 0.9189 (m-30) cc_final: 0.8766 (t0) REVERT: D 65 LEU cc_start: 0.8835 (mp) cc_final: 0.8522 (mp) REVERT: D 73 MET cc_start: 0.7065 (mmt) cc_final: 0.6788 (mmm) REVERT: D 101 TRP cc_start: 0.9042 (t60) cc_final: 0.8702 (t60) REVERT: D 164 MET cc_start: 0.9148 (tpt) cc_final: 0.8124 (tpp) REVERT: D 207 LEU cc_start: 0.8846 (mp) cc_final: 0.8105 (tp) REVERT: D 210 ILE cc_start: 0.8635 (mt) cc_final: 0.8363 (mt) REVERT: D 222 TYR cc_start: 0.8122 (m-80) cc_final: 0.7752 (m-80) REVERT: D 264 HIS cc_start: 0.7555 (p-80) cc_final: 0.6867 (p-80) REVERT: D 300 MET cc_start: 0.7514 (mtt) cc_final: 0.6694 (mmm) REVERT: D 310 TYR cc_start: 0.8792 (m-80) cc_final: 0.8505 (m-10) REVERT: D 324 LYS cc_start: 0.8456 (tttm) cc_final: 0.7919 (ttmm) REVERT: I 4 ILE cc_start: 0.9642 (mt) cc_final: 0.9342 (mm) REVERT: I 14 ASN cc_start: 0.8492 (m-40) cc_final: 0.8032 (m-40) REVERT: I 26 ASP cc_start: 0.8853 (m-30) cc_final: 0.8522 (t70) REVERT: I 65 LEU cc_start: 0.9292 (mp) cc_final: 0.8872 (mp) REVERT: I 264 HIS cc_start: 0.7550 (p-80) cc_final: 0.7128 (p-80) REVERT: I 297 LYS cc_start: 0.9164 (ptpt) cc_final: 0.8819 (ptpp) REVERT: I 310 TYR cc_start: 0.8306 (m-80) cc_final: 0.8007 (m-10) REVERT: I 324 LYS cc_start: 0.8181 (tttm) cc_final: 0.7657 (ttmm) REVERT: I 388 MET cc_start: 0.8375 (mtp) cc_final: 0.7694 (mmt) REVERT: I 406 MET cc_start: 0.7921 (tpp) cc_final: 0.7654 (mmp) REVERT: I 409 THR cc_start: 0.9250 (m) cc_final: 0.8821 (p) REVERT: B 6 HIS cc_start: 0.8358 (t70) cc_final: 0.8124 (t-170) REVERT: B 59 TYR cc_start: 0.8925 (m-80) cc_final: 0.8649 (m-80) REVERT: B 65 LEU cc_start: 0.8890 (mp) cc_final: 0.8602 (mp) REVERT: B 101 TRP cc_start: 0.8823 (t60) cc_final: 0.8275 (t60) REVERT: B 137 HIS cc_start: 0.8869 (p90) cc_final: 0.8662 (p90) REVERT: B 139 LEU cc_start: 0.8871 (mt) cc_final: 0.8503 (mp) REVERT: B 164 MET cc_start: 0.9134 (tpt) cc_final: 0.8879 (tpp) REVERT: B 187 LEU cc_start: 0.9302 (mt) cc_final: 0.8860 (tp) REVERT: B 201 CYS cc_start: 0.8830 (m) cc_final: 0.8569 (t) REVERT: B 245 GLN cc_start: 0.8481 (mt0) cc_final: 0.8191 (mm-40) REVERT: B 264 HIS cc_start: 0.7847 (p-80) cc_final: 0.6686 (p-80) REVERT: B 279 GLN cc_start: 0.8586 (pt0) cc_final: 0.8335 (pm20) REVERT: B 300 MET cc_start: 0.7678 (mtt) cc_final: 0.7397 (mtt) REVERT: B 303 CYS cc_start: 0.7230 (p) cc_final: 0.6768 (p) REVERT: B 324 LYS cc_start: 0.8174 (tttm) cc_final: 0.7799 (ttmm) REVERT: B 367 PHE cc_start: 0.8467 (t80) cc_final: 0.8219 (t80) REVERT: H 4 ILE cc_start: 0.9614 (mt) cc_final: 0.9309 (mm) REVERT: H 26 ASP cc_start: 0.9151 (m-30) cc_final: 0.8725 (t70) REVERT: H 37 HIS cc_start: 0.8689 (m90) cc_final: 0.8056 (m-70) REVERT: H 112 LEU cc_start: 0.9300 (tp) cc_final: 0.8901 (tt) REVERT: H 147 MET cc_start: 0.9021 (tpt) cc_final: 0.8742 (tpt) REVERT: H 184 ASN cc_start: 0.8376 (m-40) cc_final: 0.8149 (t0) REVERT: H 245 GLN cc_start: 0.8171 (mt0) cc_final: 0.7798 (mm-40) REVERT: H 279 GLN cc_start: 0.8792 (pt0) cc_final: 0.8532 (pm20) REVERT: H 300 MET cc_start: 0.7675 (mtt) cc_final: 0.7469 (mtt) REVERT: H 303 CYS cc_start: 0.7351 (p) cc_final: 0.6839 (p) REVERT: H 363 MET cc_start: 0.7991 (ptp) cc_final: 0.7772 (ptt) REVERT: H 388 MET cc_start: 0.8587 (mtp) cc_final: 0.7955 (mmp) REVERT: H 406 MET cc_start: 0.7813 (tpp) cc_final: 0.7569 (mmm) REVERT: E 32 PRO cc_start: 0.9416 (Cg_exo) cc_final: 0.9060 (Cg_endo) REVERT: E 33 ASP cc_start: 0.8635 (m-30) cc_final: 0.7831 (p0) REVERT: E 90 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8187 (tt0) REVERT: E 112 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8243 (ttpt) REVERT: E 121 ARG cc_start: 0.7626 (mmm160) cc_final: 0.7337 (mmp-170) REVERT: E 151 SER cc_start: 0.9065 (m) cc_final: 0.8818 (p) REVERT: E 170 SER cc_start: 0.9209 (m) cc_final: 0.8818 (p) REVERT: E 233 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8392 (mm-40) REVERT: E 254 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7826 (mt-10) REVERT: E 258 ASN cc_start: 0.8817 (m110) cc_final: 0.8580 (t0) REVERT: E 295 CYS cc_start: 0.8391 (m) cc_final: 0.7660 (m) REVERT: E 308 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8629 (ptp90) REVERT: E 368 LEU cc_start: 0.8891 (mp) cc_final: 0.8642 (pp) REVERT: E 388 TRP cc_start: 0.8726 (m100) cc_final: 0.8500 (m100) REVERT: E 398 MET cc_start: 0.7643 (mtp) cc_final: 0.7387 (mmm) REVERT: E 407 TRP cc_start: 0.8945 (m100) cc_final: 0.8437 (m100) REVERT: E 425 MET cc_start: 0.8200 (tpp) cc_final: 0.7939 (tpp) REVERT: J 21 TRP cc_start: 0.8592 (m100) cc_final: 0.7358 (m100) REVERT: J 33 ASP cc_start: 0.8571 (m-30) cc_final: 0.7871 (p0) REVERT: J 50 ASN cc_start: 0.8270 (t0) cc_final: 0.7812 (t0) REVERT: J 69 ASP cc_start: 0.7840 (t0) cc_final: 0.7601 (t0) REVERT: J 75 ILE cc_start: 0.9483 (mm) cc_final: 0.9261 (tt) REVERT: J 85 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8536 (mm110) REVERT: J 90 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7279 (tp30) REVERT: J 91 GLN cc_start: 0.8537 (mt0) cc_final: 0.7951 (mm110) REVERT: J 151 SER cc_start: 0.9330 (m) cc_final: 0.8841 (p) REVERT: J 205 ASP cc_start: 0.7807 (t0) cc_final: 0.7404 (m-30) REVERT: J 214 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7997 (ttp80) REVERT: J 271 THR cc_start: 0.8898 (m) cc_final: 0.8594 (p) REVERT: J 291 ILE cc_start: 0.9010 (pt) cc_final: 0.8322 (pt) REVERT: J 295 CYS cc_start: 0.8609 (m) cc_final: 0.8319 (m) REVERT: J 306 ASP cc_start: 0.8333 (t70) cc_final: 0.8049 (t0) REVERT: J 368 LEU cc_start: 0.9258 (mp) cc_final: 0.8940 (pp) REVERT: J 425 MET cc_start: 0.8270 (tpp) cc_final: 0.7803 (tpp) REVERT: C 31 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8143 (mp10) REVERT: C 33 ASP cc_start: 0.8517 (m-30) cc_final: 0.7987 (p0) REVERT: C 50 ASN cc_start: 0.7831 (t0) cc_final: 0.7506 (t0) REVERT: C 85 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8629 (mm-40) REVERT: C 86 LEU cc_start: 0.8701 (tp) cc_final: 0.8420 (tt) REVERT: C 109 THR cc_start: 0.8436 (m) cc_final: 0.8063 (p) REVERT: C 169 PHE cc_start: 0.8175 (m-10) cc_final: 0.7854 (m-10) REVERT: C 232 SER cc_start: 0.8947 (p) cc_final: 0.8497 (m) REVERT: C 258 ASN cc_start: 0.8476 (m110) cc_final: 0.8047 (m-40) REVERT: C 271 THR cc_start: 0.9104 (m) cc_final: 0.8771 (p) REVERT: C 285 GLN cc_start: 0.8296 (pt0) cc_final: 0.7327 (mm-40) REVERT: C 295 CYS cc_start: 0.8512 (m) cc_final: 0.8268 (m) REVERT: C 356 ASN cc_start: 0.8650 (t0) cc_final: 0.8403 (m110) REVERT: C 368 LEU cc_start: 0.8971 (mp) cc_final: 0.8639 (pp) REVERT: C 378 LEU cc_start: 0.7914 (mt) cc_final: 0.7671 (mm) REVERT: C 388 TRP cc_start: 0.8815 (m100) cc_final: 0.8315 (m100) REVERT: L 31 GLN cc_start: 0.8800 (mm-40) cc_final: 0.7803 (mt0) REVERT: L 33 ASP cc_start: 0.8630 (m-30) cc_final: 0.7935 (p0) REVERT: L 50 ASN cc_start: 0.8063 (t0) cc_final: 0.7687 (t0) REVERT: L 90 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7442 (tp30) REVERT: L 115 ILE cc_start: 0.8476 (tp) cc_final: 0.8234 (tp) REVERT: L 119 LEU cc_start: 0.8853 (mt) cc_final: 0.8557 (pp) REVERT: L 120 ASP cc_start: 0.8091 (t70) cc_final: 0.7870 (t0) REVERT: L 123 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7534 (ttm110) REVERT: L 132 LEU cc_start: 0.9054 (tp) cc_final: 0.8725 (tt) REVERT: L 138 PHE cc_start: 0.8780 (m-10) cc_final: 0.8563 (m-10) REVERT: L 151 SER cc_start: 0.8773 (m) cc_final: 0.8536 (p) REVERT: L 154 MET cc_start: 0.8903 (mmm) cc_final: 0.8442 (mmt) REVERT: L 196 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8034 (tm-30) REVERT: L 233 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8369 (mm-40) REVERT: L 271 THR cc_start: 0.9012 (m) cc_final: 0.8649 (p) REVERT: L 285 GLN cc_start: 0.8181 (pt0) cc_final: 0.7130 (mm-40) REVERT: L 290 GLU cc_start: 0.7642 (tt0) cc_final: 0.7400 (tt0) REVERT: L 326 LYS cc_start: 0.7559 (tmtm) cc_final: 0.7066 (mmtt) REVERT: L 329 ASN cc_start: 0.8421 (t0) cc_final: 0.8063 (m110) REVERT: L 368 LEU cc_start: 0.9277 (mp) cc_final: 0.8852 (pp) REVERT: L 378 LEU cc_start: 0.7977 (mt) cc_final: 0.7628 (mm) REVERT: L 402 ARG cc_start: 0.8543 (mmt-90) cc_final: 0.8327 (mmm160) REVERT: L 407 TRP cc_start: 0.8964 (m100) cc_final: 0.8683 (m100) REVERT: K 33 ASP cc_start: 0.8338 (m-30) cc_final: 0.7701 (p0) REVERT: K 90 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7457 (tp30) REVERT: K 132 LEU cc_start: 0.9101 (tp) cc_final: 0.8731 (tp) REVERT: K 154 MET cc_start: 0.9074 (mmm) cc_final: 0.8721 (mmm) REVERT: K 192 HIS cc_start: 0.7284 (t-90) cc_final: 0.7066 (t70) REVERT: K 202 PHE cc_start: 0.8178 (m-80) cc_final: 0.7766 (m-10) REVERT: K 214 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8085 (ttp80) REVERT: K 233 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8444 (mm-40) REVERT: K 249 ASN cc_start: 0.7766 (m-40) cc_final: 0.7522 (p0) REVERT: K 271 THR cc_start: 0.9023 (m) cc_final: 0.8792 (p) REVERT: K 295 CYS cc_start: 0.8990 (m) cc_final: 0.8600 (m) REVERT: K 302 MET cc_start: 0.7592 (mtt) cc_final: 0.6777 (mmm) REVERT: K 308 ARG cc_start: 0.8502 (mtm180) cc_final: 0.8000 (ptp-110) REVERT: K 368 LEU cc_start: 0.9363 (mp) cc_final: 0.8958 (pp) REVERT: K 378 LEU cc_start: 0.8053 (mt) cc_final: 0.7810 (mm) REVERT: K 388 TRP cc_start: 0.8801 (m100) cc_final: 0.8565 (m100) REVERT: K 407 TRP cc_start: 0.9063 (m100) cc_final: 0.8689 (m100) outliers start: 0 outliers final: 0 residues processed: 1778 average time/residue: 0.2618 time to fit residues: 758.2119 Evaluate side-chains 1003 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1003 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 494 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 GLN F 37 HIS F 190 HIS F 226 ASN F 307 HIS A 11 GLN A 18 ASN A 28 HIS A 88 HIS A 107 HIS A 192 HIS A 206 ASN A 266 HIS A 283 HIS A 301 GLN G 37 HIS G 190 HIS G 226 ASN G 247 ASN G 307 HIS G 423 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 37 HIS D 105 HIS D 190 HIS D 256 ASN D 307 HIS D 423 GLN I 37 HIS I 190 HIS I 264 HIS I 307 HIS I 396 HIS B 11 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS B 280 GLN B 307 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS H 190 HIS H 204 ASN H 247 ASN H 280 GLN H 307 HIS H 334 GLN E 11 GLN E 18 ASN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS E 107 HIS E 186 ASN E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN E 258 ASN E 283 HIS J 11 GLN J 18 ASN ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS J 107 HIS J 192 HIS ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN J 258 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 28 HIS C 88 HIS C 133 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS L 107 HIS L 133 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 ASN L 258 ASN K 11 GLN K 28 HIS K 88 HIS K 133 GLN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN K 258 ASN K 283 HIS ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.114613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.103379 restraints weight = 91849.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.106543 restraints weight = 46267.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.108628 restraints weight = 27039.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.110073 restraints weight = 17379.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.111041 restraints weight = 11866.614| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 41820 Z= 0.149 Angle : 0.599 9.325 56820 Z= 0.311 Chirality : 0.045 0.195 6216 Planarity : 0.005 0.043 7398 Dihedral : 11.959 179.802 5760 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.23 % Allowed : 2.35 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.10), residues: 5130 helix: -2.25 (0.08), residues: 2232 sheet: -0.88 (0.19), residues: 750 loop : -2.27 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 214 TYR 0.028 0.002 TYR J 185 PHE 0.014 0.001 PHE G 270 TRP 0.033 0.002 TRP D 344 HIS 0.011 0.001 HIS K 192 Details of bonding type rmsd covalent geometry : bond 0.00320 (41820) covalent geometry : angle 0.59913 (56820) hydrogen bonds : bond 0.05188 ( 1368) hydrogen bonds : angle 5.50383 ( 4032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1288 time to evaluate : 1.593 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: symmetry clash revert: symmetry clash REVERT: F 21 TRP cc_start: 0.8746 (m100) cc_final: 0.8436 (m100) REVERT: F 23 VAL cc_start: 0.9060 (t) cc_final: 0.8848 (p) REVERT: F 25 SER cc_start: 0.9312 (m) cc_final: 0.8763 (p) REVERT: F 26 ASP cc_start: 0.8913 (m-30) cc_final: 0.8627 (t70) REVERT: F 95 SER cc_start: 0.8971 (m) cc_final: 0.8622 (t) REVERT: F 101 TRP cc_start: 0.9189 (t60) cc_final: 0.8946 (t60) REVERT: F 163 ILE cc_start: 0.8931 (pt) cc_final: 0.8664 (pt) REVERT: F 203 ASP cc_start: 0.7718 (t0) cc_final: 0.7514 (t70) REVERT: F 205 GLU cc_start: 0.8709 (tp30) cc_final: 0.8486 (mm-30) REVERT: F 233 MET cc_start: 0.8711 (mtp) cc_final: 0.8490 (mtm) REVERT: F 264 HIS cc_start: 0.7989 (p-80) cc_final: 0.7035 (p-80) REVERT: F 268 PRO cc_start: 0.9559 (Cg_endo) cc_final: 0.9239 (Cg_exo) REVERT: F 329 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8203 (mt0) REVERT: F 330 MET cc_start: 0.8660 (tpp) cc_final: 0.8426 (tpt) REVERT: F 334 GLN cc_start: 0.8923 (tt0) cc_final: 0.8691 (tm-30) REVERT: F 367 PHE cc_start: 0.8468 (t80) cc_final: 0.7837 (t80) REVERT: F 406 MET cc_start: 0.6671 (tpt) cc_final: 0.6254 (mmm) REVERT: A 33 ASP cc_start: 0.8249 (m-30) cc_final: 0.7738 (p0) REVERT: A 69 ASP cc_start: 0.8217 (t0) cc_final: 0.7641 (t0) REVERT: A 90 GLU cc_start: 0.7919 (mm-30) cc_final: 0.6904 (tp30) REVERT: A 97 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7314 (mt-10) REVERT: A 120 ASP cc_start: 0.8269 (t70) cc_final: 0.7983 (t0) REVERT: A 151 SER cc_start: 0.9096 (m) cc_final: 0.8814 (p) REVERT: A 154 MET cc_start: 0.9064 (mmm) cc_final: 0.8572 (mmm) REVERT: A 157 LEU cc_start: 0.8860 (mt) cc_final: 0.8634 (mp) REVERT: A 213 CYS cc_start: 0.8312 (m) cc_final: 0.7598 (p) REVERT: A 254 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7864 (mt-10) REVERT: A 291 ILE cc_start: 0.8330 (pt) cc_final: 0.8094 (pt) REVERT: A 320 ARG cc_start: 0.8282 (ptm160) cc_final: 0.8060 (ptm160) REVERT: A 368 LEU cc_start: 0.8820 (mp) cc_final: 0.8448 (pp) REVERT: A 377 MET cc_start: 0.8042 (tmm) cc_final: 0.7791 (tmm) REVERT: A 398 MET cc_start: 0.7735 (mtm) cc_final: 0.7199 (ttp) REVERT: A 413 MET cc_start: 0.8202 (tpp) cc_final: 0.5141 (tpp) REVERT: A 423 GLU cc_start: 0.8182 (tp30) cc_final: 0.7924 (tp30) REVERT: G 4 ILE cc_start: 0.9618 (mt) cc_final: 0.9390 (mm) REVERT: G 12 CYS cc_start: 0.6925 (t) cc_final: 0.6682 (t) REVERT: G 37 HIS cc_start: 0.8836 (m-70) cc_final: 0.8279 (m-70) REVERT: G 67 ASP cc_start: 0.8893 (t0) cc_final: 0.8361 (t70) REVERT: G 101 TRP cc_start: 0.9305 (t60) cc_final: 0.8859 (t60) REVERT: G 147 MET cc_start: 0.8762 (tpt) cc_final: 0.8474 (tpp) REVERT: G 203 ASP cc_start: 0.8090 (t0) cc_final: 0.7725 (t70) REVERT: G 264 HIS cc_start: 0.7670 (p-80) cc_final: 0.7041 (p-80) REVERT: G 299 MET cc_start: 0.8870 (mmm) cc_final: 0.8597 (mmm) REVERT: G 300 MET cc_start: 0.7941 (mtt) cc_final: 0.7647 (mtm) REVERT: G 303 CYS cc_start: 0.8056 (p) cc_final: 0.7739 (p) REVERT: G 324 LYS cc_start: 0.8715 (tttm) cc_final: 0.8409 (ttmm) REVERT: G 406 MET cc_start: 0.6640 (mmm) cc_final: 0.5831 (tpp) REVERT: D 25 SER cc_start: 0.9343 (m) cc_final: 0.8966 (t) REVERT: D 26 ASP cc_start: 0.9010 (m-30) cc_final: 0.8794 (t0) REVERT: D 147 MET cc_start: 0.8118 (tpp) cc_final: 0.7883 (mmp) REVERT: D 222 TYR cc_start: 0.7887 (m-80) cc_final: 0.7246 (m-80) REVERT: D 264 HIS cc_start: 0.8075 (p-80) cc_final: 0.7188 (p-80) REVERT: D 297 LYS cc_start: 0.9412 (ptpp) cc_final: 0.9114 (ptmt) REVERT: D 310 TYR cc_start: 0.8785 (m-80) cc_final: 0.8436 (m-10) REVERT: D 321 MET cc_start: 0.7916 (pmm) cc_final: 0.7461 (pmm) REVERT: D 324 LYS cc_start: 0.8192 (tttm) cc_final: 0.7912 (ttmm) REVERT: D 367 PHE cc_start: 0.8510 (t80) cc_final: 0.8277 (t80) REVERT: D 403 MET cc_start: 0.7279 (ttp) cc_final: 0.5271 (ttp) REVERT: I 4 ILE cc_start: 0.9691 (mt) cc_final: 0.9377 (mm) REVERT: I 6 HIS cc_start: 0.7890 (t70) cc_final: 0.7652 (t-170) REVERT: I 25 SER cc_start: 0.9118 (m) cc_final: 0.8801 (t) REVERT: I 65 LEU cc_start: 0.9330 (mp) cc_final: 0.9057 (mp) REVERT: I 100 ASN cc_start: 0.8624 (t0) cc_final: 0.8408 (t0) REVERT: I 101 TRP cc_start: 0.8968 (t60) cc_final: 0.8664 (t60) REVERT: I 264 HIS cc_start: 0.7497 (p90) cc_final: 0.7144 (p-80) REVERT: I 310 TYR cc_start: 0.8541 (m-80) cc_final: 0.8190 (m-10) REVERT: I 324 LYS cc_start: 0.8020 (tttm) cc_final: 0.7801 (ttmm) REVERT: I 350 LYS cc_start: 0.9041 (tptp) cc_final: 0.8518 (tppt) REVERT: I 388 MET cc_start: 0.8335 (mtp) cc_final: 0.8086 (mmt) REVERT: I 406 MET cc_start: 0.7550 (tpp) cc_final: 0.7343 (mmp) REVERT: I 409 THR cc_start: 0.9329 (m) cc_final: 0.8973 (p) REVERT: I 426 GLN cc_start: 0.7928 (tp40) cc_final: 0.7546 (tp40) REVERT: I 427 ASP cc_start: 0.7986 (m-30) cc_final: 0.7599 (m-30) REVERT: B 26 ASP cc_start: 0.9157 (m-30) cc_final: 0.8799 (t70) REVERT: B 59 TYR cc_start: 0.8664 (m-80) cc_final: 0.8371 (m-10) REVERT: B 73 MET cc_start: 0.8303 (mmm) cc_final: 0.7753 (mmt) REVERT: B 101 TRP cc_start: 0.8717 (t60) cc_final: 0.8147 (t60) REVERT: B 198 GLU cc_start: 0.8651 (pm20) cc_final: 0.8144 (pm20) REVERT: B 203 ASP cc_start: 0.8206 (t0) cc_final: 0.7898 (t0) REVERT: B 256 ASN cc_start: 0.8225 (m-40) cc_final: 0.7467 (t0) REVERT: B 264 HIS cc_start: 0.8223 (p-80) cc_final: 0.7148 (p-80) REVERT: B 321 MET cc_start: 0.8025 (pmm) cc_final: 0.7733 (pmm) REVERT: B 349 VAL cc_start: 0.9456 (t) cc_final: 0.9247 (t) REVERT: H 37 HIS cc_start: 0.8857 (m-70) cc_final: 0.8462 (m-70) REVERT: H 203 ASP cc_start: 0.8269 (t0) cc_final: 0.7966 (t70) REVERT: H 204 ASN cc_start: 0.8798 (m110) cc_final: 0.8353 (t0) REVERT: H 297 LYS cc_start: 0.9369 (ptpp) cc_final: 0.8879 (mtmm) REVERT: H 349 VAL cc_start: 0.9532 (t) cc_final: 0.9260 (t) REVERT: H 367 PHE cc_start: 0.8418 (t80) cc_final: 0.8113 (t80) REVERT: H 388 MET cc_start: 0.8195 (mtp) cc_final: 0.7945 (mmt) REVERT: E 27 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7695 (mm-30) REVERT: E 33 ASP cc_start: 0.8409 (m-30) cc_final: 0.7935 (p0) REVERT: E 85 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7706 (mm-40) REVERT: E 90 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7270 (tp30) REVERT: E 151 SER cc_start: 0.9259 (m) cc_final: 0.8841 (p) REVERT: E 157 LEU cc_start: 0.8646 (mt) cc_final: 0.8412 (mt) REVERT: E 170 SER cc_start: 0.9221 (m) cc_final: 0.8129 (p) REVERT: E 210 TYR cc_start: 0.8723 (m-80) cc_final: 0.8462 (m-10) REVERT: E 230 LEU cc_start: 0.9174 (mp) cc_final: 0.8947 (tt) REVERT: E 233 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8603 (mm-40) REVERT: E 377 MET cc_start: 0.8183 (tmm) cc_final: 0.7848 (tmm) REVERT: E 407 TRP cc_start: 0.9023 (m100) cc_final: 0.8444 (m100) REVERT: E 413 MET cc_start: 0.8757 (tpp) cc_final: 0.7784 (tpp) REVERT: J 30 ILE cc_start: 0.9450 (mm) cc_final: 0.8938 (mm) REVERT: J 33 ASP cc_start: 0.8349 (m-30) cc_final: 0.7839 (p0) REVERT: J 90 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7042 (tp30) REVERT: J 91 GLN cc_start: 0.8360 (mt0) cc_final: 0.7957 (mm110) REVERT: J 123 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7762 (ttp80) REVERT: J 151 SER cc_start: 0.9318 (m) cc_final: 0.8894 (p) REVERT: J 172 TYR cc_start: 0.8181 (t80) cc_final: 0.7870 (t80) REVERT: J 233 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8523 (mm-40) REVERT: J 271 THR cc_start: 0.9295 (m) cc_final: 0.9071 (p) REVERT: J 295 CYS cc_start: 0.8247 (m) cc_final: 0.7946 (m) REVERT: J 368 LEU cc_start: 0.9187 (mp) cc_final: 0.8925 (pp) REVERT: J 413 MET cc_start: 0.8570 (tpp) cc_final: 0.6972 (tpp) REVERT: C 33 ASP cc_start: 0.8426 (m-30) cc_final: 0.8096 (p0) REVERT: C 69 ASP cc_start: 0.7145 (t0) cc_final: 0.6923 (t70) REVERT: C 86 LEU cc_start: 0.8573 (tp) cc_final: 0.8223 (tt) REVERT: C 90 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7713 (tp30) REVERT: C 96 LYS cc_start: 0.8071 (mmtp) cc_final: 0.7362 (mmmm) REVERT: C 112 LYS cc_start: 0.8933 (mptt) cc_final: 0.8697 (ttmt) REVERT: C 154 MET cc_start: 0.8990 (mmm) cc_final: 0.8746 (mmt) REVERT: C 169 PHE cc_start: 0.8237 (m-10) cc_final: 0.7623 (m-10) REVERT: C 170 SER cc_start: 0.8941 (m) cc_final: 0.7706 (p) REVERT: C 188 ILE cc_start: 0.8461 (mm) cc_final: 0.8127 (mt) REVERT: C 203 MET cc_start: 0.8276 (mmm) cc_final: 0.7857 (mmp) REVERT: C 258 ASN cc_start: 0.8340 (m110) cc_final: 0.8043 (m-40) REVERT: C 285 GLN cc_start: 0.8124 (pt0) cc_final: 0.7476 (mm110) REVERT: C 290 GLU cc_start: 0.7066 (tt0) cc_final: 0.6832 (tt0) REVERT: C 352 LYS cc_start: 0.8600 (tptp) cc_final: 0.8327 (tppt) REVERT: C 358 GLN cc_start: 0.8632 (tt0) cc_final: 0.8189 (tt0) REVERT: C 368 LEU cc_start: 0.8926 (mp) cc_final: 0.8602 (pp) REVERT: C 377 MET cc_start: 0.7358 (tmm) cc_final: 0.7152 (tmm) REVERT: L 33 ASP cc_start: 0.8517 (m-30) cc_final: 0.7897 (p0) REVERT: L 49 PHE cc_start: 0.7553 (p90) cc_final: 0.7081 (p90) REVERT: L 90 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7427 (tp30) REVERT: L 115 ILE cc_start: 0.8442 (tp) cc_final: 0.8140 (tp) REVERT: L 123 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7648 (ttm110) REVERT: L 132 LEU cc_start: 0.8960 (tp) cc_final: 0.8613 (tt) REVERT: L 138 PHE cc_start: 0.8685 (m-10) cc_final: 0.8331 (m-10) REVERT: L 154 MET cc_start: 0.8976 (mmm) cc_final: 0.8719 (mmt) REVERT: L 169 PHE cc_start: 0.7830 (m-10) cc_final: 0.7529 (m-10) REVERT: L 188 ILE cc_start: 0.8567 (mm) cc_final: 0.8341 (mt) REVERT: L 213 CYS cc_start: 0.8544 (m) cc_final: 0.8215 (p) REVERT: L 230 LEU cc_start: 0.9063 (mp) cc_final: 0.8478 (tt) REVERT: L 285 GLN cc_start: 0.8060 (pt0) cc_final: 0.7436 (mp10) REVERT: L 290 GLU cc_start: 0.7152 (tt0) cc_final: 0.6889 (tt0) REVERT: L 368 LEU cc_start: 0.9148 (mp) cc_final: 0.8809 (pp) REVERT: L 378 LEU cc_start: 0.7634 (mt) cc_final: 0.7424 (mm) REVERT: L 398 MET cc_start: 0.8088 (mtt) cc_final: 0.7563 (mtm) REVERT: L 407 TRP cc_start: 0.9045 (m100) cc_final: 0.8686 (m100) REVERT: L 413 MET cc_start: 0.8237 (tpt) cc_final: 0.7816 (tpt) REVERT: K 3 GLU cc_start: 0.7444 (mp0) cc_final: 0.7152 (mp0) REVERT: K 33 ASP cc_start: 0.8210 (m-30) cc_final: 0.7699 (p0) REVERT: K 50 ASN cc_start: 0.8420 (t0) cc_final: 0.7968 (t0) REVERT: K 69 ASP cc_start: 0.8058 (t0) cc_final: 0.7633 (t0) REVERT: K 90 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7693 (tp30) REVERT: K 120 ASP cc_start: 0.8335 (t70) cc_final: 0.8095 (t0) REVERT: K 132 LEU cc_start: 0.9039 (tp) cc_final: 0.8747 (tt) REVERT: K 154 MET cc_start: 0.9045 (mmm) cc_final: 0.8549 (mmm) REVERT: K 202 PHE cc_start: 0.8105 (m-80) cc_final: 0.7818 (m-10) REVERT: K 230 LEU cc_start: 0.9102 (mp) cc_final: 0.8681 (tt) REVERT: K 249 ASN cc_start: 0.7642 (m-40) cc_final: 0.7350 (p0) REVERT: K 338 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8669 (mtpp) REVERT: K 368 LEU cc_start: 0.9143 (mp) cc_final: 0.8908 (pp) REVERT: K 413 MET cc_start: 0.8625 (tpp) cc_final: 0.8183 (tpp) outliers start: 10 outliers final: 1 residues processed: 1297 average time/residue: 0.2488 time to fit residues: 536.5705 Evaluate side-chains 915 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 914 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 495 optimal weight: 8.9990 chunk 301 optimal weight: 0.3980 chunk 69 optimal weight: 20.0000 chunk 259 optimal weight: 8.9990 chunk 444 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 392 optimal weight: 1.9990 chunk 472 optimal weight: 20.0000 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN A 186 ASN A 258 ASN A 293 ASN A 356 ASN ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN I 423 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 HIS ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 GLN H 396 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN E 266 HIS E 309 HIS J 28 HIS J 88 HIS J 186 ASN J 192 HIS ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 HIS J 293 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN C 18 ASN C 107 HIS ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 HIS ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 HIS K 31 GLN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 266 HIS K 301 GLN ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.109792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.098676 restraints weight = 93958.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101715 restraints weight = 47370.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.103761 restraints weight = 27781.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.105169 restraints weight = 17912.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.106132 restraints weight = 12355.833| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 41820 Z= 0.165 Angle : 0.583 9.214 56820 Z= 0.301 Chirality : 0.045 0.190 6216 Planarity : 0.004 0.075 7398 Dihedral : 11.580 179.955 5760 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.11), residues: 5130 helix: -1.25 (0.10), residues: 2196 sheet: -0.87 (0.19), residues: 768 loop : -1.88 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 156 TYR 0.016 0.001 TYR I 222 PHE 0.016 0.001 PHE H 408 TRP 0.038 0.002 TRP B 344 HIS 0.008 0.001 HIS K 192 Details of bonding type rmsd covalent geometry : bond 0.00358 (41820) covalent geometry : angle 0.58291 (56820) hydrogen bonds : bond 0.04552 ( 1368) hydrogen bonds : angle 4.97097 ( 4032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1144 time to evaluate : 1.637 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 SER cc_start: 0.9360 (m) cc_final: 0.8876 (p) REVERT: F 26 ASP cc_start: 0.9031 (m-30) cc_final: 0.8819 (t70) REVERT: F 203 ASP cc_start: 0.8264 (t0) cc_final: 0.7954 (t70) REVERT: F 205 GLU cc_start: 0.8738 (tp30) cc_final: 0.8462 (mm-30) REVERT: F 264 HIS cc_start: 0.7932 (p-80) cc_final: 0.7097 (p-80) REVERT: F 329 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8199 (mt0) REVERT: F 334 GLN cc_start: 0.8987 (tt0) cc_final: 0.8692 (tm-30) REVERT: F 350 LYS cc_start: 0.8942 (tptp) cc_final: 0.8655 (tppt) REVERT: F 367 PHE cc_start: 0.8482 (t80) cc_final: 0.7777 (t80) REVERT: A 69 ASP cc_start: 0.8209 (t0) cc_final: 0.7901 (t0) REVERT: A 151 SER cc_start: 0.9136 (m) cc_final: 0.8714 (t) REVERT: A 154 MET cc_start: 0.9121 (mmm) cc_final: 0.8557 (mmm) REVERT: A 230 LEU cc_start: 0.9214 (mm) cc_final: 0.8955 (tt) REVERT: A 254 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7308 (mt-10) REVERT: A 291 ILE cc_start: 0.8506 (pt) cc_final: 0.8281 (pt) REVERT: A 320 ARG cc_start: 0.8157 (ptm160) cc_final: 0.7840 (ptm160) REVERT: A 368 LEU cc_start: 0.8912 (mp) cc_final: 0.8619 (pp) REVERT: A 413 MET cc_start: 0.8272 (tpp) cc_final: 0.8041 (tpt) REVERT: G 4 ILE cc_start: 0.9632 (mt) cc_final: 0.9348 (mm) REVERT: G 147 MET cc_start: 0.8843 (tpt) cc_final: 0.8596 (tpp) REVERT: G 203 ASP cc_start: 0.8280 (t0) cc_final: 0.7914 (t70) REVERT: G 264 HIS cc_start: 0.7678 (p-80) cc_final: 0.6587 (p-80) REVERT: G 267 MET cc_start: 0.8517 (mtp) cc_final: 0.8311 (mtp) REVERT: G 297 LYS cc_start: 0.9447 (ptpt) cc_final: 0.8891 (mtmm) REVERT: G 300 MET cc_start: 0.8146 (mtt) cc_final: 0.7710 (mtm) REVERT: G 323 MET cc_start: 0.8598 (mmm) cc_final: 0.8362 (mmm) REVERT: D 25 SER cc_start: 0.9329 (m) cc_final: 0.9000 (t) REVERT: D 26 ASP cc_start: 0.9069 (m-30) cc_final: 0.8847 (t0) REVERT: D 222 TYR cc_start: 0.7983 (m-80) cc_final: 0.7726 (m-80) REVERT: D 264 HIS cc_start: 0.7967 (p-80) cc_final: 0.7235 (p-80) REVERT: D 321 MET cc_start: 0.8034 (pmm) cc_final: 0.7085 (pmm) REVERT: D 324 LYS cc_start: 0.8272 (tttm) cc_final: 0.8016 (ttmm) REVERT: D 348 ASN cc_start: 0.8423 (p0) cc_final: 0.8117 (p0) REVERT: D 403 MET cc_start: 0.6883 (ttp) cc_final: 0.6284 (ttp) REVERT: D 426 GLN cc_start: 0.8101 (tp40) cc_final: 0.7870 (tp40) REVERT: I 4 ILE cc_start: 0.9659 (mt) cc_final: 0.9413 (mm) REVERT: I 6 HIS cc_start: 0.7845 (t70) cc_final: 0.7600 (t-170) REVERT: I 25 SER cc_start: 0.9077 (m) cc_final: 0.8861 (t) REVERT: I 65 LEU cc_start: 0.9386 (mp) cc_final: 0.9145 (mp) REVERT: I 67 ASP cc_start: 0.8938 (t0) cc_final: 0.8610 (t70) REVERT: I 203 ASP cc_start: 0.8566 (t0) cc_final: 0.8253 (t70) REVERT: I 264 HIS cc_start: 0.8091 (p90) cc_final: 0.7284 (p-80) REVERT: I 297 LYS cc_start: 0.9345 (ptpt) cc_final: 0.8828 (mtpt) REVERT: I 310 TYR cc_start: 0.8733 (m-80) cc_final: 0.8395 (m-10) REVERT: I 323 MET cc_start: 0.8403 (mmt) cc_final: 0.8129 (mmt) REVERT: I 324 LYS cc_start: 0.8073 (tttm) cc_final: 0.7825 (tttm) REVERT: I 350 LYS cc_start: 0.9062 (tptp) cc_final: 0.8701 (tppt) REVERT: I 355 ASP cc_start: 0.8644 (m-30) cc_final: 0.8245 (m-30) REVERT: I 388 MET cc_start: 0.8348 (mtp) cc_final: 0.8142 (mmt) REVERT: B 26 ASP cc_start: 0.9174 (m-30) cc_final: 0.8684 (t70) REVERT: B 65 LEU cc_start: 0.8924 (tp) cc_final: 0.7601 (tt) REVERT: B 73 MET cc_start: 0.8183 (mmm) cc_final: 0.7826 (mmm) REVERT: B 101 TRP cc_start: 0.8928 (t60) cc_final: 0.8179 (t60) REVERT: B 164 MET cc_start: 0.8301 (mmm) cc_final: 0.7944 (mmm) REVERT: B 187 LEU cc_start: 0.9567 (mt) cc_final: 0.9357 (mm) REVERT: B 198 GLU cc_start: 0.8623 (pm20) cc_final: 0.8148 (pm20) REVERT: B 203 ASP cc_start: 0.8410 (t0) cc_final: 0.8147 (t0) REVERT: B 256 ASN cc_start: 0.8182 (m-40) cc_final: 0.7826 (m-40) REVERT: B 264 HIS cc_start: 0.8109 (p-80) cc_final: 0.6963 (p90) REVERT: H 203 ASP cc_start: 0.8101 (t0) cc_final: 0.7839 (t0) REVERT: H 204 ASN cc_start: 0.8767 (m110) cc_final: 0.8417 (t0) REVERT: H 264 HIS cc_start: 0.7411 (p-80) cc_final: 0.6538 (p-80) REVERT: H 297 LYS cc_start: 0.9342 (ptpp) cc_final: 0.8812 (mtmm) REVERT: H 321 MET cc_start: 0.8214 (ptp) cc_final: 0.7844 (pmm) REVERT: H 356 ILE cc_start: 0.9341 (mm) cc_final: 0.8704 (tt) REVERT: H 367 PHE cc_start: 0.8469 (t80) cc_final: 0.8238 (t80) REVERT: H 388 MET cc_start: 0.8280 (mtp) cc_final: 0.8034 (mmp) REVERT: E 27 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7753 (mm-30) REVERT: E 33 ASP cc_start: 0.8410 (m-30) cc_final: 0.8002 (p0) REVERT: E 49 PHE cc_start: 0.7821 (p90) cc_final: 0.7451 (p90) REVERT: E 90 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7321 (tp30) REVERT: E 96 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8094 (mmmm) REVERT: E 151 SER cc_start: 0.9357 (m) cc_final: 0.9101 (p) REVERT: E 157 LEU cc_start: 0.8645 (mt) cc_final: 0.8424 (mt) REVERT: E 407 TRP cc_start: 0.8965 (m100) cc_final: 0.8520 (m100) REVERT: J 31 GLN cc_start: 0.8741 (mm-40) cc_final: 0.7601 (mt0) REVERT: J 33 ASP cc_start: 0.8453 (m-30) cc_final: 0.7954 (p0) REVERT: J 69 ASP cc_start: 0.7695 (t70) cc_final: 0.7181 (t70) REVERT: J 75 ILE cc_start: 0.9376 (mt) cc_final: 0.9165 (tt) REVERT: J 90 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7333 (tp30) REVERT: J 91 GLN cc_start: 0.8446 (mt0) cc_final: 0.8016 (mm110) REVERT: J 151 SER cc_start: 0.9423 (m) cc_final: 0.9135 (p) REVERT: J 157 LEU cc_start: 0.8883 (mt) cc_final: 0.8642 (mp) REVERT: J 172 TYR cc_start: 0.8122 (t80) cc_final: 0.7862 (t80) REVERT: J 192 HIS cc_start: 0.7755 (t70) cc_final: 0.7029 (t70) REVERT: J 205 ASP cc_start: 0.7858 (t0) cc_final: 0.7651 (t0) REVERT: J 230 LEU cc_start: 0.9348 (mp) cc_final: 0.8843 (tt) REVERT: J 271 THR cc_start: 0.9228 (m) cc_final: 0.9000 (p) REVERT: J 352 LYS cc_start: 0.8778 (tptt) cc_final: 0.7966 (tppt) REVERT: J 368 LEU cc_start: 0.9252 (mp) cc_final: 0.8984 (pp) REVERT: C 33 ASP cc_start: 0.8398 (m-30) cc_final: 0.7971 (p0) REVERT: C 96 LYS cc_start: 0.8107 (mmtp) cc_final: 0.7372 (mmmm) REVERT: C 154 MET cc_start: 0.9182 (mmm) cc_final: 0.8884 (mmt) REVERT: C 258 ASN cc_start: 0.8477 (m110) cc_final: 0.8027 (t0) REVERT: C 285 GLN cc_start: 0.7975 (pt0) cc_final: 0.7320 (mm110) REVERT: C 290 GLU cc_start: 0.6992 (tt0) cc_final: 0.6748 (tt0) REVERT: C 302 MET cc_start: 0.7676 (mtt) cc_final: 0.7431 (mtt) REVERT: C 352 LYS cc_start: 0.8667 (tptp) cc_final: 0.8343 (tptp) REVERT: C 358 GLN cc_start: 0.8559 (tt0) cc_final: 0.8066 (tt0) REVERT: C 368 LEU cc_start: 0.8942 (mp) cc_final: 0.8579 (pp) REVERT: C 402 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.7989 (mmm160) REVERT: L 33 ASP cc_start: 0.8516 (m-30) cc_final: 0.7818 (p0) REVERT: L 36 MET cc_start: 0.7849 (ppp) cc_final: 0.7542 (ppp) REVERT: L 49 PHE cc_start: 0.7632 (p90) cc_final: 0.7159 (p90) REVERT: L 123 ARG cc_start: 0.7965 (ttp-110) cc_final: 0.7710 (ttm110) REVERT: L 132 LEU cc_start: 0.8943 (tp) cc_final: 0.8584 (tt) REVERT: L 154 MET cc_start: 0.8955 (mmm) cc_final: 0.8754 (mmt) REVERT: L 169 PHE cc_start: 0.7839 (m-10) cc_final: 0.7448 (m-10) REVERT: L 213 CYS cc_start: 0.8546 (m) cc_final: 0.8180 (p) REVERT: L 230 LEU cc_start: 0.9161 (mp) cc_final: 0.8562 (tt) REVERT: L 285 GLN cc_start: 0.8080 (pt0) cc_final: 0.7389 (mp10) REVERT: L 290 GLU cc_start: 0.7128 (tt0) cc_final: 0.6911 (tt0) REVERT: L 291 ILE cc_start: 0.8844 (pt) cc_final: 0.8577 (pt) REVERT: L 338 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8770 (mtpp) REVERT: L 368 LEU cc_start: 0.9125 (mp) cc_final: 0.8760 (pp) REVERT: L 398 MET cc_start: 0.8008 (mtt) cc_final: 0.7649 (mtm) REVERT: L 407 TRP cc_start: 0.9099 (m100) cc_final: 0.8749 (m100) REVERT: K 31 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8344 (mt0) REVERT: K 33 ASP cc_start: 0.8239 (m-30) cc_final: 0.7619 (p0) REVERT: K 69 ASP cc_start: 0.8017 (t0) cc_final: 0.7528 (t0) REVERT: K 90 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7269 (tp30) REVERT: K 154 MET cc_start: 0.9136 (mmm) cc_final: 0.8684 (mmm) REVERT: K 202 PHE cc_start: 0.8277 (m-80) cc_final: 0.8070 (m-10) REVERT: K 230 LEU cc_start: 0.9066 (mp) cc_final: 0.8777 (tt) REVERT: K 233 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8639 (mm-40) REVERT: K 338 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8725 (mtpp) REVERT: K 368 LEU cc_start: 0.9162 (mp) cc_final: 0.8905 (pp) REVERT: K 398 MET cc_start: 0.7747 (mtm) cc_final: 0.7298 (ttp) outliers start: 4 outliers final: 1 residues processed: 1148 average time/residue: 0.2440 time to fit residues: 469.3218 Evaluate side-chains 834 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 832 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 32 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 399 optimal weight: 0.7980 chunk 385 optimal weight: 30.0000 chunk 388 optimal weight: 0.8980 chunk 360 optimal weight: 8.9990 chunk 124 optimal weight: 0.1980 chunk 288 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 chunk 459 optimal weight: 20.0000 overall best weight: 3.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 258 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 ASN G 375 GLN D 256 ASN D 424 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN E 28 HIS E 186 ASN E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 301 GLN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 GLN ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.110378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.099519 restraints weight = 94019.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.102534 restraints weight = 47381.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.104557 restraints weight = 27702.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.105938 restraints weight = 17794.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.106871 restraints weight = 12231.290| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41820 Z= 0.138 Angle : 0.561 8.909 56820 Z= 0.286 Chirality : 0.045 0.178 6216 Planarity : 0.004 0.080 7398 Dihedral : 11.417 179.305 5760 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.05 % Allowed : 1.89 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.11), residues: 5130 helix: -0.68 (0.10), residues: 2226 sheet: -0.77 (0.18), residues: 792 loop : -1.72 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 123 TYR 0.037 0.001 TYR A 185 PHE 0.013 0.001 PHE G 408 TRP 0.021 0.002 TRP B 397 HIS 0.007 0.001 HIS K 192 Details of bonding type rmsd covalent geometry : bond 0.00306 (41820) covalent geometry : angle 0.56067 (56820) hydrogen bonds : bond 0.03981 ( 1368) hydrogen bonds : angle 4.67547 ( 4032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1091 time to evaluate : 1.565 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 SER cc_start: 0.9352 (m) cc_final: 0.8853 (p) REVERT: F 26 ASP cc_start: 0.9130 (m-30) cc_final: 0.8863 (t70) REVERT: F 205 GLU cc_start: 0.8778 (tp30) cc_final: 0.8539 (mm-30) REVERT: F 264 HIS cc_start: 0.7808 (p-80) cc_final: 0.7427 (p-80) REVERT: F 297 LYS cc_start: 0.9475 (mtpt) cc_final: 0.8980 (mmtt) REVERT: F 334 GLN cc_start: 0.9014 (tt0) cc_final: 0.8669 (tm-30) REVERT: A 90 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7345 (tp30) REVERT: A 151 SER cc_start: 0.9170 (m) cc_final: 0.8948 (p) REVERT: A 154 MET cc_start: 0.9093 (mmm) cc_final: 0.8588 (mmm) REVERT: A 230 LEU cc_start: 0.9288 (mm) cc_final: 0.8953 (tt) REVERT: A 254 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7139 (mt-10) REVERT: A 272 TYR cc_start: 0.8478 (t80) cc_final: 0.8053 (t80) REVERT: A 291 ILE cc_start: 0.8588 (pt) cc_final: 0.8352 (pt) REVERT: A 320 ARG cc_start: 0.7903 (ptm160) cc_final: 0.7453 (ptm160) REVERT: A 368 LEU cc_start: 0.8883 (mp) cc_final: 0.8651 (pp) REVERT: A 413 MET cc_start: 0.7958 (tpp) cc_final: 0.6859 (tpp) REVERT: G 4 ILE cc_start: 0.9619 (mt) cc_final: 0.9330 (mm) REVERT: G 25 SER cc_start: 0.8203 (t) cc_final: 0.7849 (p) REVERT: G 67 ASP cc_start: 0.8894 (t0) cc_final: 0.8394 (t70) REVERT: G 147 MET cc_start: 0.8822 (tpt) cc_final: 0.8534 (tpp) REVERT: G 264 HIS cc_start: 0.7506 (p-80) cc_final: 0.6368 (p-80) REVERT: G 282 ARG cc_start: 0.7436 (tpp80) cc_final: 0.7210 (tpp80) REVERT: G 300 MET cc_start: 0.8040 (mtt) cc_final: 0.7738 (mtm) REVERT: G 323 MET cc_start: 0.8640 (mmm) cc_final: 0.8317 (mmm) REVERT: G 350 LYS cc_start: 0.9223 (tptp) cc_final: 0.8735 (tppt) REVERT: D 25 SER cc_start: 0.9252 (m) cc_final: 0.8665 (p) REVERT: D 65 LEU cc_start: 0.8708 (mp) cc_final: 0.8495 (mp) REVERT: D 157 GLU cc_start: 0.8264 (pp20) cc_final: 0.7822 (pp20) REVERT: D 183 TYR cc_start: 0.8680 (m-80) cc_final: 0.8444 (m-80) REVERT: D 222 TYR cc_start: 0.7973 (m-80) cc_final: 0.7116 (m-80) REVERT: D 257 MET cc_start: 0.7377 (mmm) cc_final: 0.7160 (mmm) REVERT: D 264 HIS cc_start: 0.7941 (p-80) cc_final: 0.7258 (p-80) REVERT: D 321 MET cc_start: 0.8059 (pmm) cc_final: 0.7366 (pmm) REVERT: D 336 LYS cc_start: 0.7810 (ptpt) cc_final: 0.7492 (ptpp) REVERT: D 348 ASN cc_start: 0.8446 (p0) cc_final: 0.8128 (p0) REVERT: D 403 MET cc_start: 0.7499 (ttp) cc_final: 0.5718 (ttp) REVERT: D 406 MET cc_start: 0.6168 (mmp) cc_final: 0.5819 (mmp) REVERT: D 426 GLN cc_start: 0.8287 (tp40) cc_final: 0.8029 (tp40) REVERT: I 4 ILE cc_start: 0.9702 (mt) cc_final: 0.9427 (mm) REVERT: I 6 HIS cc_start: 0.7628 (t70) cc_final: 0.7424 (t70) REVERT: I 65 LEU cc_start: 0.9376 (mp) cc_final: 0.9124 (mp) REVERT: I 67 ASP cc_start: 0.9035 (t0) cc_final: 0.8614 (t70) REVERT: I 264 HIS cc_start: 0.7960 (p90) cc_final: 0.7153 (p-80) REVERT: I 310 TYR cc_start: 0.8709 (m-80) cc_final: 0.8423 (m-10) REVERT: I 324 LYS cc_start: 0.8103 (tttm) cc_final: 0.7852 (tttp) REVERT: I 350 LYS cc_start: 0.9057 (tptp) cc_final: 0.8771 (tppt) REVERT: I 355 ASP cc_start: 0.8696 (m-30) cc_final: 0.8172 (m-30) REVERT: B 26 ASP cc_start: 0.9126 (m-30) cc_final: 0.8675 (t70) REVERT: B 65 LEU cc_start: 0.8901 (tp) cc_final: 0.7663 (tt) REVERT: B 73 MET cc_start: 0.8234 (mmm) cc_final: 0.7999 (mmm) REVERT: B 101 TRP cc_start: 0.8992 (t60) cc_final: 0.8150 (t60) REVERT: B 198 GLU cc_start: 0.8581 (pm20) cc_final: 0.8039 (pm20) REVERT: B 264 HIS cc_start: 0.7968 (p-80) cc_final: 0.6968 (p90) REVERT: B 406 MET cc_start: 0.7037 (mmp) cc_final: 0.6781 (mmp) REVERT: H 37 HIS cc_start: 0.8564 (m-70) cc_final: 0.7904 (m-70) REVERT: H 57 ASN cc_start: 0.9175 (m110) cc_final: 0.8767 (m110) REVERT: H 204 ASN cc_start: 0.8742 (m110) cc_final: 0.8355 (t0) REVERT: H 297 LYS cc_start: 0.9358 (ptpp) cc_final: 0.8843 (mtmm) REVERT: H 321 MET cc_start: 0.8157 (ptp) cc_final: 0.7569 (pmm) REVERT: H 356 ILE cc_start: 0.9322 (mm) cc_final: 0.8823 (tt) REVERT: H 367 PHE cc_start: 0.8476 (t80) cc_final: 0.8248 (t80) REVERT: E 27 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7731 (mm-30) REVERT: E 33 ASP cc_start: 0.8428 (m-30) cc_final: 0.8021 (p0) REVERT: E 49 PHE cc_start: 0.7788 (p90) cc_final: 0.7473 (p90) REVERT: E 90 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7579 (tp30) REVERT: E 151 SER cc_start: 0.9354 (m) cc_final: 0.9093 (p) REVERT: E 157 LEU cc_start: 0.8565 (mt) cc_final: 0.8316 (mt) REVERT: E 230 LEU cc_start: 0.9135 (mm) cc_final: 0.8732 (tt) REVERT: E 254 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7099 (mt-10) REVERT: E 256 GLN cc_start: 0.8757 (pm20) cc_final: 0.8428 (pm20) REVERT: E 407 TRP cc_start: 0.8963 (m100) cc_final: 0.8382 (m100) REVERT: J 31 GLN cc_start: 0.8657 (mm-40) cc_final: 0.7764 (mt0) REVERT: J 33 ASP cc_start: 0.8454 (m-30) cc_final: 0.7968 (p0) REVERT: J 75 ILE cc_start: 0.9371 (mt) cc_final: 0.9156 (tt) REVERT: J 90 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7384 (tp30) REVERT: J 91 GLN cc_start: 0.8414 (mt0) cc_final: 0.7963 (mm110) REVERT: J 97 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6953 (mt-10) REVERT: J 151 SER cc_start: 0.9309 (m) cc_final: 0.8971 (p) REVERT: J 230 LEU cc_start: 0.9361 (mp) cc_final: 0.8921 (tt) REVERT: J 233 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8639 (mm-40) REVERT: J 352 LYS cc_start: 0.8719 (tptt) cc_final: 0.7942 (tppt) REVERT: J 368 LEU cc_start: 0.9223 (mp) cc_final: 0.8957 (pp) REVERT: J 398 MET cc_start: 0.7764 (ttm) cc_final: 0.7525 (ttm) REVERT: C 33 ASP cc_start: 0.8428 (m-30) cc_final: 0.7936 (p0) REVERT: C 96 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7398 (mmmm) REVERT: C 112 LYS cc_start: 0.9327 (ttmt) cc_final: 0.9103 (ttpp) REVERT: C 154 MET cc_start: 0.9211 (mmm) cc_final: 0.8919 (mmt) REVERT: C 203 MET cc_start: 0.8645 (mmm) cc_final: 0.8337 (mmm) REVERT: C 210 TYR cc_start: 0.8761 (m-80) cc_final: 0.8559 (m-10) REVERT: C 233 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8581 (mm-40) REVERT: C 241 SER cc_start: 0.8509 (p) cc_final: 0.7830 (t) REVERT: C 285 GLN cc_start: 0.7920 (pt0) cc_final: 0.7090 (mm-40) REVERT: C 290 GLU cc_start: 0.6755 (tt0) cc_final: 0.6503 (tt0) REVERT: C 368 LEU cc_start: 0.8885 (mp) cc_final: 0.8451 (pp) REVERT: L 3 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7313 (mm-30) REVERT: L 31 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8284 (mt0) REVERT: L 33 ASP cc_start: 0.8554 (m-30) cc_final: 0.7752 (p0) REVERT: L 90 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7360 (tp30) REVERT: L 123 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7648 (ttm110) REVERT: L 154 MET cc_start: 0.9094 (mmm) cc_final: 0.8870 (mmt) REVERT: L 169 PHE cc_start: 0.7821 (m-10) cc_final: 0.7436 (m-10) REVERT: L 194 THR cc_start: 0.8803 (p) cc_final: 0.8564 (p) REVERT: L 230 LEU cc_start: 0.9177 (mp) cc_final: 0.8615 (tt) REVERT: L 285 GLN cc_start: 0.8070 (pt0) cc_final: 0.7364 (mp10) REVERT: L 290 GLU cc_start: 0.6956 (tt0) cc_final: 0.6727 (tt0) REVERT: L 315 CYS cc_start: 0.7694 (m) cc_final: 0.7419 (m) REVERT: L 368 LEU cc_start: 0.9098 (mp) cc_final: 0.8729 (pp) REVERT: K 31 GLN cc_start: 0.8691 (mm110) cc_final: 0.8470 (mt0) REVERT: K 69 ASP cc_start: 0.8163 (t0) cc_final: 0.7813 (t0) REVERT: K 90 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7250 (tp30) REVERT: K 120 ASP cc_start: 0.8459 (t70) cc_final: 0.8224 (t0) REVERT: K 154 MET cc_start: 0.9111 (mmm) cc_final: 0.8684 (mmm) REVERT: K 202 PHE cc_start: 0.8400 (m-80) cc_final: 0.8091 (m-10) REVERT: K 221 ARG cc_start: 0.9181 (mpt-90) cc_final: 0.8909 (mmt90) REVERT: K 230 LEU cc_start: 0.9124 (mp) cc_final: 0.8808 (tt) REVERT: K 233 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8603 (mm-40) REVERT: K 291 ILE cc_start: 0.8777 (pt) cc_final: 0.8530 (pt) REVERT: K 338 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8660 (mtpp) REVERT: K 368 LEU cc_start: 0.9223 (mp) cc_final: 0.8898 (pp) REVERT: K 398 MET cc_start: 0.7818 (mtm) cc_final: 0.7385 (ttp) outliers start: 2 outliers final: 0 residues processed: 1093 average time/residue: 0.2408 time to fit residues: 439.5457 Evaluate side-chains 800 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 800 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 383 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 196 optimal weight: 30.0000 chunk 498 optimal weight: 7.9990 chunk 303 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 339 optimal weight: 0.6980 chunk 403 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 chunk 169 optimal weight: 20.0000 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 233 GLN A 258 ASN A 300 ASN A 356 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 ASN G 375 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 256 ASN B 334 GLN B 348 ASN H 423 GLN E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 192 HIS C 256 GLN C 356 ASN ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 HIS ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.108944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.098131 restraints weight = 94787.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.101114 restraints weight = 47942.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.103159 restraints weight = 28128.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.104502 restraints weight = 18022.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.105439 restraints weight = 12434.844| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41820 Z= 0.149 Angle : 0.562 9.191 56820 Z= 0.286 Chirality : 0.045 0.193 6216 Planarity : 0.004 0.071 7398 Dihedral : 11.349 178.750 5760 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.09 % Allowed : 2.03 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.12), residues: 5130 helix: -0.20 (0.11), residues: 2196 sheet: -0.98 (0.18), residues: 852 loop : -1.52 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 214 TYR 0.016 0.001 TYR G 208 PHE 0.024 0.001 PHE H 385 TRP 0.022 0.002 TRP L 21 HIS 0.010 0.001 HIS J 192 Details of bonding type rmsd covalent geometry : bond 0.00332 (41820) covalent geometry : angle 0.56170 (56820) hydrogen bonds : bond 0.03795 ( 1368) hydrogen bonds : angle 4.61421 ( 4032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1043 time to evaluate : 1.542 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: F 25 SER cc_start: 0.9355 (m) cc_final: 0.8602 (p) REVERT: F 26 ASP cc_start: 0.9126 (m-30) cc_final: 0.8839 (t70) REVERT: F 205 GLU cc_start: 0.8861 (tp30) cc_final: 0.8587 (mm-30) REVERT: F 264 HIS cc_start: 0.7684 (p-80) cc_final: 0.7311 (p-80) REVERT: F 297 LYS cc_start: 0.9458 (mtpt) cc_final: 0.9122 (mmtt) REVERT: F 334 GLN cc_start: 0.8940 (tt0) cc_final: 0.8630 (tm-30) REVERT: A 69 ASP cc_start: 0.8142 (t0) cc_final: 0.7597 (t0) REVERT: A 90 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7401 (tp30) REVERT: A 154 MET cc_start: 0.9111 (mmm) cc_final: 0.8668 (mmm) REVERT: A 214 ARG cc_start: 0.8808 (ttp80) cc_final: 0.8319 (tmm-80) REVERT: A 233 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8407 (tp40) REVERT: A 254 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7729 (mt-10) REVERT: A 291 ILE cc_start: 0.8578 (pt) cc_final: 0.8373 (pt) REVERT: A 301 GLN cc_start: 0.9083 (mm110) cc_final: 0.8581 (mm110) REVERT: A 320 ARG cc_start: 0.7895 (ptm160) cc_final: 0.7379 (ptm160) REVERT: A 368 LEU cc_start: 0.8882 (mp) cc_final: 0.8610 (pp) REVERT: A 398 MET cc_start: 0.7995 (ttm) cc_final: 0.7472 (ttm) REVERT: A 413 MET cc_start: 0.7847 (tpp) cc_final: 0.7332 (tpp) REVERT: G 4 ILE cc_start: 0.9614 (mt) cc_final: 0.9355 (mm) REVERT: G 25 SER cc_start: 0.8356 (t) cc_final: 0.7994 (p) REVERT: G 67 ASP cc_start: 0.8980 (t0) cc_final: 0.8357 (t70) REVERT: G 147 MET cc_start: 0.8823 (tpt) cc_final: 0.8570 (tpp) REVERT: G 264 HIS cc_start: 0.7486 (p-80) cc_final: 0.6414 (p-80) REVERT: G 300 MET cc_start: 0.8208 (mtt) cc_final: 0.7826 (mtm) REVERT: G 323 MET cc_start: 0.8471 (mmm) cc_final: 0.8013 (tpp) REVERT: D 25 SER cc_start: 0.9108 (m) cc_final: 0.8644 (p) REVERT: D 183 TYR cc_start: 0.8744 (m-80) cc_final: 0.8499 (m-80) REVERT: D 222 TYR cc_start: 0.7998 (m-80) cc_final: 0.7245 (m-80) REVERT: D 257 MET cc_start: 0.7410 (mmm) cc_final: 0.7194 (mmm) REVERT: D 264 HIS cc_start: 0.7921 (p-80) cc_final: 0.7266 (p-80) REVERT: D 321 MET cc_start: 0.8085 (pmm) cc_final: 0.7412 (pmm) REVERT: D 336 LYS cc_start: 0.7814 (ptpt) cc_final: 0.7552 (ptpp) REVERT: D 348 ASN cc_start: 0.8373 (p0) cc_final: 0.8018 (p0) REVERT: D 403 MET cc_start: 0.7032 (ttp) cc_final: 0.6472 (ptp) REVERT: D 406 MET cc_start: 0.6403 (mmp) cc_final: 0.6007 (mmp) REVERT: D 426 GLN cc_start: 0.8183 (tp40) cc_final: 0.7938 (tp40) REVERT: I 4 ILE cc_start: 0.9685 (mt) cc_final: 0.9394 (mm) REVERT: I 67 ASP cc_start: 0.8963 (t0) cc_final: 0.8709 (t70) REVERT: I 147 MET cc_start: 0.8939 (mmp) cc_final: 0.8585 (mmm) REVERT: I 257 MET cc_start: 0.7595 (mmm) cc_final: 0.6578 (mmt) REVERT: I 264 HIS cc_start: 0.7849 (p90) cc_final: 0.7032 (p-80) REVERT: I 297 LYS cc_start: 0.9429 (ptpt) cc_final: 0.9220 (mtmt) REVERT: I 310 TYR cc_start: 0.8736 (m-80) cc_final: 0.8465 (m-10) REVERT: I 324 LYS cc_start: 0.8281 (tttm) cc_final: 0.8017 (ttmm) REVERT: I 350 LYS cc_start: 0.9130 (tptp) cc_final: 0.8843 (tppt) REVERT: I 355 ASP cc_start: 0.8655 (m-30) cc_final: 0.8153 (m-30) REVERT: B 26 ASP cc_start: 0.9152 (m-30) cc_final: 0.8799 (t70) REVERT: B 198 GLU cc_start: 0.8761 (pm20) cc_final: 0.8200 (pm20) REVERT: B 203 ASP cc_start: 0.8577 (t0) cc_final: 0.8306 (t0) REVERT: B 264 HIS cc_start: 0.7902 (p-80) cc_final: 0.7153 (p90) REVERT: B 293 MET cc_start: 0.8491 (mtm) cc_final: 0.8177 (mtm) REVERT: H 37 HIS cc_start: 0.8666 (m-70) cc_final: 0.8026 (m-70) REVERT: H 57 ASN cc_start: 0.9096 (m110) cc_final: 0.8722 (m110) REVERT: H 203 ASP cc_start: 0.8021 (t0) cc_final: 0.7692 (t0) REVERT: H 204 ASN cc_start: 0.8541 (m110) cc_final: 0.8076 (t0) REVERT: H 264 HIS cc_start: 0.7382 (p-80) cc_final: 0.6897 (p90) REVERT: H 297 LYS cc_start: 0.9361 (ptpp) cc_final: 0.8799 (mtmm) REVERT: H 356 ILE cc_start: 0.9282 (mm) cc_final: 0.8764 (tt) REVERT: E 33 ASP cc_start: 0.8535 (m-30) cc_final: 0.8037 (p0) REVERT: E 49 PHE cc_start: 0.7869 (p90) cc_final: 0.7571 (p90) REVERT: E 90 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7427 (tp30) REVERT: E 151 SER cc_start: 0.9347 (m) cc_final: 0.9056 (p) REVERT: E 157 LEU cc_start: 0.8564 (mt) cc_final: 0.8344 (mt) REVERT: E 213 CYS cc_start: 0.8528 (m) cc_final: 0.8282 (p) REVERT: E 230 LEU cc_start: 0.9223 (mm) cc_final: 0.8795 (tt) REVERT: E 407 TRP cc_start: 0.8926 (m100) cc_final: 0.8279 (m100) REVERT: J 24 TYR cc_start: 0.8476 (m-80) cc_final: 0.8034 (m-80) REVERT: J 31 GLN cc_start: 0.8656 (mm-40) cc_final: 0.7798 (mt0) REVERT: J 33 ASP cc_start: 0.8535 (m-30) cc_final: 0.8020 (p0) REVERT: J 90 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7416 (tp30) REVERT: J 91 GLN cc_start: 0.8423 (mt0) cc_final: 0.8022 (mm110) REVERT: J 151 SER cc_start: 0.9329 (m) cc_final: 0.9062 (p) REVERT: J 186 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7366 (m-40) REVERT: J 230 LEU cc_start: 0.9365 (mp) cc_final: 0.8907 (tt) REVERT: J 233 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8649 (mm-40) REVERT: J 305 CYS cc_start: 0.8534 (m) cc_final: 0.8186 (m) REVERT: J 313 MET cc_start: 0.7091 (mtp) cc_final: 0.6800 (mtt) REVERT: J 352 LYS cc_start: 0.8745 (tptt) cc_final: 0.7951 (tppt) REVERT: J 368 LEU cc_start: 0.9183 (mp) cc_final: 0.8905 (pp) REVERT: J 398 MET cc_start: 0.7708 (ttm) cc_final: 0.7465 (ttm) REVERT: C 33 ASP cc_start: 0.8328 (m-30) cc_final: 0.7814 (p0) REVERT: C 96 LYS cc_start: 0.8117 (mmtp) cc_final: 0.7393 (mmmm) REVERT: C 112 LYS cc_start: 0.9205 (ttmt) cc_final: 0.8964 (ttpp) REVERT: C 120 ASP cc_start: 0.8432 (t70) cc_final: 0.8117 (t0) REVERT: C 156 ARG cc_start: 0.8879 (mmm-85) cc_final: 0.8651 (mmm-85) REVERT: C 203 MET cc_start: 0.8790 (mmm) cc_final: 0.8578 (mmm) REVERT: C 210 TYR cc_start: 0.8716 (m-80) cc_final: 0.8509 (m-10) REVERT: C 233 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8632 (mm-40) REVERT: C 241 SER cc_start: 0.8581 (p) cc_final: 0.8007 (t) REVERT: C 285 GLN cc_start: 0.7884 (pt0) cc_final: 0.7150 (mm-40) REVERT: C 290 GLU cc_start: 0.6676 (tt0) cc_final: 0.6457 (tt0) REVERT: C 368 LEU cc_start: 0.8910 (mp) cc_final: 0.8520 (pp) REVERT: C 398 MET cc_start: 0.8248 (mtt) cc_final: 0.7621 (ttm) REVERT: C 402 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7927 (mmm160) REVERT: L 31 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8267 (mt0) REVERT: L 33 ASP cc_start: 0.8584 (m-30) cc_final: 0.7716 (p0) REVERT: L 90 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7408 (tp30) REVERT: L 123 ARG cc_start: 0.8073 (ttp-110) cc_final: 0.7859 (ttm110) REVERT: L 154 MET cc_start: 0.9216 (mmm) cc_final: 0.8948 (mmt) REVERT: L 169 PHE cc_start: 0.7845 (m-10) cc_final: 0.7466 (m-10) REVERT: L 233 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8633 (mm-40) REVERT: L 285 GLN cc_start: 0.8210 (pt0) cc_final: 0.7429 (mp10) REVERT: L 315 CYS cc_start: 0.7585 (m) cc_final: 0.7302 (m) REVERT: L 368 LEU cc_start: 0.9105 (mp) cc_final: 0.8709 (pp) REVERT: L 398 MET cc_start: 0.7863 (ttm) cc_final: 0.7542 (ttp) REVERT: K 31 GLN cc_start: 0.8755 (mm110) cc_final: 0.8514 (mt0) REVERT: K 69 ASP cc_start: 0.8272 (t0) cc_final: 0.7896 (t0) REVERT: K 90 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7432 (tp30) REVERT: K 120 ASP cc_start: 0.8575 (t70) cc_final: 0.8180 (t0) REVERT: K 154 MET cc_start: 0.9130 (mmm) cc_final: 0.8757 (mmm) REVERT: K 230 LEU cc_start: 0.9105 (mp) cc_final: 0.8819 (tt) REVERT: K 291 ILE cc_start: 0.8768 (pt) cc_final: 0.8567 (pt) REVERT: K 338 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8666 (mtpp) REVERT: K 368 LEU cc_start: 0.9202 (mp) cc_final: 0.8922 (pp) REVERT: K 413 MET cc_start: 0.8391 (tpp) cc_final: 0.8127 (tpp) outliers start: 4 outliers final: 0 residues processed: 1046 average time/residue: 0.2321 time to fit residues: 408.8635 Evaluate side-chains 759 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 757 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 120 optimal weight: 3.9990 chunk 378 optimal weight: 0.0670 chunk 11 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 489 optimal weight: 4.9990 chunk 423 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 258 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 ASN G 375 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 423 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 ASN H 414 ASN E 18 ASN E 186 ASN E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 192 HIS ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.109314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.098452 restraints weight = 94331.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.101481 restraints weight = 47833.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.103492 restraints weight = 27990.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.104867 restraints weight = 18004.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.105817 restraints weight = 12386.795| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 41820 Z= 0.138 Angle : 0.560 8.670 56820 Z= 0.283 Chirality : 0.045 0.224 6216 Planarity : 0.004 0.070 7398 Dihedral : 11.302 179.370 5760 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.11 % Allowed : 1.30 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.12), residues: 5130 helix: -0.00 (0.11), residues: 2190 sheet: -0.92 (0.18), residues: 852 loop : -1.40 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 221 TYR 0.019 0.001 TYR A 272 PHE 0.022 0.001 PHE D 367 TRP 0.017 0.002 TRP L 21 HIS 0.005 0.001 HIS J 192 Details of bonding type rmsd covalent geometry : bond 0.00308 (41820) covalent geometry : angle 0.55985 (56820) hydrogen bonds : bond 0.03671 ( 1368) hydrogen bonds : angle 4.54094 ( 4032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1044 time to evaluate : 1.660 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 SER cc_start: 0.9323 (m) cc_final: 0.9117 (t) REVERT: F 26 ASP cc_start: 0.9119 (m-30) cc_final: 0.8798 (t70) REVERT: F 32 PRO cc_start: 0.9300 (Cg_exo) cc_final: 0.9033 (Cg_endo) REVERT: F 59 TYR cc_start: 0.8537 (m-10) cc_final: 0.8304 (m-10) REVERT: F 157 GLU cc_start: 0.8418 (pp20) cc_final: 0.8072 (pp20) REVERT: F 205 GLU cc_start: 0.8822 (tp30) cc_final: 0.8561 (mm-30) REVERT: F 256 ASN cc_start: 0.8388 (m-40) cc_final: 0.7643 (t0) REVERT: F 264 HIS cc_start: 0.7776 (p-80) cc_final: 0.6958 (p-80) REVERT: F 334 GLN cc_start: 0.8929 (tt0) cc_final: 0.8593 (tm-30) REVERT: F 340 TYR cc_start: 0.7724 (m-10) cc_final: 0.7346 (m-10) REVERT: A 69 ASP cc_start: 0.8030 (t0) cc_final: 0.7527 (t0) REVERT: A 90 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7364 (tp30) REVERT: A 154 MET cc_start: 0.9139 (mmm) cc_final: 0.8710 (mmm) REVERT: A 214 ARG cc_start: 0.8831 (ttp80) cc_final: 0.8354 (tmm-80) REVERT: A 254 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 276 ILE cc_start: 0.9009 (pt) cc_final: 0.8770 (mt) REVERT: A 301 GLN cc_start: 0.9167 (mm110) cc_final: 0.8346 (mm-40) REVERT: A 320 ARG cc_start: 0.7910 (ptm160) cc_final: 0.7420 (ptm160) REVERT: A 368 LEU cc_start: 0.8901 (mp) cc_final: 0.8602 (pp) REVERT: A 398 MET cc_start: 0.7852 (ttm) cc_final: 0.7384 (ttm) REVERT: G 4 ILE cc_start: 0.9626 (mt) cc_final: 0.9353 (mm) REVERT: G 25 SER cc_start: 0.8352 (t) cc_final: 0.7944 (p) REVERT: G 67 ASP cc_start: 0.8939 (t0) cc_final: 0.8389 (t70) REVERT: G 147 MET cc_start: 0.8813 (tpt) cc_final: 0.8578 (tpp) REVERT: G 264 HIS cc_start: 0.7439 (p-80) cc_final: 0.6357 (p-80) REVERT: G 297 LYS cc_start: 0.9351 (ptpt) cc_final: 0.9081 (mtmt) REVERT: G 300 MET cc_start: 0.8238 (mtt) cc_final: 0.7907 (mtm) REVERT: G 323 MET cc_start: 0.8428 (mmm) cc_final: 0.8000 (tpp) REVERT: D 25 SER cc_start: 0.9174 (m) cc_final: 0.8830 (p) REVERT: D 65 LEU cc_start: 0.8872 (mp) cc_final: 0.8639 (mp) REVERT: D 222 TYR cc_start: 0.7991 (m-80) cc_final: 0.7213 (m-80) REVERT: D 257 MET cc_start: 0.7258 (mmm) cc_final: 0.7051 (mmm) REVERT: D 264 HIS cc_start: 0.7862 (p-80) cc_final: 0.7211 (p-80) REVERT: D 297 LYS cc_start: 0.9486 (mtpt) cc_final: 0.9193 (ttmm) REVERT: D 321 MET cc_start: 0.8069 (pmm) cc_final: 0.7407 (pmm) REVERT: D 330 MET cc_start: 0.8472 (mmp) cc_final: 0.8254 (mmm) REVERT: D 348 ASN cc_start: 0.8507 (p0) cc_final: 0.8142 (p0) REVERT: D 406 MET cc_start: 0.5993 (mmp) cc_final: 0.5771 (mmp) REVERT: D 407 GLU cc_start: 0.6221 (pt0) cc_final: 0.5741 (pt0) REVERT: D 409 THR cc_start: 0.8852 (m) cc_final: 0.8485 (p) REVERT: D 426 GLN cc_start: 0.8265 (tp40) cc_final: 0.7934 (tp40) REVERT: I 4 ILE cc_start: 0.9716 (mt) cc_final: 0.9429 (mm) REVERT: I 6 HIS cc_start: 0.7905 (t70) cc_final: 0.7591 (t70) REVERT: I 147 MET cc_start: 0.8905 (mmp) cc_final: 0.8567 (mmm) REVERT: I 178 THR cc_start: 0.8484 (m) cc_final: 0.8265 (m) REVERT: I 264 HIS cc_start: 0.7770 (p90) cc_final: 0.7027 (p-80) REVERT: I 310 TYR cc_start: 0.8744 (m-80) cc_final: 0.8488 (m-10) REVERT: I 355 ASP cc_start: 0.8648 (m-30) cc_final: 0.8072 (m-30) REVERT: I 356 ILE cc_start: 0.9057 (mm) cc_final: 0.8515 (tt) REVERT: B 25 SER cc_start: 0.9433 (m) cc_final: 0.9030 (p) REVERT: B 26 ASP cc_start: 0.9147 (m-30) cc_final: 0.8693 (t70) REVERT: B 37 HIS cc_start: 0.8964 (m90) cc_final: 0.8668 (m-70) REVERT: B 101 TRP cc_start: 0.9101 (t60) cc_final: 0.8706 (t60) REVERT: B 198 GLU cc_start: 0.8718 (pm20) cc_final: 0.8122 (pm20) REVERT: B 203 ASP cc_start: 0.8539 (t0) cc_final: 0.8173 (t70) REVERT: B 264 HIS cc_start: 0.7738 (p-80) cc_final: 0.7202 (p90) REVERT: B 293 MET cc_start: 0.8572 (mtm) cc_final: 0.8245 (mtm) REVERT: B 297 LYS cc_start: 0.9243 (ttmm) cc_final: 0.8696 (ttmm) REVERT: B 321 MET cc_start: 0.8410 (pmm) cc_final: 0.7828 (pmm) REVERT: H 37 HIS cc_start: 0.8797 (m-70) cc_final: 0.8257 (m-70) REVERT: H 57 ASN cc_start: 0.9119 (m110) cc_final: 0.8756 (m110) REVERT: H 116 VAL cc_start: 0.8903 (t) cc_final: 0.8690 (p) REVERT: H 203 ASP cc_start: 0.7997 (t0) cc_final: 0.7584 (t0) REVERT: H 204 ASN cc_start: 0.8478 (m110) cc_final: 0.8047 (t0) REVERT: H 264 HIS cc_start: 0.7337 (p-80) cc_final: 0.6930 (p90) REVERT: H 297 LYS cc_start: 0.9345 (ptpp) cc_final: 0.8763 (mtmm) REVERT: H 321 MET cc_start: 0.8325 (ptp) cc_final: 0.7958 (pmm) REVERT: H 356 ILE cc_start: 0.9258 (mm) cc_final: 0.8749 (tt) REVERT: E 33 ASP cc_start: 0.8541 (m-30) cc_final: 0.8027 (p0) REVERT: E 49 PHE cc_start: 0.7919 (p90) cc_final: 0.7614 (p90) REVERT: E 151 SER cc_start: 0.9373 (m) cc_final: 0.9092 (p) REVERT: E 157 LEU cc_start: 0.8624 (mt) cc_final: 0.8360 (mt) REVERT: E 213 CYS cc_start: 0.8492 (m) cc_final: 0.8274 (p) REVERT: E 230 LEU cc_start: 0.9245 (mm) cc_final: 0.8793 (tt) REVERT: E 295 CYS cc_start: 0.8063 (m) cc_final: 0.7783 (m) REVERT: E 301 GLN cc_start: 0.8618 (mp10) cc_final: 0.8190 (mm-40) REVERT: E 352 LYS cc_start: 0.8904 (tptp) cc_final: 0.8209 (tttp) REVERT: E 377 MET cc_start: 0.8019 (tmm) cc_final: 0.7676 (tmm) REVERT: E 407 TRP cc_start: 0.8867 (m100) cc_final: 0.8196 (m100) REVERT: J 24 TYR cc_start: 0.8532 (m-80) cc_final: 0.8173 (m-80) REVERT: J 31 GLN cc_start: 0.8693 (mm-40) cc_final: 0.7753 (mt0) REVERT: J 90 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7471 (tp30) REVERT: J 172 TYR cc_start: 0.8471 (t80) cc_final: 0.8211 (t80) REVERT: J 202 PHE cc_start: 0.8193 (m-10) cc_final: 0.7943 (m-10) REVERT: J 230 LEU cc_start: 0.9345 (mp) cc_final: 0.8933 (tt) REVERT: J 233 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8645 (mm-40) REVERT: J 313 MET cc_start: 0.7055 (mtp) cc_final: 0.6801 (mtt) REVERT: J 315 CYS cc_start: 0.7963 (m) cc_final: 0.7593 (m) REVERT: J 352 LYS cc_start: 0.8745 (tptt) cc_final: 0.7960 (tppt) REVERT: J 368 LEU cc_start: 0.9177 (mp) cc_final: 0.8875 (pp) REVERT: J 398 MET cc_start: 0.7684 (ttm) cc_final: 0.7402 (ttm) REVERT: C 33 ASP cc_start: 0.8345 (m-30) cc_final: 0.7798 (p0) REVERT: C 112 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8938 (ttpp) REVERT: C 120 ASP cc_start: 0.8423 (t70) cc_final: 0.8060 (t0) REVERT: C 123 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8115 (mmm-85) REVERT: C 233 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8502 (mm-40) REVERT: C 241 SER cc_start: 0.8542 (p) cc_final: 0.7948 (t) REVERT: C 285 GLN cc_start: 0.7804 (pt0) cc_final: 0.7073 (mm-40) REVERT: C 290 GLU cc_start: 0.6714 (tt0) cc_final: 0.6479 (tt0) REVERT: C 368 LEU cc_start: 0.8816 (mp) cc_final: 0.8403 (pp) REVERT: C 398 MET cc_start: 0.8248 (mtt) cc_final: 0.7672 (ttm) REVERT: C 428 LEU cc_start: 0.8592 (tt) cc_final: 0.8062 (mm) REVERT: L 31 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8257 (mt0) REVERT: L 90 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7490 (tp30) REVERT: L 123 ARG cc_start: 0.8087 (ttp-110) cc_final: 0.7852 (ttm110) REVERT: L 154 MET cc_start: 0.9215 (mmm) cc_final: 0.8935 (mmt) REVERT: L 169 PHE cc_start: 0.7844 (m-10) cc_final: 0.7526 (m-10) REVERT: L 285 GLN cc_start: 0.8288 (pt0) cc_final: 0.7330 (mp10) REVERT: L 315 CYS cc_start: 0.7626 (m) cc_final: 0.7370 (m) REVERT: L 368 LEU cc_start: 0.9058 (mp) cc_final: 0.8645 (pp) REVERT: L 398 MET cc_start: 0.7865 (ttm) cc_final: 0.7419 (ttp) REVERT: K 31 GLN cc_start: 0.8714 (mm110) cc_final: 0.8433 (mt0) REVERT: K 36 MET cc_start: 0.8218 (ppp) cc_final: 0.7974 (ppp) REVERT: K 69 ASP cc_start: 0.8165 (t0) cc_final: 0.7842 (t0) REVERT: K 90 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7420 (tp30) REVERT: K 93 ILE cc_start: 0.8590 (mm) cc_final: 0.8339 (mm) REVERT: K 96 LYS cc_start: 0.8624 (tptm) cc_final: 0.8373 (tptm) REVERT: K 120 ASP cc_start: 0.8573 (t70) cc_final: 0.8280 (t0) REVERT: K 154 MET cc_start: 0.9134 (mmm) cc_final: 0.8787 (mmm) REVERT: K 230 LEU cc_start: 0.9077 (mp) cc_final: 0.8752 (tt) REVERT: K 302 MET cc_start: 0.7976 (tpt) cc_final: 0.7758 (tpt) REVERT: K 338 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8666 (mtpp) REVERT: K 368 LEU cc_start: 0.9221 (mp) cc_final: 0.8902 (pp) outliers start: 5 outliers final: 1 residues processed: 1048 average time/residue: 0.2377 time to fit residues: 419.7309 Evaluate side-chains 775 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 774 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 490 optimal weight: 20.0000 chunk 467 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 394 optimal weight: 30.0000 chunk 375 optimal weight: 5.9990 chunk 400 optimal weight: 0.0970 chunk 67 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 280 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 overall best weight: 4.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 256 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 ASN E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 192 HIS C 258 ASN C 309 HIS ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.106128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.095248 restraints weight = 95195.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.098274 restraints weight = 47906.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.100291 restraints weight = 27946.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.101645 restraints weight = 17964.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.102602 restraints weight = 12412.741| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 41820 Z= 0.156 Angle : 0.584 9.299 56820 Z= 0.295 Chirality : 0.046 0.253 6216 Planarity : 0.004 0.069 7398 Dihedral : 11.256 179.443 5760 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.07 % Allowed : 0.93 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.12), residues: 5130 helix: 0.07 (0.11), residues: 2196 sheet: -0.95 (0.17), residues: 852 loop : -1.36 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 156 TYR 0.038 0.001 TYR K 185 PHE 0.022 0.001 PHE D 367 TRP 0.019 0.002 TRP L 21 HIS 0.006 0.001 HIS J 192 Details of bonding type rmsd covalent geometry : bond 0.00350 (41820) covalent geometry : angle 0.58365 (56820) hydrogen bonds : bond 0.03675 ( 1368) hydrogen bonds : angle 4.59852 ( 4032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1025 time to evaluate : 1.599 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: symmetry clash revert: symmetry clash REVERT: F 26 ASP cc_start: 0.9094 (m-30) cc_final: 0.8796 (t70) REVERT: F 59 TYR cc_start: 0.8536 (m-10) cc_final: 0.8261 (m-10) REVERT: F 157 GLU cc_start: 0.8524 (pp20) cc_final: 0.8165 (pp20) REVERT: F 256 ASN cc_start: 0.8149 (m-40) cc_final: 0.7737 (t0) REVERT: F 264 HIS cc_start: 0.7803 (p-80) cc_final: 0.7062 (p-80) REVERT: F 334 GLN cc_start: 0.8996 (tt0) cc_final: 0.8592 (tm-30) REVERT: F 362 LYS cc_start: 0.8474 (tttm) cc_final: 0.8182 (tttm) REVERT: F 363 MET cc_start: 0.8653 (pmm) cc_final: 0.8389 (pmm) REVERT: A 69 ASP cc_start: 0.8060 (t0) cc_final: 0.7533 (t0) REVERT: A 90 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7492 (tp30) REVERT: A 154 MET cc_start: 0.9188 (mmm) cc_final: 0.8809 (mmm) REVERT: A 168 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7454 (tt0) REVERT: A 214 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8332 (tmm-80) REVERT: A 241 SER cc_start: 0.8037 (p) cc_final: 0.7766 (p) REVERT: A 254 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 320 ARG cc_start: 0.7941 (ptm160) cc_final: 0.7590 (ptm160) REVERT: A 368 LEU cc_start: 0.8935 (mp) cc_final: 0.8637 (pp) REVERT: A 398 MET cc_start: 0.7943 (ttm) cc_final: 0.7416 (ttm) REVERT: A 407 TRP cc_start: 0.8967 (m100) cc_final: 0.8683 (m100) REVERT: G 4 ILE cc_start: 0.9618 (mt) cc_final: 0.9332 (mm) REVERT: G 147 MET cc_start: 0.8869 (tpt) cc_final: 0.8617 (tpp) REVERT: G 264 HIS cc_start: 0.7313 (p-80) cc_final: 0.6358 (p-80) REVERT: G 300 MET cc_start: 0.8491 (mtt) cc_final: 0.8112 (mtm) REVERT: G 323 MET cc_start: 0.8471 (mmm) cc_final: 0.8097 (tpp) REVERT: G 406 MET cc_start: 0.7181 (mmp) cc_final: 0.6161 (tpp) REVERT: D 25 SER cc_start: 0.9252 (m) cc_final: 0.8849 (p) REVERT: D 65 LEU cc_start: 0.8972 (mp) cc_final: 0.8766 (mp) REVERT: D 222 TYR cc_start: 0.7993 (m-80) cc_final: 0.7421 (m-80) REVERT: D 257 MET cc_start: 0.7489 (mmm) cc_final: 0.7224 (mmm) REVERT: D 297 LYS cc_start: 0.9474 (mtpt) cc_final: 0.9209 (ttmm) REVERT: D 321 MET cc_start: 0.8081 (pmm) cc_final: 0.7758 (pmm) REVERT: D 330 MET cc_start: 0.8507 (mmp) cc_final: 0.8294 (mmm) REVERT: D 348 ASN cc_start: 0.8492 (p0) cc_final: 0.8165 (p0) REVERT: D 426 GLN cc_start: 0.8249 (tp40) cc_final: 0.7842 (tp40) REVERT: I 4 ILE cc_start: 0.9660 (mt) cc_final: 0.9400 (mm) REVERT: I 147 MET cc_start: 0.8941 (mmp) cc_final: 0.8455 (mmm) REVERT: I 178 THR cc_start: 0.8523 (m) cc_final: 0.8289 (m) REVERT: I 257 MET cc_start: 0.7609 (mmm) cc_final: 0.6673 (mmt) REVERT: I 264 HIS cc_start: 0.7830 (p90) cc_final: 0.7018 (p-80) REVERT: I 310 TYR cc_start: 0.8768 (m-80) cc_final: 0.8478 (m-10) REVERT: I 355 ASP cc_start: 0.8676 (m-30) cc_final: 0.8090 (m-30) REVERT: I 356 ILE cc_start: 0.9077 (mm) cc_final: 0.8586 (tt) REVERT: B 26 ASP cc_start: 0.9167 (m-30) cc_final: 0.7935 (t70) REVERT: B 37 HIS cc_start: 0.8977 (m90) cc_final: 0.8713 (m-70) REVERT: B 101 TRP cc_start: 0.9121 (t60) cc_final: 0.8733 (t60) REVERT: B 198 GLU cc_start: 0.8778 (pm20) cc_final: 0.8058 (pm20) REVERT: B 203 ASP cc_start: 0.8542 (t0) cc_final: 0.8262 (t0) REVERT: B 264 HIS cc_start: 0.7788 (p-80) cc_final: 0.7131 (p90) REVERT: B 282 ARG cc_start: 0.7394 (ttm-80) cc_final: 0.7158 (ttm-80) REVERT: B 321 MET cc_start: 0.8386 (pmm) cc_final: 0.7663 (pmm) REVERT: B 330 MET cc_start: 0.8495 (tpp) cc_final: 0.8217 (mmm) REVERT: B 359 ARG cc_start: 0.7300 (mtm180) cc_final: 0.6676 (mtm180) REVERT: B 388 MET cc_start: 0.8252 (mtp) cc_final: 0.8007 (mtp) REVERT: H 37 HIS cc_start: 0.8756 (m-70) cc_final: 0.8183 (m-70) REVERT: H 57 ASN cc_start: 0.9118 (m110) cc_final: 0.8769 (m110) REVERT: H 178 THR cc_start: 0.8118 (m) cc_final: 0.7870 (p) REVERT: H 203 ASP cc_start: 0.8031 (t0) cc_final: 0.7792 (t0) REVERT: H 204 ASN cc_start: 0.8442 (m110) cc_final: 0.8081 (t0) REVERT: H 264 HIS cc_start: 0.7397 (p-80) cc_final: 0.7010 (p90) REVERT: H 297 LYS cc_start: 0.9332 (ptpp) cc_final: 0.8746 (mtmm) REVERT: H 321 MET cc_start: 0.8454 (ptp) cc_final: 0.8027 (pmm) REVERT: H 406 MET cc_start: 0.7575 (mmm) cc_final: 0.7015 (mmm) REVERT: E 24 TYR cc_start: 0.8583 (m-80) cc_final: 0.8380 (m-80) REVERT: E 49 PHE cc_start: 0.7962 (p90) cc_final: 0.7649 (p90) REVERT: E 151 SER cc_start: 0.9411 (m) cc_final: 0.9133 (p) REVERT: E 157 LEU cc_start: 0.8651 (mt) cc_final: 0.8387 (mt) REVERT: E 213 CYS cc_start: 0.8571 (m) cc_final: 0.8336 (p) REVERT: E 230 LEU cc_start: 0.9291 (mm) cc_final: 0.8760 (tt) REVERT: E 254 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7168 (mt-10) REVERT: E 352 LYS cc_start: 0.8911 (tptp) cc_final: 0.8240 (tttp) REVERT: E 407 TRP cc_start: 0.8745 (m100) cc_final: 0.8045 (m100) REVERT: J 24 TYR cc_start: 0.8548 (m-80) cc_final: 0.8181 (m-80) REVERT: J 31 GLN cc_start: 0.8655 (mm-40) cc_final: 0.7719 (mt0) REVERT: J 90 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7602 (tp30) REVERT: J 172 TYR cc_start: 0.8556 (t80) cc_final: 0.8305 (t80) REVERT: J 230 LEU cc_start: 0.9384 (mp) cc_final: 0.8929 (tt) REVERT: J 233 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8561 (mm-40) REVERT: J 237 SER cc_start: 0.8644 (m) cc_final: 0.8432 (p) REVERT: J 313 MET cc_start: 0.7201 (mtp) cc_final: 0.6886 (mtt) REVERT: J 352 LYS cc_start: 0.8776 (tptt) cc_final: 0.7990 (tppt) REVERT: J 368 LEU cc_start: 0.9191 (mp) cc_final: 0.8908 (pp) REVERT: J 398 MET cc_start: 0.7733 (ttm) cc_final: 0.7429 (ttm) REVERT: C 36 MET cc_start: 0.8162 (ppp) cc_final: 0.7913 (ppp) REVERT: C 120 ASP cc_start: 0.8428 (t70) cc_final: 0.8061 (t0) REVERT: C 123 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8129 (mmm-85) REVERT: C 203 MET cc_start: 0.8692 (mmm) cc_final: 0.8423 (mmm) REVERT: C 233 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8444 (mm-40) REVERT: C 241 SER cc_start: 0.8554 (p) cc_final: 0.7979 (t) REVERT: C 285 GLN cc_start: 0.7834 (pt0) cc_final: 0.7079 (mm-40) REVERT: C 290 GLU cc_start: 0.6769 (tt0) cc_final: 0.6562 (tt0) REVERT: C 291 ILE cc_start: 0.8767 (pt) cc_final: 0.8391 (pt) REVERT: C 368 LEU cc_start: 0.8890 (mp) cc_final: 0.8523 (pp) REVERT: C 398 MET cc_start: 0.8336 (mtt) cc_final: 0.7692 (ttm) REVERT: C 402 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.7977 (mmm160) REVERT: L 31 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8302 (mt0) REVERT: L 90 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7517 (tp30) REVERT: L 123 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7925 (ttm110) REVERT: L 154 MET cc_start: 0.9235 (mmm) cc_final: 0.8955 (mmt) REVERT: L 169 PHE cc_start: 0.7890 (m-10) cc_final: 0.7581 (m-10) REVERT: L 285 GLN cc_start: 0.8251 (pt0) cc_final: 0.7358 (mp10) REVERT: L 315 CYS cc_start: 0.7579 (m) cc_final: 0.7306 (m) REVERT: L 368 LEU cc_start: 0.9058 (mp) cc_final: 0.8646 (pp) REVERT: L 398 MET cc_start: 0.7919 (ttm) cc_final: 0.7440 (ttp) REVERT: K 31 GLN cc_start: 0.8813 (mm110) cc_final: 0.8250 (mt0) REVERT: K 69 ASP cc_start: 0.8285 (t0) cc_final: 0.7912 (t0) REVERT: K 90 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7226 (tp30) REVERT: K 93 ILE cc_start: 0.8579 (mm) cc_final: 0.8334 (mm) REVERT: K 96 LYS cc_start: 0.8584 (tptm) cc_final: 0.8382 (tptm) REVERT: K 120 ASP cc_start: 0.8623 (t70) cc_final: 0.8311 (t0) REVERT: K 154 MET cc_start: 0.9173 (mmm) cc_final: 0.8814 (mmm) REVERT: K 230 LEU cc_start: 0.9081 (mp) cc_final: 0.8730 (tt) REVERT: K 338 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8649 (mtpp) REVERT: K 368 LEU cc_start: 0.9119 (mp) cc_final: 0.8864 (pp) outliers start: 3 outliers final: 0 residues processed: 1028 average time/residue: 0.2378 time to fit residues: 412.3408 Evaluate side-chains 751 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 751 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 22 optimal weight: 10.0000 chunk 278 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 309 optimal weight: 5.9990 chunk 301 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 273 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 405 optimal weight: 0.7980 chunk 264 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 ASN E 186 ASN E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** J 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 192 HIS ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.107022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.095929 restraints weight = 95071.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.098963 restraints weight = 48459.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.100990 restraints weight = 28508.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.102374 restraints weight = 18490.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.103279 restraints weight = 12854.122| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41820 Z= 0.137 Angle : 0.583 9.560 56820 Z= 0.291 Chirality : 0.045 0.251 6216 Planarity : 0.004 0.070 7398 Dihedral : 11.127 179.963 5760 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.11 % Allowed : 0.73 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.12), residues: 5130 helix: 0.15 (0.11), residues: 2232 sheet: -0.87 (0.17), residues: 864 loop : -1.30 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 156 TYR 0.026 0.001 TYR K 272 PHE 0.026 0.001 PHE B 260 TRP 0.019 0.002 TRP L 21 HIS 0.005 0.001 HIS J 192 Details of bonding type rmsd covalent geometry : bond 0.00310 (41820) covalent geometry : angle 0.58290 (56820) hydrogen bonds : bond 0.03576 ( 1368) hydrogen bonds : angle 4.52157 ( 4032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1005 time to evaluate : 1.580 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: symmetry clash REVERT: F 25 SER cc_start: 0.8909 (t) cc_final: 0.8162 (p) REVERT: F 26 ASP cc_start: 0.9086 (m-30) cc_final: 0.8816 (t70) REVERT: F 157 GLU cc_start: 0.8543 (pp20) cc_final: 0.8194 (pp20) REVERT: F 256 ASN cc_start: 0.8262 (m-40) cc_final: 0.7750 (t0) REVERT: F 297 LYS cc_start: 0.9400 (mtpt) cc_final: 0.9163 (mtpp) REVERT: F 300 MET cc_start: 0.8508 (mmm) cc_final: 0.8288 (mtt) REVERT: F 334 GLN cc_start: 0.8994 (tt0) cc_final: 0.8545 (tm-30) REVERT: F 340 TYR cc_start: 0.7871 (m-10) cc_final: 0.7481 (m-10) REVERT: F 362 LYS cc_start: 0.8469 (tttm) cc_final: 0.8133 (tttm) REVERT: F 363 MET cc_start: 0.8564 (pmm) cc_final: 0.8253 (pmm) REVERT: A 3 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 36 MET cc_start: 0.8222 (ppp) cc_final: 0.7955 (ppp) REVERT: A 69 ASP cc_start: 0.8051 (t0) cc_final: 0.7765 (t0) REVERT: A 90 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7464 (tp30) REVERT: A 154 MET cc_start: 0.9211 (mmm) cc_final: 0.8801 (mmm) REVERT: A 157 LEU cc_start: 0.9026 (mt) cc_final: 0.8673 (mt) REVERT: A 168 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7418 (tt0) REVERT: A 214 ARG cc_start: 0.8814 (ttp80) cc_final: 0.8180 (ttp80) REVERT: A 241 SER cc_start: 0.8019 (p) cc_final: 0.7742 (p) REVERT: A 254 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 258 ASN cc_start: 0.8776 (m110) cc_final: 0.8564 (t0) REVERT: A 276 ILE cc_start: 0.9012 (pt) cc_final: 0.8780 (mt) REVERT: A 291 ILE cc_start: 0.8662 (pt) cc_final: 0.8459 (pt) REVERT: A 320 ARG cc_start: 0.7847 (ptm160) cc_final: 0.7285 (ptm160) REVERT: A 368 LEU cc_start: 0.8943 (mp) cc_final: 0.8644 (pp) REVERT: A 398 MET cc_start: 0.8039 (ttm) cc_final: 0.7540 (ttm) REVERT: A 407 TRP cc_start: 0.8811 (m100) cc_final: 0.8542 (m100) REVERT: G 4 ILE cc_start: 0.9612 (mt) cc_final: 0.9330 (mm) REVERT: G 21 TRP cc_start: 0.8929 (m100) cc_final: 0.8281 (m100) REVERT: G 147 MET cc_start: 0.8823 (tpt) cc_final: 0.8562 (tpp) REVERT: G 264 HIS cc_start: 0.7401 (p-80) cc_final: 0.6391 (p-80) REVERT: G 300 MET cc_start: 0.8379 (mtt) cc_final: 0.8047 (mtm) REVERT: G 323 MET cc_start: 0.8494 (mmm) cc_final: 0.8112 (mmm) REVERT: G 406 MET cc_start: 0.7156 (mmp) cc_final: 0.6157 (tpp) REVERT: D 25 SER cc_start: 0.9208 (m) cc_final: 0.8825 (p) REVERT: D 65 LEU cc_start: 0.9097 (mp) cc_final: 0.8886 (mt) REVERT: D 222 TYR cc_start: 0.7945 (m-80) cc_final: 0.7394 (m-80) REVERT: D 321 MET cc_start: 0.8032 (pmm) cc_final: 0.7644 (pmm) REVERT: D 330 MET cc_start: 0.8435 (mmp) cc_final: 0.8224 (mmm) REVERT: D 348 ASN cc_start: 0.8513 (p0) cc_final: 0.8240 (p0) REVERT: I 4 ILE cc_start: 0.9675 (mt) cc_final: 0.9396 (mm) REVERT: I 147 MET cc_start: 0.8914 (mmp) cc_final: 0.8455 (mmm) REVERT: I 257 MET cc_start: 0.7583 (mmm) cc_final: 0.6544 (mmm) REVERT: I 264 HIS cc_start: 0.7799 (p90) cc_final: 0.6979 (p-80) REVERT: I 310 TYR cc_start: 0.8757 (m-80) cc_final: 0.8511 (m-10) REVERT: I 313 VAL cc_start: 0.8947 (t) cc_final: 0.8718 (t) REVERT: I 355 ASP cc_start: 0.8633 (m-30) cc_final: 0.8220 (m-30) REVERT: B 26 ASP cc_start: 0.9152 (m-30) cc_final: 0.7919 (t70) REVERT: B 37 HIS cc_start: 0.8977 (m90) cc_final: 0.8703 (m-70) REVERT: B 101 TRP cc_start: 0.9146 (t60) cc_final: 0.8746 (t60) REVERT: B 198 GLU cc_start: 0.8764 (pm20) cc_final: 0.8086 (pm20) REVERT: B 202 ILE cc_start: 0.9477 (tp) cc_final: 0.9196 (tp) REVERT: B 203 ASP cc_start: 0.8571 (t0) cc_final: 0.8261 (t0) REVERT: B 263 LEU cc_start: 0.8486 (mp) cc_final: 0.8283 (pp) REVERT: B 264 HIS cc_start: 0.7753 (p-80) cc_final: 0.7236 (p90) REVERT: B 282 ARG cc_start: 0.7406 (ttm-80) cc_final: 0.7185 (ttm-80) REVERT: B 321 MET cc_start: 0.8355 (pmm) cc_final: 0.7683 (pmm) REVERT: B 330 MET cc_start: 0.8428 (tpp) cc_final: 0.8146 (mmm) REVERT: B 359 ARG cc_start: 0.7311 (mtm180) cc_final: 0.6692 (mtm180) REVERT: B 403 MET cc_start: 0.8267 (mmm) cc_final: 0.7828 (tpp) REVERT: H 37 HIS cc_start: 0.8803 (m-70) cc_final: 0.8287 (m-70) REVERT: H 57 ASN cc_start: 0.9124 (m110) cc_final: 0.8780 (m110) REVERT: H 74 ASP cc_start: 0.9230 (m-30) cc_final: 0.9020 (m-30) REVERT: H 203 ASP cc_start: 0.8049 (t0) cc_final: 0.7481 (t0) REVERT: H 204 ASN cc_start: 0.8420 (m110) cc_final: 0.8090 (t0) REVERT: H 264 HIS cc_start: 0.7389 (p-80) cc_final: 0.7050 (p90) REVERT: H 297 LYS cc_start: 0.9320 (ptpp) cc_final: 0.8720 (mtmm) REVERT: H 321 MET cc_start: 0.8437 (ptp) cc_final: 0.8076 (pmm) REVERT: H 367 PHE cc_start: 0.8145 (t80) cc_final: 0.7754 (t80) REVERT: H 406 MET cc_start: 0.7585 (mmm) cc_final: 0.7018 (mmm) REVERT: E 24 TYR cc_start: 0.8578 (m-80) cc_final: 0.8318 (m-80) REVERT: E 49 PHE cc_start: 0.7956 (p90) cc_final: 0.7642 (p90) REVERT: E 90 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7867 (tp30) REVERT: E 151 SER cc_start: 0.9492 (m) cc_final: 0.9179 (p) REVERT: E 157 LEU cc_start: 0.8670 (mt) cc_final: 0.8409 (mt) REVERT: E 213 CYS cc_start: 0.8545 (m) cc_final: 0.8301 (p) REVERT: E 254 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7450 (mt-10) REVERT: E 352 LYS cc_start: 0.8776 (tptp) cc_final: 0.8278 (tttp) REVERT: E 407 TRP cc_start: 0.8721 (m100) cc_final: 0.8143 (m100) REVERT: J 24 TYR cc_start: 0.8515 (m-80) cc_final: 0.8207 (m-80) REVERT: J 90 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7693 (tp30) REVERT: J 213 CYS cc_start: 0.8592 (m) cc_final: 0.8389 (p) REVERT: J 233 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8562 (mm-40) REVERT: J 313 MET cc_start: 0.7203 (mtp) cc_final: 0.6912 (mtt) REVERT: J 352 LYS cc_start: 0.8782 (tptt) cc_final: 0.7991 (tppt) REVERT: J 368 LEU cc_start: 0.9114 (mp) cc_final: 0.8872 (pp) REVERT: J 398 MET cc_start: 0.7754 (ttm) cc_final: 0.7401 (ttm) REVERT: C 120 ASP cc_start: 0.8400 (t70) cc_final: 0.8044 (t0) REVERT: C 123 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8229 (mmm-85) REVERT: C 203 MET cc_start: 0.8697 (mmm) cc_final: 0.8412 (mmm) REVERT: C 221 ARG cc_start: 0.8901 (mtt-85) cc_final: 0.8647 (mmm-85) REVERT: C 233 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8469 (mm-40) REVERT: C 241 SER cc_start: 0.8536 (p) cc_final: 0.7988 (t) REVERT: C 285 GLN cc_start: 0.7920 (pt0) cc_final: 0.7100 (mm-40) REVERT: C 290 GLU cc_start: 0.6744 (tt0) cc_final: 0.6516 (tt0) REVERT: C 291 ILE cc_start: 0.8755 (pt) cc_final: 0.8356 (pt) REVERT: C 368 LEU cc_start: 0.8860 (mp) cc_final: 0.8496 (pp) REVERT: C 398 MET cc_start: 0.8311 (mtt) cc_final: 0.7644 (ttm) REVERT: C 428 LEU cc_start: 0.8535 (tt) cc_final: 0.8012 (mm) REVERT: L 3 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6937 (mm-30) REVERT: L 31 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8352 (mt0) REVERT: L 90 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7500 (tp30) REVERT: L 123 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7915 (ttm110) REVERT: L 129 CYS cc_start: 0.7372 (m) cc_final: 0.6677 (m) REVERT: L 169 PHE cc_start: 0.7883 (m-10) cc_final: 0.7553 (m-10) REVERT: L 285 GLN cc_start: 0.8253 (pt0) cc_final: 0.7356 (mp10) REVERT: L 291 ILE cc_start: 0.8890 (pt) cc_final: 0.8658 (pt) REVERT: L 305 CYS cc_start: 0.8775 (m) cc_final: 0.8531 (m) REVERT: L 315 CYS cc_start: 0.7591 (m) cc_final: 0.7325 (m) REVERT: L 372 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7974 (tt0) REVERT: L 398 MET cc_start: 0.7919 (ttm) cc_final: 0.7402 (ttp) REVERT: K 31 GLN cc_start: 0.8776 (mm110) cc_final: 0.8182 (mt0) REVERT: K 69 ASP cc_start: 0.8270 (t0) cc_final: 0.7953 (t0) REVERT: K 90 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7471 (tp30) REVERT: K 93 ILE cc_start: 0.8550 (mm) cc_final: 0.8307 (mm) REVERT: K 96 LYS cc_start: 0.8592 (tptm) cc_final: 0.8384 (tptm) REVERT: K 120 ASP cc_start: 0.8568 (t70) cc_final: 0.8364 (t0) REVERT: K 154 MET cc_start: 0.9170 (mmm) cc_final: 0.8806 (mmm) REVERT: K 230 LEU cc_start: 0.9072 (mp) cc_final: 0.8720 (tt) REVERT: K 291 ILE cc_start: 0.8777 (pt) cc_final: 0.8571 (pt) REVERT: K 338 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8638 (mtpp) REVERT: K 368 LEU cc_start: 0.9129 (mp) cc_final: 0.8840 (pp) outliers start: 5 outliers final: 0 residues processed: 1009 average time/residue: 0.2298 time to fit residues: 394.9505 Evaluate side-chains 756 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 756 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 97 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 397 optimal weight: 9.9990 chunk 410 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 218 optimal weight: 8.9990 chunk 480 optimal weight: 30.0000 chunk 454 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 350 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 192 HIS ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** 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 = 0.3704 r_free = 0.3704 target = 0.106872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.095696 restraints weight = 95626.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.098753 restraints weight = 48637.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.100806 restraints weight = 28624.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.102207 restraints weight = 18501.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.103182 restraints weight = 12820.696| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41820 Z= 0.137 Angle : 0.586 9.996 56820 Z= 0.293 Chirality : 0.046 0.241 6216 Planarity : 0.004 0.071 7398 Dihedral : 11.036 179.412 5760 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.05 % Allowed : 0.39 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.12), residues: 5130 helix: 0.25 (0.11), residues: 2190 sheet: -0.88 (0.17), residues: 852 loop : -1.24 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 221 TYR 0.024 0.001 TYR K 272 PHE 0.020 0.001 PHE B 260 TRP 0.020 0.002 TRP A 21 HIS 0.005 0.001 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00310 (41820) covalent geometry : angle 0.58570 (56820) hydrogen bonds : bond 0.03545 ( 1368) hydrogen bonds : angle 4.54395 ( 4032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 996 time to evaluate : 1.559 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: F 25 SER cc_start: 0.8891 (t) cc_final: 0.8114 (p) REVERT: F 26 ASP cc_start: 0.9110 (m-30) cc_final: 0.8827 (t70) REVERT: F 157 GLU cc_start: 0.8589 (pp20) cc_final: 0.8231 (pp20) REVERT: F 256 ASN cc_start: 0.8184 (m-40) cc_final: 0.7660 (t0) REVERT: F 264 HIS cc_start: 0.7497 (p-80) cc_final: 0.6993 (p-80) REVERT: F 297 LYS cc_start: 0.9376 (mtpt) cc_final: 0.9157 (mtpp) REVERT: F 334 GLN cc_start: 0.9007 (tt0) cc_final: 0.8529 (tm-30) REVERT: F 362 LYS cc_start: 0.8451 (tttm) cc_final: 0.8157 (tttm) REVERT: F 363 MET cc_start: 0.8554 (pmm) cc_final: 0.8187 (pmm) REVERT: F 426 GLN cc_start: 0.7838 (tt0) cc_final: 0.7637 (tp40) REVERT: A 3 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 90 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7445 (tp30) REVERT: A 154 MET cc_start: 0.9239 (mmm) cc_final: 0.8791 (mmm) REVERT: A 157 LEU cc_start: 0.9022 (mt) cc_final: 0.8659 (mt) REVERT: A 168 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7454 (tt0) REVERT: A 214 ARG cc_start: 0.8850 (ttp80) cc_final: 0.8227 (ttp80) REVERT: A 241 SER cc_start: 0.8028 (p) cc_final: 0.7806 (p) REVERT: A 254 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7763 (mt-10) REVERT: A 291 ILE cc_start: 0.8696 (pt) cc_final: 0.8490 (pt) REVERT: A 301 GLN cc_start: 0.9246 (mm110) cc_final: 0.8484 (mm-40) REVERT: A 320 ARG cc_start: 0.7843 (ptm160) cc_final: 0.7446 (ptm160) REVERT: A 368 LEU cc_start: 0.8956 (mp) cc_final: 0.8662 (pp) REVERT: A 398 MET cc_start: 0.8066 (ttm) cc_final: 0.7541 (ttm) REVERT: A 407 TRP cc_start: 0.8880 (m100) cc_final: 0.8661 (m100) REVERT: G 4 ILE cc_start: 0.9600 (mt) cc_final: 0.9312 (mm) REVERT: G 21 TRP cc_start: 0.8817 (m100) cc_final: 0.8267 (m100) REVERT: G 147 MET cc_start: 0.8842 (tpt) cc_final: 0.8572 (tpp) REVERT: G 264 HIS cc_start: 0.7445 (p-80) cc_final: 0.6629 (p-80) REVERT: G 300 MET cc_start: 0.8424 (mtt) cc_final: 0.7995 (mtm) REVERT: G 323 MET cc_start: 0.8472 (mmm) cc_final: 0.8164 (tpp) REVERT: G 406 MET cc_start: 0.7221 (mmp) cc_final: 0.6253 (tpp) REVERT: D 25 SER cc_start: 0.9204 (m) cc_final: 0.8831 (p) REVERT: D 65 LEU cc_start: 0.9107 (mp) cc_final: 0.8863 (mt) REVERT: D 111 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7986 (mt-10) REVERT: D 222 TYR cc_start: 0.7931 (m-80) cc_final: 0.7396 (m-80) REVERT: D 330 MET cc_start: 0.8460 (mmp) cc_final: 0.8254 (mmm) REVERT: D 348 ASN cc_start: 0.8450 (p0) cc_final: 0.8145 (p0) REVERT: D 426 GLN cc_start: 0.8397 (tp40) cc_final: 0.7956 (tm-30) REVERT: I 4 ILE cc_start: 0.9656 (mt) cc_final: 0.9401 (mm) REVERT: I 101 TRP cc_start: 0.8936 (t60) cc_final: 0.8479 (t60) REVERT: I 178 THR cc_start: 0.8411 (m) cc_final: 0.8166 (m) REVERT: I 257 MET cc_start: 0.7699 (mmm) cc_final: 0.6771 (mmm) REVERT: I 264 HIS cc_start: 0.7802 (p90) cc_final: 0.7017 (p-80) REVERT: I 297 LYS cc_start: 0.9402 (mtmt) cc_final: 0.9026 (mtmt) REVERT: I 310 TYR cc_start: 0.8766 (m-80) cc_final: 0.8507 (m-10) REVERT: I 355 ASP cc_start: 0.8597 (m-30) cc_final: 0.7983 (m-30) REVERT: I 356 ILE cc_start: 0.9220 (mp) cc_final: 0.8590 (tt) REVERT: B 26 ASP cc_start: 0.9148 (m-30) cc_final: 0.7908 (t70) REVERT: B 37 HIS cc_start: 0.8955 (m90) cc_final: 0.8674 (m-70) REVERT: B 59 TYR cc_start: 0.8318 (m-10) cc_final: 0.8056 (m-10) REVERT: B 101 TRP cc_start: 0.9158 (t60) cc_final: 0.8812 (t60) REVERT: B 145 SER cc_start: 0.9175 (p) cc_final: 0.8827 (p) REVERT: B 198 GLU cc_start: 0.8789 (pm20) cc_final: 0.7997 (pm20) REVERT: B 202 ILE cc_start: 0.9479 (tp) cc_final: 0.9210 (tp) REVERT: B 203 ASP cc_start: 0.8443 (t0) cc_final: 0.8126 (t0) REVERT: B 264 HIS cc_start: 0.7726 (p-80) cc_final: 0.7119 (p90) REVERT: B 282 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.7209 (ttm-80) REVERT: B 321 MET cc_start: 0.8337 (pmm) cc_final: 0.7707 (pmm) REVERT: B 359 ARG cc_start: 0.7320 (mtm180) cc_final: 0.6757 (mtm180) REVERT: B 403 MET cc_start: 0.8284 (mmm) cc_final: 0.8068 (mmp) REVERT: H 37 HIS cc_start: 0.8815 (m-70) cc_final: 0.8292 (m-70) REVERT: H 57 ASN cc_start: 0.9119 (m110) cc_final: 0.8781 (m110) REVERT: H 74 ASP cc_start: 0.9239 (m-30) cc_final: 0.9029 (m-30) REVERT: H 203 ASP cc_start: 0.8064 (t0) cc_final: 0.7646 (t0) REVERT: H 204 ASN cc_start: 0.8394 (m110) cc_final: 0.8115 (t0) REVERT: H 264 HIS cc_start: 0.7341 (p-80) cc_final: 0.7004 (p90) REVERT: H 297 LYS cc_start: 0.9328 (ptpp) cc_final: 0.8719 (mtmm) REVERT: H 321 MET cc_start: 0.8426 (ptp) cc_final: 0.8124 (pmm) REVERT: H 406 MET cc_start: 0.7652 (mmm) cc_final: 0.7186 (mmm) REVERT: E 24 TYR cc_start: 0.8577 (m-80) cc_final: 0.8313 (m-80) REVERT: E 49 PHE cc_start: 0.7984 (p90) cc_final: 0.7648 (p90) REVERT: E 90 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7771 (tp30) REVERT: E 151 SER cc_start: 0.9482 (m) cc_final: 0.9185 (p) REVERT: E 157 LEU cc_start: 0.8697 (mt) cc_final: 0.8441 (mt) REVERT: E 213 CYS cc_start: 0.8562 (m) cc_final: 0.8303 (p) REVERT: E 230 LEU cc_start: 0.9264 (mm) cc_final: 0.8805 (tt) REVERT: E 233 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8843 (mm-40) REVERT: E 295 CYS cc_start: 0.8205 (m) cc_final: 0.7967 (m) REVERT: E 352 LYS cc_start: 0.8903 (tptp) cc_final: 0.8244 (tttp) REVERT: J 24 TYR cc_start: 0.8527 (m-80) cc_final: 0.8215 (m-80) REVERT: J 66 VAL cc_start: 0.9238 (p) cc_final: 0.9028 (m) REVERT: J 90 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7705 (tp30) REVERT: J 213 CYS cc_start: 0.8640 (m) cc_final: 0.8403 (p) REVERT: J 305 CYS cc_start: 0.8280 (m) cc_final: 0.7964 (m) REVERT: J 313 MET cc_start: 0.7196 (mtp) cc_final: 0.6852 (mtt) REVERT: J 352 LYS cc_start: 0.8758 (tptt) cc_final: 0.7979 (tppt) REVERT: J 368 LEU cc_start: 0.9080 (mp) cc_final: 0.8868 (pp) REVERT: J 398 MET cc_start: 0.7746 (ttm) cc_final: 0.7369 (ttm) REVERT: C 90 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7489 (tp30) REVERT: C 120 ASP cc_start: 0.8440 (t70) cc_final: 0.8048 (t0) REVERT: C 221 ARG cc_start: 0.8914 (mtt-85) cc_final: 0.8682 (mmm-85) REVERT: C 233 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8549 (mm-40) REVERT: C 241 SER cc_start: 0.8531 (p) cc_final: 0.7973 (t) REVERT: C 285 GLN cc_start: 0.7917 (pt0) cc_final: 0.7166 (mm110) REVERT: C 368 LEU cc_start: 0.8841 (mp) cc_final: 0.8495 (pp) REVERT: C 402 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.8024 (mmm160) REVERT: C 428 LEU cc_start: 0.8547 (tt) cc_final: 0.8009 (mm) REVERT: L 3 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6908 (mm-30) REVERT: L 31 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8209 (mt0) REVERT: L 90 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7502 (tp30) REVERT: L 123 ARG cc_start: 0.8152 (ttp-110) cc_final: 0.7935 (ttm110) REVERT: L 129 CYS cc_start: 0.7361 (m) cc_final: 0.6959 (m) REVERT: L 169 PHE cc_start: 0.7881 (m-10) cc_final: 0.7556 (m-10) REVERT: L 213 CYS cc_start: 0.8717 (m) cc_final: 0.8314 (p) REVERT: L 233 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8416 (mm-40) REVERT: L 285 GLN cc_start: 0.8230 (pt0) cc_final: 0.7395 (mp10) REVERT: L 291 ILE cc_start: 0.8876 (pt) cc_final: 0.8625 (pt) REVERT: L 315 CYS cc_start: 0.7579 (m) cc_final: 0.7281 (m) REVERT: L 372 GLN cc_start: 0.8220 (tp-100) cc_final: 0.7952 (tt0) REVERT: L 398 MET cc_start: 0.7949 (ttm) cc_final: 0.7411 (ttp) REVERT: K 31 GLN cc_start: 0.8747 (mm110) cc_final: 0.8145 (mt0) REVERT: K 69 ASP cc_start: 0.8285 (t0) cc_final: 0.7988 (t0) REVERT: K 90 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7446 (tp30) REVERT: K 93 ILE cc_start: 0.8583 (mm) cc_final: 0.8314 (mm) REVERT: K 154 MET cc_start: 0.9192 (mmm) cc_final: 0.8907 (mmm) REVERT: K 157 LEU cc_start: 0.9051 (mt) cc_final: 0.8845 (mt) REVERT: K 230 LEU cc_start: 0.9070 (mp) cc_final: 0.8716 (tt) REVERT: K 338 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8646 (mtpp) REVERT: K 368 LEU cc_start: 0.9125 (mp) cc_final: 0.8840 (pp) outliers start: 2 outliers final: 1 residues processed: 998 average time/residue: 0.2376 time to fit residues: 403.3327 Evaluate side-chains 756 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 755 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 417 optimal weight: 2.9990 chunk 491 optimal weight: 9.9990 chunk 441 optimal weight: 2.9990 chunk 270 optimal weight: 20.0000 chunk 460 optimal weight: 9.9990 chunk 357 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 329 optimal weight: 20.0000 chunk 471 optimal weight: 0.0370 chunk 108 optimal weight: 20.0000 chunk 192 optimal weight: 8.9990 overall best weight: 2.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 192 HIS ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** 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 = 0.3741 r_free = 0.3741 target = 0.108984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.097809 restraints weight = 94123.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.100871 restraints weight = 47876.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.102925 restraints weight = 28191.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.104308 restraints weight = 18257.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.105302 restraints weight = 12716.504| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41820 Z= 0.112 Angle : 0.581 10.078 56820 Z= 0.288 Chirality : 0.045 0.243 6216 Planarity : 0.004 0.070 7398 Dihedral : 10.816 177.892 5760 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.05 % Allowed : 0.18 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.12), residues: 5130 helix: 0.40 (0.11), residues: 2184 sheet: -0.73 (0.17), residues: 858 loop : -1.21 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 221 TYR 0.021 0.001 TYR K 272 PHE 0.024 0.001 PHE B 385 TRP 0.020 0.002 TRP A 21 HIS 0.009 0.001 HIS L 28 Details of bonding type rmsd covalent geometry : bond 0.00253 (41820) covalent geometry : angle 0.58101 (56820) hydrogen bonds : bond 0.03402 ( 1368) hydrogen bonds : angle 4.41063 ( 4032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1022 time to evaluate : 1.663 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: symmetry clash revert: symmetry clash REVERT: F 25 SER cc_start: 0.8842 (t) cc_final: 0.8058 (p) REVERT: F 26 ASP cc_start: 0.9061 (m-30) cc_final: 0.8809 (t70) REVERT: F 53 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7997 (mm-30) REVERT: F 157 GLU cc_start: 0.8588 (pp20) cc_final: 0.8215 (pp20) REVERT: F 256 ASN cc_start: 0.8130 (m-40) cc_final: 0.7501 (t0) REVERT: F 264 HIS cc_start: 0.7462 (p-80) cc_final: 0.6922 (p-80) REVERT: F 321 MET cc_start: 0.8358 (ptp) cc_final: 0.7954 (pmm) REVERT: F 334 GLN cc_start: 0.8983 (tt0) cc_final: 0.8587 (tm-30) REVERT: F 340 TYR cc_start: 0.7804 (m-10) cc_final: 0.7539 (m-10) REVERT: F 362 LYS cc_start: 0.8494 (tttm) cc_final: 0.8130 (tttm) REVERT: F 363 MET cc_start: 0.8546 (pmm) cc_final: 0.8274 (pmm) REVERT: A 3 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7459 (mm-30) REVERT: A 90 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7374 (tp30) REVERT: A 154 MET cc_start: 0.9221 (mmm) cc_final: 0.8750 (mmm) REVERT: A 214 ARG cc_start: 0.8895 (ttp80) cc_final: 0.8314 (tmm-80) REVERT: A 230 LEU cc_start: 0.9259 (mm) cc_final: 0.8816 (tt) REVERT: A 241 SER cc_start: 0.8084 (p) cc_final: 0.7882 (p) REVERT: A 291 ILE cc_start: 0.8615 (pt) cc_final: 0.8407 (pt) REVERT: A 301 GLN cc_start: 0.9217 (mm110) cc_final: 0.8454 (mm-40) REVERT: A 320 ARG cc_start: 0.7862 (ptm160) cc_final: 0.7321 (ptm160) REVERT: A 368 LEU cc_start: 0.8939 (mp) cc_final: 0.8685 (pp) REVERT: A 398 MET cc_start: 0.7942 (ttm) cc_final: 0.7496 (ttm) REVERT: G 4 ILE cc_start: 0.9601 (mt) cc_final: 0.9342 (mm) REVERT: G 21 TRP cc_start: 0.8836 (m100) cc_final: 0.8318 (m100) REVERT: G 67 ASP cc_start: 0.8867 (t0) cc_final: 0.8591 (t0) REVERT: G 147 MET cc_start: 0.8800 (tpt) cc_final: 0.8519 (tpp) REVERT: G 264 HIS cc_start: 0.7331 (p-80) cc_final: 0.6551 (p-80) REVERT: G 297 LYS cc_start: 0.9501 (ptpt) cc_final: 0.9001 (mtmt) REVERT: G 300 MET cc_start: 0.8368 (mtt) cc_final: 0.8077 (mtm) REVERT: G 323 MET cc_start: 0.8471 (mmm) cc_final: 0.8151 (tpp) REVERT: G 406 MET cc_start: 0.7093 (mmp) cc_final: 0.6079 (tpp) REVERT: D 25 SER cc_start: 0.9143 (m) cc_final: 0.8774 (p) REVERT: D 101 TRP cc_start: 0.9140 (t60) cc_final: 0.8875 (t60) REVERT: D 222 TYR cc_start: 0.7869 (m-80) cc_final: 0.7297 (m-80) REVERT: D 256 ASN cc_start: 0.8666 (m-40) cc_final: 0.7454 (t0) REVERT: D 340 TYR cc_start: 0.7646 (m-10) cc_final: 0.7381 (m-10) REVERT: D 348 ASN cc_start: 0.8387 (p0) cc_final: 0.8110 (p0) REVERT: D 426 GLN cc_start: 0.8371 (tp40) cc_final: 0.7954 (tm-30) REVERT: I 4 ILE cc_start: 0.9685 (mt) cc_final: 0.9441 (mm) REVERT: I 101 TRP cc_start: 0.8961 (t60) cc_final: 0.8519 (t60) REVERT: I 147 MET cc_start: 0.8854 (mmm) cc_final: 0.8647 (mmp) REVERT: I 257 MET cc_start: 0.7681 (mmm) cc_final: 0.6770 (mmm) REVERT: I 264 HIS cc_start: 0.7687 (p90) cc_final: 0.6901 (p-80) REVERT: I 293 MET cc_start: 0.8194 (mtm) cc_final: 0.7717 (ptp) REVERT: I 310 TYR cc_start: 0.8717 (m-80) cc_final: 0.8425 (m-10) REVERT: I 324 LYS cc_start: 0.8278 (tttm) cc_final: 0.7995 (ttmm) REVERT: I 340 TYR cc_start: 0.7986 (m-10) cc_final: 0.7763 (m-10) REVERT: I 356 ILE cc_start: 0.9087 (mp) cc_final: 0.8629 (tt) REVERT: B 25 SER cc_start: 0.9407 (m) cc_final: 0.8931 (p) REVERT: B 26 ASP cc_start: 0.9124 (m-30) cc_final: 0.7837 (t70) REVERT: B 37 HIS cc_start: 0.8946 (m90) cc_final: 0.8650 (m-70) REVERT: B 101 TRP cc_start: 0.9178 (t60) cc_final: 0.8851 (t60) REVERT: B 145 SER cc_start: 0.9167 (p) cc_final: 0.8861 (p) REVERT: B 198 GLU cc_start: 0.8699 (pm20) cc_final: 0.8025 (pm20) REVERT: B 203 ASP cc_start: 0.8242 (t0) cc_final: 0.7830 (t70) REVERT: B 264 HIS cc_start: 0.7533 (p-80) cc_final: 0.7289 (p90) REVERT: B 321 MET cc_start: 0.8371 (pmm) cc_final: 0.7798 (pmm) REVERT: B 359 ARG cc_start: 0.7231 (mtm180) cc_final: 0.6621 (mtm180) REVERT: B 388 MET cc_start: 0.8276 (mtp) cc_final: 0.8054 (mtp) REVERT: H 37 HIS cc_start: 0.8763 (m-70) cc_final: 0.8273 (m-70) REVERT: H 57 ASN cc_start: 0.9110 (m110) cc_final: 0.8779 (m110) REVERT: H 74 ASP cc_start: 0.9206 (m-30) cc_final: 0.8998 (m-30) REVERT: H 233 MET cc_start: 0.8385 (ttp) cc_final: 0.8102 (ttp) REVERT: H 264 HIS cc_start: 0.7325 (p-80) cc_final: 0.6999 (p90) REVERT: H 297 LYS cc_start: 0.9300 (ptpp) cc_final: 0.8699 (mtmm) REVERT: H 367 PHE cc_start: 0.8209 (t80) cc_final: 0.7981 (t80) REVERT: H 403 MET cc_start: 0.7966 (mmm) cc_final: 0.7739 (mmp) REVERT: H 406 MET cc_start: 0.7718 (mmm) cc_final: 0.7278 (mmm) REVERT: H 425 TYR cc_start: 0.8909 (m-80) cc_final: 0.8613 (m-10) REVERT: E 24 TYR cc_start: 0.8498 (m-80) cc_final: 0.8170 (m-80) REVERT: E 33 ASP cc_start: 0.8617 (m-30) cc_final: 0.7875 (p0) REVERT: E 49 PHE cc_start: 0.8023 (p90) cc_final: 0.7718 (p90) REVERT: E 90 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7761 (tp30) REVERT: E 151 SER cc_start: 0.9443 (m) cc_final: 0.9173 (p) REVERT: E 157 LEU cc_start: 0.8664 (mt) cc_final: 0.8384 (mt) REVERT: E 230 LEU cc_start: 0.9194 (mm) cc_final: 0.8758 (tt) REVERT: E 295 CYS cc_start: 0.8202 (m) cc_final: 0.7958 (m) REVERT: E 352 LYS cc_start: 0.8700 (tptp) cc_final: 0.8290 (tttp) REVERT: J 24 TYR cc_start: 0.8474 (m-80) cc_final: 0.8242 (m-80) REVERT: J 90 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7636 (tp30) REVERT: J 313 MET cc_start: 0.7118 (mtp) cc_final: 0.6792 (mtt) REVERT: J 398 MET cc_start: 0.7719 (ttm) cc_final: 0.7404 (ttm) REVERT: C 86 LEU cc_start: 0.8322 (tp) cc_final: 0.8114 (tt) REVERT: C 90 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7490 (tp30) REVERT: C 120 ASP cc_start: 0.8466 (t70) cc_final: 0.8089 (t0) REVERT: C 169 PHE cc_start: 0.7946 (m-10) cc_final: 0.7737 (m-10) REVERT: C 203 MET cc_start: 0.8513 (mmm) cc_final: 0.8240 (mmm) REVERT: C 221 ARG cc_start: 0.8900 (mtt-85) cc_final: 0.8660 (mmm-85) REVERT: C 233 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8496 (mm-40) REVERT: C 241 SER cc_start: 0.8543 (p) cc_final: 0.7955 (t) REVERT: C 285 GLN cc_start: 0.7935 (pt0) cc_final: 0.7227 (mm110) REVERT: C 372 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7784 (tt0) REVERT: C 402 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.7999 (mmm160) REVERT: C 428 LEU cc_start: 0.8492 (tt) cc_final: 0.7869 (mm) REVERT: L 3 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6895 (mm-30) REVERT: L 31 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8188 (mt0) REVERT: L 90 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7450 (tp30) REVERT: L 119 LEU cc_start: 0.9183 (pp) cc_final: 0.8975 (pp) REVERT: L 123 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7798 (ttm110) REVERT: L 129 CYS cc_start: 0.7490 (m) cc_final: 0.6876 (m) REVERT: L 169 PHE cc_start: 0.7807 (m-10) cc_final: 0.7586 (m-10) REVERT: L 213 CYS cc_start: 0.8634 (m) cc_final: 0.8110 (p) REVERT: L 233 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8530 (mm-40) REVERT: L 285 GLN cc_start: 0.8213 (pt0) cc_final: 0.7073 (mm-40) REVERT: L 291 ILE cc_start: 0.8789 (pt) cc_final: 0.8486 (pt) REVERT: L 297 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8274 (tm-30) REVERT: L 315 CYS cc_start: 0.7667 (m) cc_final: 0.7419 (m) REVERT: L 368 LEU cc_start: 0.9063 (mm) cc_final: 0.8636 (pp) REVERT: L 372 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7995 (tt0) REVERT: L 398 MET cc_start: 0.7913 (ttm) cc_final: 0.7400 (ttp) REVERT: L 407 TRP cc_start: 0.8953 (m100) cc_final: 0.8372 (m100) REVERT: K 31 GLN cc_start: 0.8691 (mm110) cc_final: 0.8088 (mt0) REVERT: K 69 ASP cc_start: 0.8184 (t0) cc_final: 0.7837 (t0) REVERT: K 90 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7516 (tp30) REVERT: K 93 ILE cc_start: 0.8680 (mm) cc_final: 0.8408 (mm) REVERT: K 120 ASP cc_start: 0.8688 (t0) cc_final: 0.8485 (t0) REVERT: K 154 MET cc_start: 0.9176 (mmm) cc_final: 0.8891 (mmm) REVERT: K 230 LEU cc_start: 0.9111 (mp) cc_final: 0.8774 (tt) REVERT: K 233 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8725 (mm-40) REVERT: K 291 ILE cc_start: 0.8772 (pt) cc_final: 0.8281 (pt) REVERT: K 338 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8638 (mtpp) REVERT: K 368 LEU cc_start: 0.9070 (mp) cc_final: 0.8805 (pp) outliers start: 2 outliers final: 1 residues processed: 1024 average time/residue: 0.2344 time to fit residues: 408.7219 Evaluate side-chains 770 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 769 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 291 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 443 optimal weight: 20.0000 chunk 167 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 438 optimal weight: 20.0000 chunk 503 optimal weight: 0.0050 chunk 137 optimal weight: 0.6980 overall best weight: 2.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN F 347 ASN ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS D 256 ASN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 192 HIS ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.109277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.098177 restraints weight = 94798.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.101211 restraints weight = 47937.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.103263 restraints weight = 28190.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.104657 restraints weight = 18190.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.105631 restraints weight = 12617.823| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 41820 Z= 0.113 Angle : 0.578 10.483 56820 Z= 0.287 Chirality : 0.045 0.226 6216 Planarity : 0.004 0.071 7398 Dihedral : 10.661 179.506 5760 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.11 % Allowed : 0.14 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.12), residues: 5130 helix: 0.49 (0.11), residues: 2178 sheet: -0.58 (0.18), residues: 828 loop : -1.21 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 105 TYR 0.022 0.001 TYR K 185 PHE 0.024 0.001 PHE B 385 TRP 0.053 0.002 TRP B 397 HIS 0.015 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00255 (41820) covalent geometry : angle 0.57783 (56820) hydrogen bonds : bond 0.03312 ( 1368) hydrogen bonds : angle 4.39441 ( 4032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8405.99 seconds wall clock time: 145 minutes 43.31 seconds (8743.31 seconds total)