Starting phenix.real_space_refine on Tue Sep 15 13:52:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6evx_3962/09_2026/6evx_3962.cif Found real_map, /net/cci-nas-00/data/ceres_data/6evx_3962/09_2026/6evx_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_3962/09_2026/6evx_3962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6evx_3962/09_2026/6evx_3962.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6evx_3962/09_2026/6evx_3962.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6evx_3962/09_2026/6evx_3962.cif" model { file = "/net/cci-nas-00/data/ceres_data/6evx_3962/09_2026/6evx_3962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6evx_3962/09_2026/6evx_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40896 Number of models: 1 Model: "" Number of chains: 24 Chain: "F" 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: "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: "G" 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: "D" 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: "I" 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: "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: "H" 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: "E" 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: "J" 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: "C" 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: "L" 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: "K" 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: "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} Time building chain proxies: 8.26, per 1000 atoms: 0.20 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: 3.06 Conformation dependent library (CDL) restraints added in 1.6 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: 1.01 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: 8.57 Time building geometry restraints manager: 4.13 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: 0.080 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 34.380 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.080 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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/Z covalent geometry : bond 0.00492 / 0.24 (41820) covalent geometry : angle 0.78860 / 0.40 (56820) hydrogen bonds : bond 0.31767 / 21.29 ( 1368) hydrogen bonds : angle 9.91774 / 6.93 ( 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 : 1.530 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: 0.8656 (m100) REVERT: F 59 TYR cc_start: 0.8924 (m-80) cc_final: 0.8631 (m-80) REVERT: F 65 LEU cc_start: 0.8665 (mp) cc_final: 0.8428 (mp) REVERT: F 95 SER cc_start: 0.9066 (m) cc_final: 0.8757 (t) REVERT: F 101 TRP cc_start: 0.9134 (t60) cc_final: 0.8930 (t60) REVERT: F 125 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7937 (mt-10) REVERT: F 162 ARG cc_start: 0.8354 (mmt-90) cc_final: 0.8038 (mmp80) REVERT: F 164 MET cc_start: 0.9118 (tpt) cc_final: 0.8634 (mmm) REVERT: F 205 GLU cc_start: 0.8900 (tp30) cc_final: 0.8646 (mm-30) REVERT: F 233 MET cc_start: 0.8730 (mtp) cc_final: 0.8452 (mtm) REVERT: F 264 HIS cc_start: 0.8044 (p-80) cc_final: 0.7222 (p-80) REVERT: F 288 GLU cc_start: 0.6311 (tm-30) cc_final: 0.5837 (tm-30) REVERT: F 300 MET cc_start: 0.7738 (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: 0.8389 (t) REVERT: F 334 GLN cc_start: 0.8848 (tt0) cc_final: 0.8620 (tm-30) REVERT: F 340 TYR cc_start: 0.7798 (m-80) cc_final: 0.7562 (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: 0.8307 (m-80) REVERT: A 31 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8237 (mm-40) REVERT: A 33 ASP cc_start: 0.8444 (m-30) cc_final: 0.7510 (p0) REVERT: A 50 ASN cc_start: 0.8405 (t0) cc_final: 0.7762 (t0) REVERT: A 56 THR cc_start: 0.7959 (p) cc_final: 0.7649 (t) REVERT: A 85 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8385 (mm110) REVERT: A 90 GLU cc_start: 0.7788 (mm-30) cc_final: 0.6898 (tp30) REVERT: A 93 ILE cc_start: 0.8904 (mt) cc_final: 0.8665 (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: 0.7639 (t0) REVERT: A 151 SER cc_start: 0.8970 (m) cc_final: 0.8454 (p) REVERT: A 154 MET cc_start: 0.9037 (mmm) cc_final: 0.8604 (mmm) REVERT: A 172 TYR cc_start: 0.8099 (t80) cc_final: 0.7887 (t80) REVERT: A 188 ILE cc_start: 0.8710 (mm) cc_final: 0.8404 (mt) REVERT: A 210 TYR cc_start: 0.8929 (m-80) cc_final: 0.8577 (m-10) REVERT: A 233 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8293 (mm-40) REVERT: A 252 LEU cc_start: 0.8962 (mp) cc_final: 0.8692 (mt) REVERT: A 258 ASN cc_start: 0.8902 (m110) cc_final: 0.8669 (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: 0.8450 (ptp-110) REVERT: A 368 LEU cc_start: 0.9035 (mp) cc_final: 0.8628 (pp) REVERT: A 378 LEU cc_start: 0.8085 (mt) cc_final: 0.7566 (mm) REVERT: A 388 TRP cc_start: 0.8860 (m100) cc_final: 0.8619 (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: 0.7991 (t) REVERT: G 4 ILE cc_start: 0.9553 (mt) cc_final: 0.9344 (mm) REVERT: G 26 ASP cc_start: 0.9016 (m-30) cc_final: 0.8746 (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: 0.8659 (tpp) REVERT: G 184 ASN cc_start: 0.8456 (m-40) cc_final: 0.7857 (t0) REVERT: G 245 GLN cc_start: 0.8275 (mt0) cc_final: 0.7984 (mm110) REVERT: G 264 HIS cc_start: 0.7639 (p-80) cc_final: 0.7227 (p-80) REVERT: G 300 MET cc_start: 0.7873 (mtt) cc_final: 0.6844 (mtm) REVERT: G 324 LYS cc_start: 0.8455 (tttm) cc_final: 0.8104 (ttmm) REVERT: G 388 MET cc_start: 0.8316 (mtp) cc_final: 0.7808 (mmp) REVERT: G 408 PHE cc_start: 0.8679 (m-80) cc_final: 0.8363 (m-10) REVERT: D 6 HIS cc_start: 0.8231 (t70) cc_final: 0.7845 (t70) REVERT: D 26 ASP cc_start: 0.9189 (m-30) cc_final: 0.8765 (t0) REVERT: D 65 LEU cc_start: 0.8835 (mp) cc_final: 0.8521 (mp) REVERT: D 73 MET cc_start: 0.7065 (mmt) cc_final: 0.6783 (mmm) REVERT: D 101 TRP cc_start: 0.9042 (t60) cc_final: 0.8703 (t60) REVERT: D 164 MET cc_start: 0.9148 (tpt) cc_final: 0.8121 (tpp) REVERT: D 207 LEU cc_start: 0.8846 (mp) cc_final: 0.8077 (tt) REVERT: D 210 ILE cc_start: 0.8635 (mt) cc_final: 0.8424 (mt) REVERT: D 222 TYR cc_start: 0.8122 (m-80) cc_final: 0.7764 (m-80) REVERT: D 264 HIS cc_start: 0.7555 (p-80) cc_final: 0.6870 (p-80) REVERT: D 300 MET cc_start: 0.7514 (mtt) cc_final: 0.7081 (mmm) REVERT: D 310 TYR cc_start: 0.8792 (m-80) cc_final: 0.8503 (m-10) REVERT: D 324 LYS cc_start: 0.8456 (tttm) cc_final: 0.7918 (ttmm) REVERT: I 4 ILE cc_start: 0.9642 (mt) cc_final: 0.9384 (mm) REVERT: I 14 ASN cc_start: 0.8492 (m-40) cc_final: 0.8041 (m-40) REVERT: I 26 ASP cc_start: 0.8853 (m-30) cc_final: 0.8520 (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: 0.7125 (p-80) REVERT: I 297 LYS cc_start: 0.9164 (ptpt) cc_final: 0.8818 (ptpp) REVERT: I 310 TYR cc_start: 0.8306 (m-80) cc_final: 0.8005 (m-10) REVERT: I 324 LYS cc_start: 0.8182 (tttm) cc_final: 0.7657 (ttmm) REVERT: I 388 MET cc_start: 0.8375 (mtp) cc_final: 0.7692 (mmt) REVERT: I 406 MET cc_start: 0.7921 (tpp) cc_final: 0.7644 (mmp) REVERT: I 409 THR cc_start: 0.9250 (m) cc_final: 0.8831 (p) REVERT: B 6 HIS cc_start: 0.8358 (t70) cc_final: 0.8070 (t-170) REVERT: B 59 TYR cc_start: 0.8925 (m-80) cc_final: 0.8629 (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: 0.8273 (t60) REVERT: B 139 LEU cc_start: 0.8871 (mt) cc_final: 0.8507 (mp) REVERT: B 164 MET cc_start: 0.9134 (tpt) cc_final: 0.8891 (tpp) REVERT: B 187 LEU cc_start: 0.9302 (mt) cc_final: 0.8874 (tp) REVERT: B 201 CYS cc_start: 0.8830 (m) cc_final: 0.8564 (t) REVERT: B 245 GLN cc_start: 0.8481 (mt0) cc_final: 0.8187 (mm-40) REVERT: B 264 HIS cc_start: 0.7847 (p-80) cc_final: 0.6690 (p-80) REVERT: B 279 GLN cc_start: 0.8586 (pt0) cc_final: 0.8336 (pm20) REVERT: B 300 MET cc_start: 0.7678 (mtt) cc_final: 0.7400 (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: 0.7802 (ttmm) REVERT: B 367 PHE cc_start: 0.8467 (t80) cc_final: 0.8221 (t80) REVERT: H 4 ILE cc_start: 0.9614 (mt) cc_final: 0.9311 (mm) REVERT: H 26 ASP cc_start: 0.9151 (m-30) cc_final: 0.8724 (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: 0.8764 (tpt) REVERT: H 184 ASN cc_start: 0.8376 (m-40) cc_final: 0.8160 (t0) REVERT: H 245 GLN cc_start: 0.8171 (mt0) cc_final: 0.7795 (mm-40) REVERT: H 279 GLN cc_start: 0.8792 (pt0) cc_final: 0.8534 (pm20) REVERT: H 300 MET cc_start: 0.7675 (mtt) cc_final: 0.7417 (mtt) REVERT: H 303 CYS cc_start: 0.7351 (p) cc_final: 0.6841 (p) REVERT: H 363 MET cc_start: 0.7991 (ptp) cc_final: 0.7773 (ptt) REVERT: H 388 MET cc_start: 0.8587 (mtp) cc_final: 0.7951 (mmp) REVERT: H 406 MET cc_start: 0.7813 (tpp) cc_final: 0.7558 (mmm) REVERT: E 32 PRO cc_start: 0.9416 (Cg_exo) cc_final: 0.9061 (Cg_endo) REVERT: E 33 ASP cc_start: 0.8635 (m-30) cc_final: 0.7833 (p0) REVERT: E 90 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8184 (tt0) REVERT: E 112 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8242 (ttpt) REVERT: E 121 ARG cc_start: 0.7626 (mmm160) cc_final: 0.7336 (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: 0.8404 (mm-40) REVERT: E 254 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7832 (mt-10) REVERT: E 258 ASN cc_start: 0.8817 (m110) cc_final: 0.8589 (t0) REVERT: E 295 CYS cc_start: 0.8391 (m) cc_final: 0.7656 (m) REVERT: E 308 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8627 (ptp90) REVERT: E 368 LEU cc_start: 0.8891 (mp) cc_final: 0.8638 (pp) REVERT: E 388 TRP cc_start: 0.8726 (m100) cc_final: 0.8513 (m100) REVERT: E 407 TRP cc_start: 0.8945 (m100) cc_final: 0.8427 (m100) REVERT: E 425 MET cc_start: 0.8200 (tpp) cc_final: 0.7942 (tpp) REVERT: J 21 TRP cc_start: 0.8592 (m100) cc_final: 0.7360 (m100) REVERT: J 33 ASP cc_start: 0.8571 (m-30) cc_final: 0.7874 (p0) REVERT: J 50 ASN cc_start: 0.8270 (t0) cc_final: 0.7809 (t0) REVERT: J 85 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8541 (mm110) REVERT: J 90 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7281 (tp30) REVERT: J 91 GLN cc_start: 0.8537 (mt0) cc_final: 0.7955 (mm110) REVERT: J 151 SER cc_start: 0.9330 (m) cc_final: 0.8842 (p) REVERT: J 205 ASP cc_start: 0.7807 (t0) cc_final: 0.7431 (m-30) REVERT: J 214 ARG cc_start: 0.8207 (ttp80) cc_final: 0.8000 (ttp80) REVERT: J 271 THR cc_start: 0.8898 (m) cc_final: 0.8595 (p) REVERT: J 291 ILE cc_start: 0.9010 (pt) cc_final: 0.8324 (pt) REVERT: J 295 CYS cc_start: 0.8609 (m) cc_final: 0.8317 (m) REVERT: J 306 ASP cc_start: 0.8333 (t70) cc_final: 0.8051 (t0) REVERT: J 368 LEU cc_start: 0.9258 (mp) cc_final: 0.8942 (pp) REVERT: J 391 LEU cc_start: 0.9078 (tp) cc_final: 0.8741 (tt) REVERT: J 425 MET cc_start: 0.8270 (tpp) cc_final: 0.7815 (tpp) REVERT: C 31 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8141 (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: 0.7507 (t0) REVERT: C 85 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8630 (mm-40) REVERT: C 86 LEU cc_start: 0.8701 (tp) cc_final: 0.8421 (tt) REVERT: C 109 THR cc_start: 0.8436 (m) cc_final: 0.8065 (p) REVERT: C 169 PHE cc_start: 0.8175 (m-10) cc_final: 0.7856 (m-10) REVERT: C 232 SER cc_start: 0.8947 (p) cc_final: 0.8496 (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: 0.8772 (p) REVERT: C 285 GLN cc_start: 0.8296 (pt0) cc_final: 0.7328 (mm-40) REVERT: C 295 CYS cc_start: 0.8512 (m) cc_final: 0.8265 (m) REVERT: C 356 ASN cc_start: 0.8650 (t0) cc_final: 0.8402 (m110) REVERT: C 368 LEU cc_start: 0.8971 (mp) cc_final: 0.8638 (pp) REVERT: C 378 LEU cc_start: 0.7915 (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: 0.7802 (mt0) REVERT: L 33 ASP cc_start: 0.8630 (m-30) cc_final: 0.7937 (p0) REVERT: L 50 ASN cc_start: 0.8063 (t0) cc_final: 0.7687 (t0) REVERT: L 90 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7441 (tp30) REVERT: L 115 ILE cc_start: 0.8476 (tp) cc_final: 0.8233 (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: 0.7868 (t0) REVERT: L 123 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7535 (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: 0.8535 (p) REVERT: L 154 MET cc_start: 0.8903 (mmm) cc_final: 0.8440 (mmt) REVERT: L 196 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8035 (tm-30) REVERT: L 233 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8370 (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: 0.7131 (mm-40) REVERT: L 290 GLU cc_start: 0.7642 (tt0) cc_final: 0.7399 (tt0) REVERT: L 326 LYS cc_start: 0.7559 (tmtm) cc_final: 0.7067 (mmtt) REVERT: L 329 ASN cc_start: 0.8421 (t0) cc_final: 0.8061 (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: 0.7631 (mm) REVERT: L 402 ARG cc_start: 0.8543 (mmt-90) cc_final: 0.8326 (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: 0.7456 (tp30) REVERT: K 132 LEU cc_start: 0.9101 (tp) cc_final: 0.8720 (tt) REVERT: K 154 MET cc_start: 0.9074 (mmm) cc_final: 0.8723 (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: 0.7764 (m-10) REVERT: K 214 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8087 (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: 0.9022 (m) cc_final: 0.8791 (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: 0.7999 (ptp-110) REVERT: K 368 LEU cc_start: 0.9363 (mp) cc_final: 0.8959 (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: 0.8561 (m100) REVERT: K 407 TRP cc_start: 0.9063 (m100) cc_final: 0.8693 (m100) outliers start: 0 outliers final: 0 residues processed: 1778 average time/residue: 0.2413 time to fit residues: 702.8293 Evaluate side-chains 1002 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1002 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 11 GLN F 37 HIS F 190 HIS F 226 ASN F 307 HIS A 11 GLN A 18 ASN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 396 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 226 ASN H 247 ASN H 280 GLN H 307 HIS H 334 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 75 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.115158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.103618 restraints weight = 93537.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.106753 restraints weight = 47948.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.108869 restraints weight = 28468.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.110292 restraints weight = 18507.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.111288 restraints weight = 12898.503| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3412 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= 0.160 Angle : 0.605 9.506 56820 Z= 0.315 Chirality : 0.045 0.189 6216 Planarity : 0.005 0.044 7398 Dihedral : 11.972 179.448 5760 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.16 % Allowed : 2.35 % Favored : 97.50 % 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: -0.90 (0.18), residues: 750 loop : -2.27 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 121 TYR 0.029 0.002 TYR J 185 PHE 0.014 0.001 PHE D 260 TRP 0.031 0.002 TRP D 344 HIS 0.010 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (41820) covalent geometry : angle 0.60464 / 0.32 (56820) hydrogen bonds : bond 0.05289 / 3.55 ( 1368) hydrogen bonds : angle 5.53362 / 3.86 ( 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 1286 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1279 time to evaluate : 1.554 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 21 TRP cc_start: 0.8763 (m100) cc_final: 0.8447 (m100) REVERT: F 23 VAL cc_start: 0.9066 (t) cc_final: 0.8865 (p) REVERT: F 25 SER cc_start: 0.9321 (m) cc_final: 0.8778 (p) REVERT: F 26 ASP cc_start: 0.8920 (m-30) cc_final: 0.8633 (t70) REVERT: F 95 SER cc_start: 0.8987 (m) cc_final: 0.8623 (t) REVERT: F 101 TRP cc_start: 0.9246 (t60) cc_final: 0.8979 (t60) REVERT: F 163 ILE cc_start: 0.8952 (pt) cc_final: 0.8683 (pt) REVERT: F 203 ASP cc_start: 0.7873 (t0) cc_final: 0.7639 (t70) REVERT: F 205 GLU cc_start: 0.8710 (tp30) cc_final: 0.8484 (mm-30) REVERT: F 250 LEU cc_start: 0.9265 (mm) cc_final: 0.9007 (mt) REVERT: F 264 HIS cc_start: 0.7988 (p-80) cc_final: 0.7027 (p-80) REVERT: F 268 PRO cc_start: 0.9563 (Cg_endo) cc_final: 0.9243 (Cg_exo) REVERT: F 329 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8189 (mt0) REVERT: F 330 MET cc_start: 0.8668 (tpp) cc_final: 0.8419 (tpt) REVERT: F 334 GLN cc_start: 0.8929 (tt0) cc_final: 0.8688 (tm-30) REVERT: F 367 PHE cc_start: 0.8465 (t80) cc_final: 0.7845 (t80) REVERT: F 406 MET cc_start: 0.6734 (tpt) cc_final: 0.6292 (mmm) REVERT: A 33 ASP cc_start: 0.8256 (m-30) cc_final: 0.7737 (p0) REVERT: A 69 ASP cc_start: 0.8216 (t0) cc_final: 0.7669 (t0) REVERT: A 90 GLU cc_start: 0.7925 (mm-30) cc_final: 0.6913 (tp30) REVERT: A 120 ASP cc_start: 0.8195 (t70) cc_final: 0.7957 (t0) REVERT: A 123 ARG cc_start: 0.8066 (ttp-110) cc_final: 0.7755 (ttm170) REVERT: A 151 SER cc_start: 0.9111 (m) cc_final: 0.8722 (p) REVERT: A 154 MET cc_start: 0.9038 (mmm) cc_final: 0.8610 (mmm) REVERT: A 157 LEU cc_start: 0.8878 (mt) cc_final: 0.8646 (mp) REVERT: A 213 CYS cc_start: 0.8321 (m) cc_final: 0.7598 (p) REVERT: A 233 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8432 (mm-40) REVERT: A 254 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7856 (mt-10) REVERT: A 291 ILE cc_start: 0.8347 (pt) cc_final: 0.8097 (pt) REVERT: A 320 ARG cc_start: 0.8294 (ptm160) cc_final: 0.8047 (ptm160) REVERT: A 368 LEU cc_start: 0.8851 (mp) cc_final: 0.8469 (pp) REVERT: A 377 MET cc_start: 0.8048 (tmm) cc_final: 0.7808 (tmm) REVERT: A 398 MET cc_start: 0.7730 (mtm) cc_final: 0.7184 (ttp) REVERT: A 413 MET cc_start: 0.8111 (tpp) cc_final: 0.5084 (tpp) REVERT: A 423 GLU cc_start: 0.8189 (tp30) cc_final: 0.7936 (tp30) REVERT: G 4 ILE cc_start: 0.9622 (mt) cc_final: 0.9390 (mm) REVERT: G 12 CYS cc_start: 0.6971 (t) cc_final: 0.6722 (t) REVERT: G 37 HIS cc_start: 0.8845 (m-70) cc_final: 0.8297 (m-70) REVERT: G 67 ASP cc_start: 0.8894 (t0) cc_final: 0.8359 (t70) REVERT: G 101 TRP cc_start: 0.9278 (t60) cc_final: 0.8774 (t60) REVERT: G 147 MET cc_start: 0.8772 (tpt) cc_final: 0.8481 (tpp) REVERT: G 187 LEU cc_start: 0.9445 (mt) cc_final: 0.9226 (mm) REVERT: G 264 HIS cc_start: 0.7700 (p-80) cc_final: 0.7060 (p-80) REVERT: G 300 MET cc_start: 0.7969 (mtt) cc_final: 0.7622 (mtm) REVERT: G 324 LYS cc_start: 0.8721 (tttm) cc_final: 0.8414 (ttmm) REVERT: D 25 SER cc_start: 0.9352 (m) cc_final: 0.8990 (t) REVERT: D 26 ASP cc_start: 0.8977 (m-30) cc_final: 0.8752 (t0) REVERT: D 147 MET cc_start: 0.8144 (tpp) cc_final: 0.7921 (mmp) REVERT: D 222 TYR cc_start: 0.7907 (m-80) cc_final: 0.7257 (m-80) REVERT: D 264 HIS cc_start: 0.8089 (p-80) cc_final: 0.7185 (p-80) REVERT: D 297 LYS cc_start: 0.9391 (ptpp) cc_final: 0.9091 (ptmt) REVERT: D 310 TYR cc_start: 0.8804 (m-80) cc_final: 0.8477 (m-10) REVERT: D 321 MET cc_start: 0.7942 (pmm) cc_final: 0.7456 (pmm) REVERT: D 324 LYS cc_start: 0.8187 (tttm) cc_final: 0.7962 (ttmm) REVERT: D 367 PHE cc_start: 0.8517 (t80) cc_final: 0.8283 (t80) REVERT: D 403 MET cc_start: 0.7287 (ttp) cc_final: 0.5238 (ttp) REVERT: I 4 ILE cc_start: 0.9695 (mt) cc_final: 0.9382 (mm) REVERT: I 6 HIS cc_start: 0.7896 (t70) cc_final: 0.7671 (t-170) REVERT: I 25 SER cc_start: 0.9137 (m) cc_final: 0.8819 (t) REVERT: I 65 LEU cc_start: 0.9337 (mp) cc_final: 0.9066 (mp) REVERT: I 100 ASN cc_start: 0.8632 (t0) cc_final: 0.8379 (t0) REVERT: I 264 HIS cc_start: 0.7541 (p90) cc_final: 0.7153 (p-80) REVERT: I 297 LYS cc_start: 0.9354 (ptpt) cc_final: 0.9103 (ptpp) REVERT: I 310 TYR cc_start: 0.8560 (m-80) cc_final: 0.8219 (m-10) REVERT: I 324 LYS cc_start: 0.8039 (tttm) cc_final: 0.7812 (tttp) REVERT: I 350 LYS cc_start: 0.9047 (tptp) cc_final: 0.8541 (tppt) REVERT: I 388 MET cc_start: 0.8365 (mtp) cc_final: 0.8140 (mmt) REVERT: I 409 THR cc_start: 0.9333 (m) cc_final: 0.8981 (p) REVERT: I 426 GLN cc_start: 0.7976 (tp40) cc_final: 0.7519 (tp40) REVERT: I 427 ASP cc_start: 0.8002 (m-30) cc_final: 0.7590 (m-30) REVERT: B 26 ASP cc_start: 0.9163 (m-30) cc_final: 0.8797 (t70) REVERT: B 73 MET cc_start: 0.8318 (mmm) cc_final: 0.7715 (mmt) REVERT: B 101 TRP cc_start: 0.8733 (t60) cc_final: 0.8151 (t60) REVERT: B 187 LEU cc_start: 0.9521 (mt) cc_final: 0.8916 (tp) REVERT: B 198 GLU cc_start: 0.8644 (pm20) cc_final: 0.8164 (pm20) REVERT: B 203 ASP cc_start: 0.8218 (t0) cc_final: 0.7888 (t0) REVERT: B 256 ASN cc_start: 0.8229 (m-40) cc_final: 0.7541 (t0) REVERT: B 264 HIS cc_start: 0.8103 (p-80) cc_final: 0.7237 (p-80) REVERT: B 321 MET cc_start: 0.8045 (pmm) cc_final: 0.7730 (pmm) REVERT: B 349 VAL cc_start: 0.9464 (t) cc_final: 0.9248 (t) REVERT: H 37 HIS cc_start: 0.8873 (m-70) cc_final: 0.8483 (m-70) REVERT: H 203 ASP cc_start: 0.8267 (t0) cc_final: 0.7992 (t70) REVERT: H 204 ASN cc_start: 0.8807 (m110) cc_final: 0.8363 (t0) REVERT: H 297 LYS cc_start: 0.9369 (ptpp) cc_final: 0.8872 (mtmm) REVERT: H 349 VAL cc_start: 0.9536 (t) cc_final: 0.9262 (t) REVERT: H 367 PHE cc_start: 0.8434 (t80) cc_final: 0.8158 (t80) REVERT: H 388 MET cc_start: 0.8195 (mtp) cc_final: 0.7936 (mmt) REVERT: E 27 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7658 (mm-30) REVERT: E 33 ASP cc_start: 0.8406 (m-30) cc_final: 0.7916 (p0) REVERT: E 85 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7710 (mm-40) REVERT: E 90 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7249 (tp30) REVERT: E 151 SER cc_start: 0.9263 (m) cc_final: 0.8897 (p) REVERT: E 157 LEU cc_start: 0.8656 (mt) cc_final: 0.8390 (mt) REVERT: E 170 SER cc_start: 0.9221 (m) cc_final: 0.8149 (p) REVERT: E 210 TYR cc_start: 0.8737 (m-80) cc_final: 0.8490 (m-10) REVERT: E 233 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8603 (mm-40) REVERT: E 254 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7807 (mt-10) REVERT: E 368 LEU cc_start: 0.8776 (mp) cc_final: 0.8550 (pp) REVERT: E 377 MET cc_start: 0.8190 (tmm) cc_final: 0.7761 (tmm) REVERT: E 407 TRP cc_start: 0.8974 (m100) cc_final: 0.8428 (m100) REVERT: J 30 ILE cc_start: 0.9457 (mm) cc_final: 0.8930 (mm) REVERT: J 33 ASP cc_start: 0.8306 (m-30) cc_final: 0.7800 (p0) REVERT: J 69 ASP cc_start: 0.7758 (t70) cc_final: 0.7196 (t70) REVERT: J 75 ILE cc_start: 0.9337 (mt) cc_final: 0.9122 (tt) REVERT: J 90 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7040 (tp30) REVERT: J 91 GLN cc_start: 0.8377 (mt0) cc_final: 0.7966 (mm110) REVERT: J 151 SER cc_start: 0.9323 (m) cc_final: 0.8902 (p) REVERT: J 172 TYR cc_start: 0.8185 (t80) cc_final: 0.7858 (t80) REVERT: J 233 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8527 (mm-40) REVERT: J 271 THR cc_start: 0.9319 (m) cc_final: 0.9087 (p) REVERT: J 295 CYS cc_start: 0.8259 (m) cc_final: 0.7959 (m) REVERT: J 368 LEU cc_start: 0.9186 (mp) cc_final: 0.8925 (pp) REVERT: J 413 MET cc_start: 0.8577 (tpp) cc_final: 0.6967 (tpp) REVERT: C 27 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7934 (mm-30) REVERT: C 33 ASP cc_start: 0.8426 (m-30) cc_final: 0.8095 (p0) REVERT: C 69 ASP cc_start: 0.7181 (t0) cc_final: 0.6960 (t70) REVERT: C 86 LEU cc_start: 0.8586 (tp) cc_final: 0.8235 (tt) REVERT: C 90 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7715 (tp30) REVERT: C 96 LYS cc_start: 0.8086 (mmtp) cc_final: 0.7377 (mmmm) REVERT: C 112 LYS cc_start: 0.8928 (mptt) cc_final: 0.8703 (ttmt) REVERT: C 154 MET cc_start: 0.8981 (mmm) cc_final: 0.8734 (mmt) REVERT: C 169 PHE cc_start: 0.8233 (m-10) cc_final: 0.7659 (m-10) REVERT: C 170 SER cc_start: 0.8925 (m) cc_final: 0.7638 (p) REVERT: C 188 ILE cc_start: 0.8474 (mm) cc_final: 0.8137 (mt) REVERT: C 203 MET cc_start: 0.8246 (mmm) cc_final: 0.7802 (mmp) REVERT: C 258 ASN cc_start: 0.8355 (m110) cc_final: 0.8025 (m-40) REVERT: C 285 GLN cc_start: 0.8046 (pt0) cc_final: 0.7443 (mm110) REVERT: C 290 GLU cc_start: 0.7082 (tt0) cc_final: 0.6855 (tt0) REVERT: C 352 LYS cc_start: 0.8557 (tptp) cc_final: 0.8311 (tppt) REVERT: C 358 GLN cc_start: 0.8615 (tt0) cc_final: 0.8161 (tt0) REVERT: C 368 LEU cc_start: 0.8934 (mp) cc_final: 0.8602 (pp) REVERT: C 377 MET cc_start: 0.7363 (tmm) cc_final: 0.7162 (tmm) REVERT: C 413 MET cc_start: 0.8384 (tpp) cc_final: 0.8146 (tpp) REVERT: L 33 ASP cc_start: 0.8524 (m-30) cc_final: 0.7884 (p0) REVERT: L 49 PHE cc_start: 0.7688 (p90) cc_final: 0.7183 (p90) REVERT: L 90 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7434 (tp30) REVERT: L 115 ILE cc_start: 0.8461 (tp) cc_final: 0.8218 (tp) REVERT: L 123 ARG cc_start: 0.8017 (ttp-110) cc_final: 0.7677 (ttm110) REVERT: L 132 LEU cc_start: 0.8969 (tp) cc_final: 0.8637 (tt) REVERT: L 138 PHE cc_start: 0.8703 (m-10) cc_final: 0.8436 (m-10) REVERT: L 154 MET cc_start: 0.8950 (mmm) cc_final: 0.8718 (mmt) REVERT: L 169 PHE cc_start: 0.7847 (m-10) cc_final: 0.7469 (m-10) REVERT: L 172 TYR cc_start: 0.8164 (t80) cc_final: 0.7960 (t80) REVERT: L 188 ILE cc_start: 0.8574 (mm) cc_final: 0.8357 (mt) REVERT: L 213 CYS cc_start: 0.8498 (m) cc_final: 0.8183 (p) REVERT: L 230 LEU cc_start: 0.9127 (mp) cc_final: 0.8509 (tt) REVERT: L 285 GLN cc_start: 0.8065 (pt0) cc_final: 0.7261 (mm-40) REVERT: L 290 GLU cc_start: 0.7173 (tt0) cc_final: 0.6901 (tt0) REVERT: L 368 LEU cc_start: 0.9155 (mp) cc_final: 0.8813 (pp) REVERT: L 378 LEU cc_start: 0.7644 (mt) cc_final: 0.7442 (mm) REVERT: L 398 MET cc_start: 0.8143 (mtt) cc_final: 0.7608 (mtm) REVERT: L 407 TRP cc_start: 0.9047 (m100) cc_final: 0.8695 (m100) REVERT: L 413 MET cc_start: 0.8248 (tpt) cc_final: 0.7879 (tpt) REVERT: K 3 GLU cc_start: 0.7448 (mp0) cc_final: 0.7156 (mp0) REVERT: K 33 ASP cc_start: 0.8232 (m-30) cc_final: 0.7691 (p0) REVERT: K 50 ASN cc_start: 0.8427 (t0) cc_final: 0.7970 (t0) REVERT: K 69 ASP cc_start: 0.8063 (t0) cc_final: 0.7645 (t0) REVERT: K 90 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7714 (tp30) REVERT: K 120 ASP cc_start: 0.8363 (t70) cc_final: 0.8106 (t0) REVERT: K 132 LEU cc_start: 0.9047 (tp) cc_final: 0.8769 (tt) REVERT: K 154 MET cc_start: 0.9060 (mmm) cc_final: 0.8584 (mmm) REVERT: K 202 PHE cc_start: 0.8111 (m-80) cc_final: 0.7787 (m-10) REVERT: K 230 LEU cc_start: 0.9103 (mp) cc_final: 0.8692 (tt) REVERT: K 249 ASN cc_start: 0.7632 (m-40) cc_final: 0.7431 (p0) REVERT: K 271 THR cc_start: 0.9211 (m) cc_final: 0.8958 (p) REVERT: K 338 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8676 (mtpp) REVERT: K 368 LEU cc_start: 0.9245 (mp) cc_final: 0.8916 (pp) REVERT: K 407 TRP cc_start: 0.8967 (m100) cc_final: 0.8614 (m100) REVERT: K 413 MET cc_start: 0.8590 (tpp) cc_final: 0.7737 (tpp) outliers start: 7 outliers final: 1 residues processed: 1285 average time/residue: 0.2260 time to fit residues: 483.6981 Evaluate side-chains 917 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 916 time to evaluate : 1.521 ------------------------------------------------------------------------------- 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: 7.9990 chunk 301 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 259 optimal weight: 5.9990 chunk 444 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 392 optimal weight: 6.9990 chunk 472 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN A 28 HIS A 258 ASN A 293 ASN A 301 GLN A 356 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 11 GLN ** 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 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 J 283 HIS J 293 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN C 18 ASN C 28 HIS C 107 HIS ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN L 18 ASN 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 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3816 r_free = 0.3816 target = 0.112964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.101866 restraints weight = 92749.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.104962 restraints weight = 46672.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.107024 restraints weight = 27177.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.108435 restraints weight = 17438.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.109399 restraints weight = 11968.054| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41820 Z= 0.127 Angle : 0.560 9.444 56820 Z= 0.284 Chirality : 0.044 0.209 6216 Planarity : 0.004 0.076 7398 Dihedral : 11.534 179.693 5760 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.11 % 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: -2.31 (0.11), residues: 5130 helix: -1.37 (0.10), residues: 2220 sheet: -0.83 (0.18), residues: 810 loop : -1.84 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 318 TYR 0.015 0.001 TYR I 208 PHE 0.013 0.001 PHE H 133 TRP 0.036 0.002 TRP B 344 HIS 0.006 0.001 HIS D 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (41820) covalent geometry : angle 0.55980 / 0.28 (56820) hydrogen bonds : bond 0.04403 / 2.95 ( 1368) hydrogen bonds : angle 4.88859 / 3.42 ( 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 1204 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1200 time to evaluate : 1.529 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: 0.9320 (m) cc_final: 0.8789 (p) REVERT: F 95 SER cc_start: 0.9048 (m) cc_final: 0.8596 (t) REVERT: F 101 TRP cc_start: 0.9324 (t60) cc_final: 0.9083 (t60) REVERT: F 187 LEU cc_start: 0.9598 (mt) cc_final: 0.9364 (mm) REVERT: F 203 ASP cc_start: 0.8102 (t0) cc_final: 0.7874 (t70) REVERT: F 205 GLU cc_start: 0.8685 (tp30) cc_final: 0.8450 (mm-30) REVERT: F 264 HIS cc_start: 0.7893 (p-80) cc_final: 0.6996 (p-80) REVERT: F 280 GLN cc_start: 0.8074 (tp40) cc_final: 0.7544 (tp40) REVERT: F 281 TYR cc_start: 0.8385 (m-80) cc_final: 0.8170 (m-10) REVERT: F 297 LYS cc_start: 0.9516 (ptpt) cc_final: 0.9261 (mtmm) REVERT: F 323 MET cc_start: 0.8471 (mmm) cc_final: 0.8261 (mmm) REVERT: F 329 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8253 (mt0) REVERT: F 334 GLN cc_start: 0.8963 (tt0) cc_final: 0.8669 (tm-30) REVERT: F 367 PHE cc_start: 0.8376 (t80) cc_final: 0.7654 (t80) REVERT: A 33 ASP cc_start: 0.8302 (m-30) cc_final: 0.7753 (p0) REVERT: A 69 ASP cc_start: 0.8127 (t0) cc_final: 0.7639 (t0) REVERT: A 76 ASP cc_start: 0.8513 (m-30) cc_final: 0.8297 (t70) REVERT: A 125 LEU cc_start: 0.8846 (mt) cc_final: 0.8596 (tp) REVERT: A 151 SER cc_start: 0.9123 (m) cc_final: 0.8875 (p) REVERT: A 154 MET cc_start: 0.9063 (mmm) cc_final: 0.8515 (mmm) REVERT: A 157 LEU cc_start: 0.8961 (mt) cc_final: 0.8760 (mp) REVERT: A 213 CYS cc_start: 0.8466 (m) cc_final: 0.7812 (p) REVERT: A 254 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7654 (mt-10) REVERT: A 291 ILE cc_start: 0.8345 (pt) cc_final: 0.8120 (pt) REVERT: A 320 ARG cc_start: 0.8118 (ptm160) cc_final: 0.7606 (ptm160) REVERT: A 368 LEU cc_start: 0.8863 (mp) cc_final: 0.8585 (pp) REVERT: A 413 MET cc_start: 0.8272 (tpp) cc_final: 0.8005 (tpt) REVERT: G 4 ILE cc_start: 0.9628 (mt) cc_final: 0.9393 (mm) REVERT: G 67 ASP cc_start: 0.8902 (t0) cc_final: 0.8339 (t70) REVERT: G 101 TRP cc_start: 0.9290 (t60) cc_final: 0.8748 (t60) REVERT: G 147 MET cc_start: 0.8816 (tpt) cc_final: 0.8572 (tpp) REVERT: G 187 LEU cc_start: 0.9490 (mt) cc_final: 0.9281 (mm) REVERT: G 203 ASP cc_start: 0.8249 (t0) cc_final: 0.7872 (t70) REVERT: G 263 LEU cc_start: 0.8727 (mt) cc_final: 0.8515 (mt) REVERT: G 264 HIS cc_start: 0.7727 (p-80) cc_final: 0.6723 (p-80) REVERT: G 297 LYS cc_start: 0.9410 (ptpt) cc_final: 0.8858 (mtmm) REVERT: G 300 MET cc_start: 0.8186 (mtt) cc_final: 0.7808 (mtm) REVERT: G 303 CYS cc_start: 0.7955 (p) cc_final: 0.7626 (p) REVERT: G 323 MET cc_start: 0.8446 (mmm) cc_final: 0.8189 (mmm) REVERT: D 25 SER cc_start: 0.9281 (m) cc_final: 0.8917 (t) REVERT: D 187 LEU cc_start: 0.9473 (mt) cc_final: 0.9083 (tp) REVERT: D 222 TYR cc_start: 0.7907 (m-80) cc_final: 0.6931 (m-80) REVERT: D 263 LEU cc_start: 0.8567 (mt) cc_final: 0.8223 (mt) REVERT: D 264 HIS cc_start: 0.7798 (p-80) cc_final: 0.7081 (p-80) REVERT: D 310 TYR cc_start: 0.8775 (m-80) cc_final: 0.8503 (m-10) REVERT: D 321 MET cc_start: 0.7975 (pmm) cc_final: 0.7403 (pmm) REVERT: D 324 LYS cc_start: 0.8157 (tttm) cc_final: 0.7868 (ttmt) REVERT: D 348 ASN cc_start: 0.8329 (p0) cc_final: 0.8031 (p0) REVERT: D 426 GLN cc_start: 0.8070 (tp40) cc_final: 0.7826 (tp40) REVERT: I 4 ILE cc_start: 0.9663 (mt) cc_final: 0.9454 (mm) REVERT: I 25 SER cc_start: 0.9040 (m) cc_final: 0.8810 (t) REVERT: I 65 LEU cc_start: 0.9349 (mp) cc_final: 0.9091 (mp) REVERT: I 67 ASP cc_start: 0.8821 (t0) cc_final: 0.8495 (t70) REVERT: I 100 ASN cc_start: 0.8555 (t0) cc_final: 0.8311 (t0) REVERT: I 203 ASP cc_start: 0.8492 (t0) cc_final: 0.8102 (t70) REVERT: I 264 HIS cc_start: 0.7924 (p90) cc_final: 0.7240 (p-80) REVERT: I 297 LYS cc_start: 0.9265 (ptpt) cc_final: 0.9027 (ptpp) REVERT: I 310 TYR cc_start: 0.8658 (m-80) cc_final: 0.8246 (m-10) REVERT: I 323 MET cc_start: 0.8432 (mmt) cc_final: 0.8102 (mmt) REVERT: I 324 LYS cc_start: 0.7971 (tttm) cc_final: 0.7722 (ttmm) REVERT: I 350 LYS cc_start: 0.9020 (tptp) cc_final: 0.8628 (tppt) REVERT: I 355 ASP cc_start: 0.8535 (m-30) cc_final: 0.8141 (m-30) REVERT: I 388 MET cc_start: 0.8326 (mtp) cc_final: 0.8119 (mmt) REVERT: B 26 ASP cc_start: 0.9128 (m-30) cc_final: 0.8793 (t70) REVERT: B 65 LEU cc_start: 0.8809 (tp) cc_final: 0.7493 (tt) REVERT: B 73 MET cc_start: 0.8108 (mmm) cc_final: 0.7841 (mmm) REVERT: B 101 TRP cc_start: 0.8820 (t60) cc_final: 0.8199 (t60) REVERT: B 187 LEU cc_start: 0.9566 (mt) cc_final: 0.9009 (tp) REVERT: B 198 GLU cc_start: 0.8515 (pm20) cc_final: 0.7688 (pt0) REVERT: B 203 ASP cc_start: 0.8262 (t0) cc_final: 0.7896 (t0) REVERT: B 256 ASN cc_start: 0.8201 (m-40) cc_final: 0.7845 (m-40) REVERT: B 264 HIS cc_start: 0.7914 (p-80) cc_final: 0.6759 (p90) REVERT: B 321 MET cc_start: 0.8264 (pmm) cc_final: 0.7984 (pmm) REVERT: H 204 ASN cc_start: 0.8756 (m110) cc_final: 0.8404 (t0) REVERT: H 297 LYS cc_start: 0.9329 (ptpp) cc_final: 0.8813 (mtmm) REVERT: H 321 MET cc_start: 0.8254 (ptp) cc_final: 0.7733 (pmm) REVERT: H 356 ILE cc_start: 0.9477 (mm) cc_final: 0.8834 (tt) REVERT: H 367 PHE cc_start: 0.8412 (t80) cc_final: 0.8208 (t80) REVERT: H 388 MET cc_start: 0.8197 (mtp) cc_final: 0.7900 (mmp) REVERT: H 406 MET cc_start: 0.7561 (mmm) cc_final: 0.7142 (mmm) REVERT: E 27 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7697 (mm-30) REVERT: E 33 ASP cc_start: 0.8356 (m-30) cc_final: 0.7993 (p0) REVERT: E 49 PHE cc_start: 0.7774 (p90) cc_final: 0.7435 (p90) REVERT: E 90 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7249 (tp30) REVERT: E 96 LYS cc_start: 0.8431 (mmmt) cc_final: 0.8077 (mmmm) REVERT: E 151 SER cc_start: 0.9337 (m) cc_final: 0.9055 (p) REVERT: E 157 LEU cc_start: 0.8593 (mt) cc_final: 0.8322 (mt) REVERT: E 205 ASP cc_start: 0.7574 (t70) cc_final: 0.7371 (t0) REVERT: E 210 TYR cc_start: 0.8743 (m-80) cc_final: 0.8525 (m-10) REVERT: E 254 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7826 (mt-10) REVERT: E 352 LYS cc_start: 0.8872 (tptp) cc_final: 0.8042 (tppt) REVERT: E 407 TRP cc_start: 0.8971 (m100) cc_final: 0.8380 (m100) REVERT: E 413 MET cc_start: 0.8339 (tpp) cc_final: 0.7138 (tpp) REVERT: J 31 GLN cc_start: 0.8735 (mm-40) cc_final: 0.7558 (mt0) REVERT: J 33 ASP cc_start: 0.8341 (m-30) cc_final: 0.7930 (p0) REVERT: J 69 ASP cc_start: 0.7694 (t70) cc_final: 0.7077 (t70) REVERT: J 90 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7325 (tp30) REVERT: J 91 GLN cc_start: 0.8360 (mt0) cc_final: 0.7971 (mm110) REVERT: J 151 SER cc_start: 0.9345 (m) cc_final: 0.9027 (p) REVERT: J 172 TYR cc_start: 0.8209 (t80) cc_final: 0.7822 (t80) REVERT: J 192 HIS cc_start: 0.7585 (t70) cc_final: 0.6938 (t70) REVERT: J 205 ASP cc_start: 0.7648 (t0) cc_final: 0.7282 (m-30) REVERT: J 233 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8672 (mm-40) REVERT: J 271 THR cc_start: 0.9265 (m) cc_final: 0.9041 (p) REVERT: J 352 LYS cc_start: 0.8927 (tptt) cc_final: 0.8048 (tppt) REVERT: J 368 LEU cc_start: 0.9210 (mp) cc_final: 0.8910 (pp) REVERT: J 415 GLU cc_start: 0.7832 (tp30) cc_final: 0.7589 (tp30) REVERT: C 33 ASP cc_start: 0.8422 (m-30) cc_final: 0.8084 (p0) REVERT: C 86 LEU cc_start: 0.8547 (tp) cc_final: 0.8180 (tt) REVERT: C 154 MET cc_start: 0.9161 (mmm) cc_final: 0.8863 (mmt) REVERT: C 170 SER cc_start: 0.8951 (m) cc_final: 0.7409 (p) REVERT: C 203 MET cc_start: 0.8253 (mmm) cc_final: 0.7711 (mmm) REVERT: C 210 TYR cc_start: 0.8693 (m-80) cc_final: 0.8433 (m-10) REVERT: C 233 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8575 (mm-40) REVERT: C 258 ASN cc_start: 0.8457 (m110) cc_final: 0.8020 (t0) REVERT: C 285 GLN cc_start: 0.7980 (pt0) cc_final: 0.7392 (mm110) REVERT: C 290 GLU cc_start: 0.6927 (tt0) cc_final: 0.6661 (tt0) REVERT: C 352 LYS cc_start: 0.8685 (tptp) cc_final: 0.8373 (tptp) REVERT: C 358 GLN cc_start: 0.8478 (tt0) cc_final: 0.7949 (tt0) REVERT: C 368 LEU cc_start: 0.8909 (mp) cc_final: 0.8519 (pp) REVERT: C 402 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7879 (mmm160) REVERT: C 428 LEU cc_start: 0.8504 (tt) cc_final: 0.8047 (mm) REVERT: L 33 ASP cc_start: 0.8466 (m-30) cc_final: 0.7876 (p0) REVERT: L 49 PHE cc_start: 0.7595 (p90) cc_final: 0.7103 (p90) REVERT: L 123 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7707 (ttm110) REVERT: L 154 MET cc_start: 0.8923 (mmm) cc_final: 0.8680 (mmt) REVERT: L 169 PHE cc_start: 0.7713 (m-10) cc_final: 0.7318 (m-10) REVERT: L 194 THR cc_start: 0.8811 (p) cc_final: 0.8605 (p) REVERT: L 213 CYS cc_start: 0.8459 (m) cc_final: 0.8069 (p) REVERT: L 214 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7694 (ttp80) REVERT: L 230 LEU cc_start: 0.9136 (mp) cc_final: 0.8452 (tt) REVERT: L 285 GLN cc_start: 0.8064 (pt0) cc_final: 0.7409 (mp10) REVERT: L 290 GLU cc_start: 0.7057 (tt0) cc_final: 0.6840 (tt0) REVERT: L 368 LEU cc_start: 0.9105 (mp) cc_final: 0.8769 (pp) REVERT: L 398 MET cc_start: 0.8055 (mtt) cc_final: 0.7626 (ttm) REVERT: L 407 TRP cc_start: 0.9045 (m100) cc_final: 0.8706 (m100) REVERT: L 413 MET cc_start: 0.8167 (tpt) cc_final: 0.7965 (tpt) REVERT: K 33 ASP cc_start: 0.8224 (m-30) cc_final: 0.7721 (p0) REVERT: K 69 ASP cc_start: 0.7971 (t0) cc_final: 0.7473 (t0) REVERT: K 90 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7243 (tp30) REVERT: K 154 MET cc_start: 0.9091 (mmm) cc_final: 0.8603 (mmm) REVERT: K 202 PHE cc_start: 0.8258 (m-80) cc_final: 0.7930 (m-10) REVERT: K 230 LEU cc_start: 0.8977 (mp) cc_final: 0.8677 (tt) REVERT: K 233 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8590 (mm-40) REVERT: K 271 THR cc_start: 0.9337 (m) cc_final: 0.8811 (p) REVERT: K 338 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8693 (mtpp) REVERT: K 368 LEU cc_start: 0.9190 (mp) cc_final: 0.8897 (pp) outliers start: 4 outliers final: 0 residues processed: 1203 average time/residue: 0.2250 time to fit residues: 455.7141 Evaluate side-chains 860 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 860 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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: 8.9990 chunk 45 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 399 optimal weight: 9.9990 chunk 385 optimal weight: 20.0000 chunk 388 optimal weight: 20.0000 chunk 360 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 459 optimal weight: 30.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 300 ASN A 309 HIS G 191 GLN G 227 HIS G 247 ASN ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 424 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN I 226 ASN I 292 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 226 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 GLN H 256 ASN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 186 ASN E 258 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS C 356 ASN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** K 192 HIS ** 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 309 HIS ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.103574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092672 restraints weight = 96738.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095594 restraints weight = 49455.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.097551 restraints weight = 29255.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.098889 restraints weight = 19097.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099828 restraints weight = 13378.817| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 41820 Z= 0.250 Angle : 0.667 8.931 56820 Z= 0.348 Chirality : 0.049 0.203 6216 Planarity : 0.005 0.085 7398 Dihedral : 11.624 179.273 5760 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % 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: -1.99 (0.11), residues: 5130 helix: -0.81 (0.10), residues: 2214 sheet: -1.11 (0.18), residues: 798 loop : -1.85 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 213 TYR 0.043 0.002 TYR A 185 PHE 0.024 0.002 PHE H 385 TRP 0.023 0.002 TRP B 397 HIS 0.008 0.001 HIS J 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.25 (41820) covalent geometry : angle 0.66729 / 0.35 (56820) hydrogen bonds : bond 0.04570 / 3.06 ( 1368) hydrogen bonds : angle 5.20509 / 3.63 ( 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 1025 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1022 time to evaluate : 1.218 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: F 25 SER cc_start: 0.9240 (m) cc_final: 0.8890 (p) REVERT: F 205 GLU cc_start: 0.8823 (tp30) cc_final: 0.8572 (mm-30) REVERT: F 264 HIS cc_start: 0.7997 (p-80) cc_final: 0.7203 (p-80) REVERT: F 293 MET cc_start: 0.8256 (mtm) cc_final: 0.8033 (mtm) REVERT: F 297 LYS cc_start: 0.9543 (ptpt) cc_final: 0.9246 (mtmt) REVERT: F 334 GLN cc_start: 0.9000 (tt0) cc_final: 0.8692 (tm-30) REVERT: A 69 ASP cc_start: 0.8204 (t0) cc_final: 0.7916 (t0) REVERT: A 154 MET cc_start: 0.9162 (mmm) cc_final: 0.8744 (mmm) REVERT: A 192 HIS cc_start: 0.7831 (t70) cc_final: 0.7566 (t70) REVERT: A 254 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7563 (mt-10) REVERT: A 301 GLN cc_start: 0.9211 (mm110) cc_final: 0.8984 (mm110) REVERT: A 368 LEU cc_start: 0.8927 (mp) cc_final: 0.8704 (pp) REVERT: A 407 TRP cc_start: 0.9226 (m100) cc_final: 0.9012 (m100) REVERT: A 413 MET cc_start: 0.8056 (tpp) cc_final: 0.7716 (tpt) REVERT: G 4 ILE cc_start: 0.9638 (mt) cc_final: 0.9335 (mm) REVERT: G 67 ASP cc_start: 0.9010 (t0) cc_final: 0.8449 (t70) REVERT: G 147 MET cc_start: 0.8899 (tpt) cc_final: 0.8632 (tpp) REVERT: G 203 ASP cc_start: 0.8408 (t0) cc_final: 0.8098 (t0) REVERT: G 213 ARG cc_start: 0.7774 (ptp-170) cc_final: 0.7540 (ttp-110) REVERT: G 264 HIS cc_start: 0.7596 (p-80) cc_final: 0.6577 (p-80) REVERT: G 300 MET cc_start: 0.8283 (mtt) cc_final: 0.7862 (mtm) REVERT: G 323 MET cc_start: 0.8631 (mmm) cc_final: 0.8328 (mmm) REVERT: G 406 MET cc_start: 0.7149 (mmp) cc_final: 0.6613 (mmm) REVERT: G 412 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8380 (tm-30) REVERT: D 187 LEU cc_start: 0.9501 (mt) cc_final: 0.9125 (tp) REVERT: D 222 TYR cc_start: 0.8017 (m-80) cc_final: 0.7434 (m-80) REVERT: D 264 HIS cc_start: 0.8006 (p-80) cc_final: 0.7397 (p-80) REVERT: D 293 MET cc_start: 0.8316 (mpp) cc_final: 0.8005 (mpp) REVERT: D 409 THR cc_start: 0.9199 (m) cc_final: 0.8934 (p) REVERT: D 426 GLN cc_start: 0.8419 (tp40) cc_final: 0.7983 (tp40) REVERT: I 4 ILE cc_start: 0.9679 (mt) cc_final: 0.9401 (mm) REVERT: I 264 HIS cc_start: 0.7968 (p90) cc_final: 0.7578 (p-80) REVERT: I 297 LYS cc_start: 0.9402 (ptpt) cc_final: 0.9151 (ptpp) REVERT: I 321 MET cc_start: 0.8315 (pmm) cc_final: 0.8046 (pmm) REVERT: I 324 LYS cc_start: 0.8334 (tttm) cc_final: 0.8072 (ttmm) REVERT: I 355 ASP cc_start: 0.8769 (m-30) cc_final: 0.8397 (m-30) REVERT: I 426 GLN cc_start: 0.8156 (tp40) cc_final: 0.7936 (tm-30) REVERT: B 26 ASP cc_start: 0.9195 (m-30) cc_final: 0.8821 (t0) REVERT: B 101 TRP cc_start: 0.9223 (t60) cc_final: 0.8897 (t60) REVERT: B 187 LEU cc_start: 0.9645 (mt) cc_final: 0.9414 (mm) REVERT: B 198 GLU cc_start: 0.8944 (pm20) cc_final: 0.8266 (pm20) REVERT: B 264 HIS cc_start: 0.8000 (p-80) cc_final: 0.7382 (p90) REVERT: B 285 THR cc_start: 0.8803 (t) cc_final: 0.8559 (m) REVERT: B 293 MET cc_start: 0.8562 (mtm) cc_final: 0.8350 (mtm) REVERT: B 321 MET cc_start: 0.8536 (pmm) cc_final: 0.8051 (pmm) REVERT: B 388 MET cc_start: 0.8278 (mtp) cc_final: 0.8057 (mtp) REVERT: H 37 HIS cc_start: 0.8850 (m-70) cc_final: 0.8425 (m-70) REVERT: H 112 LEU cc_start: 0.9442 (tp) cc_final: 0.9018 (tp) REVERT: H 178 THR cc_start: 0.8207 (m) cc_final: 0.7789 (p) REVERT: H 203 ASP cc_start: 0.8276 (t0) cc_final: 0.7957 (t0) REVERT: H 204 ASN cc_start: 0.8753 (m110) cc_final: 0.8355 (t0) REVERT: H 264 HIS cc_start: 0.7514 (p-80) cc_final: 0.7160 (p-80) REVERT: H 297 LYS cc_start: 0.9337 (ptpp) cc_final: 0.8750 (mtmm) REVERT: H 356 ILE cc_start: 0.9307 (mm) cc_final: 0.8745 (tt) REVERT: H 367 PHE cc_start: 0.8634 (t80) cc_final: 0.8405 (t80) REVERT: E 27 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7783 (mm-30) REVERT: E 49 PHE cc_start: 0.7967 (p90) cc_final: 0.7611 (p90) REVERT: E 90 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7420 (tp30) REVERT: E 151 SER cc_start: 0.9379 (m) cc_final: 0.8873 (t) REVERT: E 233 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8777 (mm-40) REVERT: E 258 ASN cc_start: 0.8358 (m-40) cc_final: 0.8028 (m110) REVERT: E 265 ILE cc_start: 0.8988 (mp) cc_final: 0.8775 (mp) REVERT: E 297 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7661 (tm-30) REVERT: E 301 GLN cc_start: 0.8765 (mp10) cc_final: 0.8285 (mm-40) REVERT: E 352 LYS cc_start: 0.9019 (tptp) cc_final: 0.8481 (tttp) REVERT: E 407 TRP cc_start: 0.8955 (m100) cc_final: 0.8418 (m100) REVERT: J 90 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7354 (tp30) REVERT: J 91 GLN cc_start: 0.8596 (mt0) cc_final: 0.8145 (mm110) REVERT: J 151 SER cc_start: 0.9415 (m) cc_final: 0.9105 (p) REVERT: J 172 TYR cc_start: 0.8113 (t80) cc_final: 0.7846 (t80) REVERT: J 230 LEU cc_start: 0.9386 (mp) cc_final: 0.8937 (tt) REVERT: J 233 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8592 (mm-40) REVERT: J 352 LYS cc_start: 0.9048 (tptt) cc_final: 0.8161 (tppt) REVERT: J 368 LEU cc_start: 0.9142 (mp) cc_final: 0.8815 (pp) REVERT: J 398 MET cc_start: 0.7724 (ttm) cc_final: 0.7492 (ttm) REVERT: C 96 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7527 (mmmm) REVERT: C 154 MET cc_start: 0.9276 (mmm) cc_final: 0.9068 (mmt) REVERT: C 233 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8546 (mm-40) REVERT: C 241 SER cc_start: 0.8621 (p) cc_final: 0.7805 (t) REVERT: C 285 GLN cc_start: 0.7740 (pt0) cc_final: 0.7008 (mm-40) REVERT: C 290 GLU cc_start: 0.6820 (tt0) cc_final: 0.6594 (tt0) REVERT: C 291 ILE cc_start: 0.8965 (pt) cc_final: 0.8628 (pt) REVERT: C 368 LEU cc_start: 0.9027 (mp) cc_final: 0.8617 (pp) REVERT: C 398 MET cc_start: 0.8395 (mtt) cc_final: 0.7675 (ttm) REVERT: L 31 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8208 (mt0) REVERT: L 49 PHE cc_start: 0.7740 (p90) cc_final: 0.7353 (p90) REVERT: L 123 ARG cc_start: 0.8049 (ttp-110) cc_final: 0.7820 (ttm110) REVERT: L 154 MET cc_start: 0.9255 (mmm) cc_final: 0.9030 (mmt) REVERT: L 213 CYS cc_start: 0.8746 (m) cc_final: 0.8217 (p) REVERT: L 233 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8526 (mm-40) REVERT: L 285 GLN cc_start: 0.8103 (pt0) cc_final: 0.7392 (mp10) REVERT: L 315 CYS cc_start: 0.7610 (m) cc_final: 0.7343 (m) REVERT: L 368 LEU cc_start: 0.9166 (mp) cc_final: 0.8652 (pp) REVERT: L 407 TRP cc_start: 0.9067 (m100) cc_final: 0.8665 (m100) REVERT: K 31 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8614 (mt0) REVERT: K 36 MET cc_start: 0.8122 (ppp) cc_final: 0.7882 (ppp) REVERT: K 69 ASP cc_start: 0.8135 (t0) cc_final: 0.7662 (t0) REVERT: K 90 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7553 (tp30) REVERT: K 96 LYS cc_start: 0.8647 (tptm) cc_final: 0.8069 (tppt) REVERT: K 154 MET cc_start: 0.9215 (mmm) cc_final: 0.8901 (mmm) REVERT: K 230 LEU cc_start: 0.9131 (mp) cc_final: 0.8788 (tt) REVERT: K 233 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8603 (mm-40) REVERT: K 271 THR cc_start: 0.9302 (m) cc_final: 0.8578 (p) REVERT: K 338 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8682 (mtpp) REVERT: K 368 LEU cc_start: 0.9227 (mp) cc_final: 0.8865 (pp) outliers start: 3 outliers final: 1 residues processed: 1025 average time/residue: 0.2271 time to fit residues: 390.4694 Evaluate side-chains 744 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 742 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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: 3.9990 chunk 160 optimal weight: 20.0000 chunk 196 optimal weight: 0.9990 chunk 498 optimal weight: 4.9990 chunk 303 optimal weight: 20.0000 chunk 217 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 339 optimal weight: 3.9990 chunk 403 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 169 optimal weight: 20.0000 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN I 247 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 ASN H 423 GLN E 18 ASN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 266 HIS ** 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.109713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.098821 restraints weight = 94227.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.101856 restraints weight = 47568.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.103876 restraints weight = 27778.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.105255 restraints weight = 17849.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.106203 restraints weight = 12265.831| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5155 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= 0.118 Angle : 0.562 10.594 56820 Z= 0.283 Chirality : 0.045 0.210 6216 Planarity : 0.004 0.074 7398 Dihedral : 11.364 177.808 5760 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.07 % Allowed : 1.55 % Favored : 98.38 % 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: -1.54 (0.11), residues: 5130 helix: -0.36 (0.11), residues: 2226 sheet: -1.02 (0.18), residues: 852 loop : -1.63 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 156 TYR 0.024 0.001 TYR F 222 PHE 0.018 0.001 PHE H 385 TRP 0.020 0.002 TRP D 101 HIS 0.007 0.001 HIS D 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (41820) covalent geometry : angle 0.56202 / 0.28 (56820) hydrogen bonds : bond 0.03805 / 2.55 ( 1368) hydrogen bonds : angle 4.63798 / 3.23 ( 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 1091 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1088 time to evaluate : 1.268 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: 0.9180 (m) cc_final: 0.8731 (p) REVERT: F 53 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7746 (mt-10) REVERT: F 59 TYR cc_start: 0.8806 (m-80) cc_final: 0.8117 (m-10) REVERT: F 264 HIS cc_start: 0.7681 (p-80) cc_final: 0.6900 (p-80) REVERT: F 334 GLN cc_start: 0.8978 (tt0) cc_final: 0.8627 (tm-30) REVERT: F 356 ILE cc_start: 0.9257 (mm) cc_final: 0.8730 (tt) REVERT: A 90 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7328 (tp30) REVERT: A 154 MET cc_start: 0.9121 (mmm) cc_final: 0.8695 (mmm) REVERT: A 291 ILE cc_start: 0.8552 (pt) cc_final: 0.8347 (pt) REVERT: A 377 MET cc_start: 0.7690 (tmm) cc_final: 0.7115 (tmm) REVERT: A 407 TRP cc_start: 0.9252 (m100) cc_final: 0.8905 (m100) REVERT: G 4 ILE cc_start: 0.9619 (mt) cc_final: 0.9360 (mm) REVERT: G 25 SER cc_start: 0.8247 (t) cc_final: 0.7841 (p) REVERT: G 67 ASP cc_start: 0.8853 (t0) cc_final: 0.8483 (t70) REVERT: G 147 MET cc_start: 0.8793 (tpt) cc_final: 0.8557 (tpp) REVERT: G 203 ASP cc_start: 0.8025 (t0) cc_final: 0.7775 (t70) REVERT: G 213 ARG cc_start: 0.8076 (ptp-170) cc_final: 0.7768 (ttp-110) REVERT: G 264 HIS cc_start: 0.7431 (p-80) cc_final: 0.6351 (p-80) REVERT: G 300 MET cc_start: 0.8215 (mtt) cc_final: 0.7951 (mtm) REVERT: G 323 MET cc_start: 0.8435 (mmm) cc_final: 0.8051 (tpp) REVERT: G 406 MET cc_start: 0.6815 (mmp) cc_final: 0.6536 (tpp) REVERT: D 183 TYR cc_start: 0.8699 (m-80) cc_final: 0.8485 (m-80) REVERT: D 187 LEU cc_start: 0.9448 (mt) cc_final: 0.9117 (tp) REVERT: D 222 TYR cc_start: 0.7918 (m-80) cc_final: 0.7167 (m-80) REVERT: D 257 MET cc_start: 0.7384 (mmm) cc_final: 0.7101 (mmm) REVERT: D 264 HIS cc_start: 0.7931 (p-80) cc_final: 0.7288 (p-80) REVERT: D 336 LYS cc_start: 0.7831 (ptpt) cc_final: 0.7591 (ptpp) REVERT: D 406 MET cc_start: 0.6784 (mmp) cc_final: 0.6442 (mmp) REVERT: D 409 THR cc_start: 0.9135 (m) cc_final: 0.8748 (p) REVERT: D 426 GLN cc_start: 0.8405 (tp40) cc_final: 0.7943 (tp40) REVERT: I 4 ILE cc_start: 0.9720 (mt) cc_final: 0.9426 (mm) REVERT: I 257 MET cc_start: 0.7504 (mmm) cc_final: 0.6461 (mmt) REVERT: I 264 HIS cc_start: 0.7873 (p90) cc_final: 0.7112 (p-80) REVERT: I 293 MET cc_start: 0.8313 (mtm) cc_final: 0.8013 (mtm) REVERT: I 310 TYR cc_start: 0.8751 (m-80) cc_final: 0.8467 (m-10) REVERT: I 324 LYS cc_start: 0.8199 (tttm) cc_final: 0.7968 (ttmm) REVERT: I 355 ASP cc_start: 0.8781 (m-30) cc_final: 0.8198 (m-30) REVERT: B 26 ASP cc_start: 0.9147 (m-30) cc_final: 0.8798 (t70) REVERT: B 101 TRP cc_start: 0.9119 (t60) cc_final: 0.8916 (t60) REVERT: B 198 GLU cc_start: 0.8649 (pm20) cc_final: 0.8076 (pm20) REVERT: B 203 ASP cc_start: 0.8507 (t0) cc_final: 0.8092 (t0) REVERT: B 264 HIS cc_start: 0.7721 (p-80) cc_final: 0.7159 (p90) REVERT: B 293 MET cc_start: 0.8275 (mtm) cc_final: 0.8064 (mtm) REVERT: B 321 MET cc_start: 0.8494 (pmm) cc_final: 0.8100 (pmm) REVERT: H 37 HIS cc_start: 0.8748 (m-70) cc_final: 0.8189 (m-70) REVERT: H 57 ASN cc_start: 0.9157 (m110) cc_final: 0.8798 (m110) REVERT: H 116 VAL cc_start: 0.8832 (t) cc_final: 0.8589 (p) REVERT: H 203 ASP cc_start: 0.8024 (t0) cc_final: 0.7640 (t0) REVERT: H 204 ASN cc_start: 0.8407 (m110) cc_final: 0.8043 (t0) REVERT: H 256 ASN cc_start: 0.8203 (m-40) cc_final: 0.7307 (t0) REVERT: H 264 HIS cc_start: 0.7356 (p-80) cc_final: 0.6864 (p90) REVERT: H 297 LYS cc_start: 0.9350 (ptpp) cc_final: 0.8777 (mtmm) REVERT: H 321 MET cc_start: 0.8337 (ptp) cc_final: 0.7939 (pmm) REVERT: H 350 LYS cc_start: 0.9019 (tppt) cc_final: 0.8507 (tppt) REVERT: H 356 ILE cc_start: 0.9285 (mm) cc_final: 0.8776 (tt) REVERT: E 33 ASP cc_start: 0.8586 (m-30) cc_final: 0.7920 (p0) REVERT: E 49 PHE cc_start: 0.7821 (p90) cc_final: 0.7546 (p90) REVERT: E 90 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7594 (tp30) REVERT: E 91 GLN cc_start: 0.8677 (mt0) cc_final: 0.8472 (mp10) REVERT: E 151 SER cc_start: 0.9330 (m) cc_final: 0.8772 (t) REVERT: E 205 ASP cc_start: 0.7955 (t70) cc_final: 0.7747 (t0) REVERT: E 352 LYS cc_start: 0.8920 (tptp) cc_final: 0.7964 (tppt) REVERT: E 407 TRP cc_start: 0.8856 (m100) cc_final: 0.8218 (m100) REVERT: E 413 MET cc_start: 0.8555 (tpp) cc_final: 0.8181 (tpp) REVERT: J 24 TYR cc_start: 0.8406 (m-80) cc_final: 0.8058 (m-80) REVERT: J 31 GLN cc_start: 0.8665 (mm-40) cc_final: 0.7845 (mt0) REVERT: J 33 ASP cc_start: 0.8471 (m-30) cc_final: 0.7861 (p0) REVERT: J 49 PHE cc_start: 0.7736 (p90) cc_final: 0.7535 (p90) REVERT: J 90 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7358 (tp30) REVERT: J 91 GLN cc_start: 0.8351 (mt0) cc_final: 0.8014 (mm110) REVERT: J 170 SER cc_start: 0.9154 (m) cc_final: 0.8918 (p) REVERT: J 172 TYR cc_start: 0.8437 (t80) cc_final: 0.8086 (t80) REVERT: J 205 ASP cc_start: 0.8140 (t70) cc_final: 0.7603 (m-30) REVERT: J 230 LEU cc_start: 0.9368 (mp) cc_final: 0.8923 (tt) REVERT: J 233 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8672 (mm-40) REVERT: J 305 CYS cc_start: 0.8501 (m) cc_final: 0.8212 (m) REVERT: J 368 LEU cc_start: 0.9130 (mp) cc_final: 0.8887 (pp) REVERT: J 398 MET cc_start: 0.7726 (ttm) cc_final: 0.7511 (ttm) REVERT: C 96 LYS cc_start: 0.8107 (mmtp) cc_final: 0.7328 (mmmm) REVERT: C 112 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8989 (ttpp) REVERT: C 115 ILE cc_start: 0.8991 (tp) cc_final: 0.8609 (tp) REVERT: C 169 PHE cc_start: 0.8037 (m-10) cc_final: 0.7609 (m-10) REVERT: C 170 SER cc_start: 0.8945 (m) cc_final: 0.7860 (p) REVERT: C 203 MET cc_start: 0.8734 (mmm) cc_final: 0.7776 (mmm) REVERT: C 210 TYR cc_start: 0.8393 (m-10) cc_final: 0.7977 (m-80) REVERT: C 241 SER cc_start: 0.8426 (p) cc_final: 0.7869 (t) REVERT: C 285 GLN cc_start: 0.7896 (pt0) cc_final: 0.7126 (mm-40) REVERT: C 290 GLU cc_start: 0.6686 (tt0) cc_final: 0.6478 (tt0) REVERT: C 368 LEU cc_start: 0.8860 (mp) cc_final: 0.8532 (pp) REVERT: C 398 MET cc_start: 0.8284 (mtt) cc_final: 0.7617 (ttm) REVERT: C 402 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.7932 (mmm160) REVERT: C 428 LEU cc_start: 0.8611 (tt) cc_final: 0.8120 (mm) REVERT: L 31 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8309 (mt0) REVERT: L 49 PHE cc_start: 0.7710 (p90) cc_final: 0.7279 (p90) REVERT: L 90 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7351 (tp30) REVERT: L 123 ARG cc_start: 0.7999 (ttp-110) cc_final: 0.7725 (ttm110) REVERT: L 154 MET cc_start: 0.9180 (mmm) cc_final: 0.8928 (mmt) REVERT: L 157 LEU cc_start: 0.9062 (mt) cc_final: 0.8823 (mt) REVERT: L 169 PHE cc_start: 0.7895 (m-10) cc_final: 0.7531 (m-10) REVERT: L 213 CYS cc_start: 0.8454 (m) cc_final: 0.8056 (p) REVERT: L 285 GLN cc_start: 0.8312 (pt0) cc_final: 0.7354 (mp10) REVERT: L 315 CYS cc_start: 0.7545 (m) cc_final: 0.7267 (m) REVERT: L 368 LEU cc_start: 0.9139 (mp) cc_final: 0.8679 (pp) REVERT: L 372 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7858 (tt0) REVERT: L 398 MET cc_start: 0.8016 (mtt) cc_final: 0.7551 (ttm) REVERT: K 69 ASP cc_start: 0.8143 (t0) cc_final: 0.7809 (t0) REVERT: K 90 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7295 (tp30) REVERT: K 154 MET cc_start: 0.9154 (mmm) cc_final: 0.8775 (mmm) REVERT: K 221 ARG cc_start: 0.9075 (mmt90) cc_final: 0.8834 (mmt90) REVERT: K 230 LEU cc_start: 0.9095 (mp) cc_final: 0.8813 (tt) REVERT: K 233 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8593 (mm-40) REVERT: K 271 THR cc_start: 0.9161 (m) cc_final: 0.8630 (p) REVERT: K 291 ILE cc_start: 0.8775 (pt) cc_final: 0.8533 (pt) REVERT: K 338 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8642 (mtpp) REVERT: K 368 LEU cc_start: 0.9185 (mp) cc_final: 0.8893 (pp) REVERT: K 372 GLN cc_start: 0.8158 (tp-100) cc_final: 0.7897 (tp-100) outliers start: 3 outliers final: 0 residues processed: 1091 average time/residue: 0.2244 time to fit residues: 413.6338 Evaluate side-chains 778 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 778 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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: 9.9990 chunk 378 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 279 optimal weight: 9.9990 chunk 230 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 489 optimal weight: 0.8980 chunk 423 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 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 191 GLN D 256 ASN D 414 ASN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 414 ASN E 18 ASN E 28 HIS E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 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 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.108357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097387 restraints weight = 94462.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.100431 restraints weight = 47523.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.102472 restraints weight = 27664.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.103854 restraints weight = 17738.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.104817 restraints weight = 12190.774| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5411 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= 0.118 Angle : 0.554 8.046 56820 Z= 0.279 Chirality : 0.045 0.214 6216 Planarity : 0.004 0.070 7398 Dihedral : 11.296 179.874 5760 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.14 % Allowed : 1.46 % Favored : 98.41 % 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: -0.04 (0.11), residues: 2226 sheet: -0.86 (0.18), residues: 840 loop : -1.42 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 123 TYR 0.020 0.001 TYR A 185 PHE 0.017 0.001 PHE I 167 TRP 0.021 0.002 TRP D 101 HIS 0.005 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (41820) covalent geometry : angle 0.55369 / 0.28 (56820) hydrogen bonds : bond 0.03612 / 2.43 ( 1368) hydrogen bonds : angle 4.48954 / 3.12 ( 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 1047 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1041 time to evaluate : 1.626 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: F 25 SER cc_start: 0.9186 (m) cc_final: 0.8716 (p) REVERT: F 59 TYR cc_start: 0.8777 (m-80) cc_final: 0.8552 (m-10) REVERT: F 164 MET cc_start: 0.8181 (tpp) cc_final: 0.7937 (mmm) REVERT: F 256 ASN cc_start: 0.8017 (m-40) cc_final: 0.7515 (t0) REVERT: F 264 HIS cc_start: 0.7639 (p-80) cc_final: 0.6821 (p-80) REVERT: F 297 LYS cc_start: 0.9500 (mtpt) cc_final: 0.9137 (ttmm) REVERT: F 334 GLN cc_start: 0.9095 (tt0) cc_final: 0.8572 (tm-30) REVERT: F 356 ILE cc_start: 0.9279 (mm) cc_final: 0.8741 (tt) REVERT: F 362 LYS cc_start: 0.8531 (tttm) cc_final: 0.8253 (tttm) REVERT: F 363 MET cc_start: 0.8455 (pmm) cc_final: 0.8203 (pmm) REVERT: F 426 GLN cc_start: 0.8002 (tt0) cc_final: 0.7733 (tp40) REVERT: A 3 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 69 ASP cc_start: 0.7981 (t0) cc_final: 0.7479 (t0) REVERT: A 90 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7320 (tp30) REVERT: A 120 ASP cc_start: 0.8406 (t0) cc_final: 0.8146 (t0) REVERT: A 154 MET cc_start: 0.9116 (mmm) cc_final: 0.8668 (mmm) REVERT: A 254 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7651 (mt-10) REVERT: A 291 ILE cc_start: 0.8568 (pt) cc_final: 0.8280 (pt) REVERT: A 341 ILE cc_start: 0.9094 (mp) cc_final: 0.8878 (mp) REVERT: A 407 TRP cc_start: 0.9073 (m100) cc_final: 0.8533 (m100) REVERT: G 4 ILE cc_start: 0.9620 (mt) cc_final: 0.9351 (mm) REVERT: G 25 SER cc_start: 0.8279 (t) cc_final: 0.7835 (p) REVERT: G 147 MET cc_start: 0.8840 (tpt) cc_final: 0.8619 (tpp) REVERT: G 203 ASP cc_start: 0.8301 (t0) cc_final: 0.8054 (t0) REVERT: G 213 ARG cc_start: 0.8034 (ptp-170) cc_final: 0.7749 (ttp-110) REVERT: G 263 LEU cc_start: 0.9020 (mt) cc_final: 0.8816 (mt) REVERT: G 264 HIS cc_start: 0.7377 (p-80) cc_final: 0.6229 (p-80) REVERT: G 300 MET cc_start: 0.8426 (mtt) cc_final: 0.8122 (mtm) REVERT: G 323 MET cc_start: 0.8503 (mmm) cc_final: 0.8107 (tpp) REVERT: G 406 MET cc_start: 0.6907 (mmp) cc_final: 0.6664 (tpp) REVERT: D 65 LEU cc_start: 0.8714 (tp) cc_final: 0.8411 (tt) REVERT: D 183 TYR cc_start: 0.8663 (m-80) cc_final: 0.8443 (m-80) REVERT: D 222 TYR cc_start: 0.7978 (m-80) cc_final: 0.7257 (m-80) REVERT: D 256 ASN cc_start: 0.8379 (m110) cc_final: 0.7428 (t0) REVERT: D 264 HIS cc_start: 0.7860 (p-80) cc_final: 0.7246 (p-80) REVERT: D 409 THR cc_start: 0.9128 (m) cc_final: 0.8689 (p) REVERT: D 426 GLN cc_start: 0.8451 (tp40) cc_final: 0.7942 (tp40) REVERT: I 4 ILE cc_start: 0.9683 (mt) cc_final: 0.9414 (mm) REVERT: I 178 THR cc_start: 0.8348 (m) cc_final: 0.8142 (p) REVERT: I 203 ASP cc_start: 0.8369 (t0) cc_final: 0.8050 (t70) REVERT: I 264 HIS cc_start: 0.7747 (p90) cc_final: 0.7004 (p-80) REVERT: I 293 MET cc_start: 0.8289 (mtm) cc_final: 0.8038 (mtm) REVERT: I 310 TYR cc_start: 0.8688 (m-80) cc_final: 0.8433 (m-10) REVERT: I 355 ASP cc_start: 0.8647 (m-30) cc_final: 0.8207 (m-30) REVERT: B 26 ASP cc_start: 0.9129 (m-30) cc_final: 0.7951 (t70) REVERT: B 37 HIS cc_start: 0.8962 (m90) cc_final: 0.8680 (m-70) REVERT: B 198 GLU cc_start: 0.8616 (pm20) cc_final: 0.7976 (pm20) REVERT: B 203 ASP cc_start: 0.8472 (t0) cc_final: 0.7907 (t0) REVERT: B 264 HIS cc_start: 0.7681 (p-80) cc_final: 0.7118 (p90) REVERT: B 293 MET cc_start: 0.8386 (mtm) cc_final: 0.8144 (mtm) REVERT: B 321 MET cc_start: 0.8461 (pmm) cc_final: 0.8087 (pmm) REVERT: H 37 HIS cc_start: 0.8721 (m-70) cc_final: 0.8195 (m-70) REVERT: H 57 ASN cc_start: 0.9114 (m110) cc_final: 0.8770 (m110) REVERT: H 116 VAL cc_start: 0.8916 (t) cc_final: 0.8657 (p) REVERT: H 203 ASP cc_start: 0.8013 (t0) cc_final: 0.7614 (t0) REVERT: H 204 ASN cc_start: 0.8488 (m110) cc_final: 0.8111 (t0) REVERT: H 256 ASN cc_start: 0.8295 (m-40) cc_final: 0.7840 (t0) REVERT: H 264 HIS cc_start: 0.7335 (p-80) cc_final: 0.6924 (p90) REVERT: H 297 LYS cc_start: 0.9358 (ptpp) cc_final: 0.8787 (mtmm) REVERT: H 321 MET cc_start: 0.8261 (ptp) cc_final: 0.7897 (pmm) REVERT: H 356 ILE cc_start: 0.9250 (mm) cc_final: 0.8825 (tt) REVERT: H 403 MET cc_start: 0.7907 (mmp) cc_final: 0.7588 (mmp) REVERT: H 412 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8467 (tm-30) REVERT: E 33 ASP cc_start: 0.8607 (m-30) cc_final: 0.7940 (p0) REVERT: E 49 PHE cc_start: 0.7869 (p90) cc_final: 0.7577 (p90) REVERT: E 90 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7508 (tp30) REVERT: E 91 GLN cc_start: 0.8684 (mt0) cc_final: 0.8421 (mp10) REVERT: E 151 SER cc_start: 0.9287 (m) cc_final: 0.8941 (p) REVERT: E 205 ASP cc_start: 0.7865 (t70) cc_final: 0.7550 (t70) REVERT: E 352 LYS cc_start: 0.8716 (tptp) cc_final: 0.8228 (tttp) REVERT: E 407 TRP cc_start: 0.8817 (m100) cc_final: 0.8106 (m100) REVERT: E 413 MET cc_start: 0.8641 (tpp) cc_final: 0.7722 (tpp) REVERT: J 24 TYR cc_start: 0.8400 (m-80) cc_final: 0.8063 (m-80) REVERT: J 33 ASP cc_start: 0.8508 (m-30) cc_final: 0.7863 (p0) REVERT: J 49 PHE cc_start: 0.7792 (p90) cc_final: 0.7531 (p90) REVERT: J 90 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7409 (tp30) REVERT: J 172 TYR cc_start: 0.8454 (t80) cc_final: 0.8124 (t80) REVERT: J 205 ASP cc_start: 0.8064 (t70) cc_final: 0.7523 (m-30) REVERT: J 230 LEU cc_start: 0.9372 (mp) cc_final: 0.8806 (tt) REVERT: J 272 TYR cc_start: 0.8840 (t80) cc_final: 0.8431 (t80) REVERT: J 368 LEU cc_start: 0.9164 (mp) cc_final: 0.8856 (pp) REVERT: J 398 MET cc_start: 0.7740 (ttm) cc_final: 0.7462 (ttm) REVERT: C 112 LYS cc_start: 0.9222 (ttmt) cc_final: 0.8986 (ttpp) REVERT: C 169 PHE cc_start: 0.8029 (m-10) cc_final: 0.7600 (m-10) REVERT: C 203 MET cc_start: 0.8674 (mmm) cc_final: 0.8432 (mmm) REVERT: C 210 TYR cc_start: 0.8372 (m-10) cc_final: 0.7980 (m-80) REVERT: C 233 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8667 (mm-40) REVERT: C 241 SER cc_start: 0.8522 (p) cc_final: 0.8079 (t) REVERT: C 285 GLN cc_start: 0.7889 (pt0) cc_final: 0.7092 (mm-40) REVERT: C 290 GLU cc_start: 0.6789 (tt0) cc_final: 0.6584 (tt0) REVERT: C 291 ILE cc_start: 0.8776 (pt) cc_final: 0.8375 (pt) REVERT: C 368 LEU cc_start: 0.8817 (mp) cc_final: 0.8461 (pp) REVERT: C 398 MET cc_start: 0.8309 (mtt) cc_final: 0.7652 (ttm) REVERT: C 428 LEU cc_start: 0.8575 (tt) cc_final: 0.8067 (mm) REVERT: L 31 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8292 (mt0) REVERT: L 49 PHE cc_start: 0.7747 (p90) cc_final: 0.7330 (p90) REVERT: L 90 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7395 (tp30) REVERT: L 123 ARG cc_start: 0.8003 (ttp-110) cc_final: 0.7786 (ttm110) REVERT: L 154 MET cc_start: 0.9207 (mmm) cc_final: 0.9007 (mmt) REVERT: L 169 PHE cc_start: 0.7866 (m-10) cc_final: 0.7590 (m-10) REVERT: L 213 CYS cc_start: 0.8490 (m) cc_final: 0.8133 (p) REVERT: L 285 GLN cc_start: 0.8231 (pt0) cc_final: 0.7411 (mp10) REVERT: L 315 CYS cc_start: 0.7639 (m) cc_final: 0.7385 (m) REVERT: L 368 LEU cc_start: 0.9121 (mp) cc_final: 0.8697 (pp) REVERT: L 372 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7770 (tt0) REVERT: K 33 ASP cc_start: 0.8273 (m-30) cc_final: 0.7788 (p0) REVERT: K 36 MET cc_start: 0.8045 (ppp) cc_final: 0.7841 (ppp) REVERT: K 69 ASP cc_start: 0.8323 (t0) cc_final: 0.7941 (t0) REVERT: K 90 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7398 (tp30) REVERT: K 93 ILE cc_start: 0.8624 (mm) cc_final: 0.8391 (mm) REVERT: K 120 ASP cc_start: 0.8562 (t70) cc_final: 0.8081 (t0) REVERT: K 154 MET cc_start: 0.9131 (mmm) cc_final: 0.8725 (mmm) REVERT: K 221 ARG cc_start: 0.9107 (mmt90) cc_final: 0.8821 (mmt90) REVERT: K 230 LEU cc_start: 0.9074 (mp) cc_final: 0.8805 (tt) REVERT: K 233 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8629 (mm-40) REVERT: K 291 ILE cc_start: 0.8761 (pt) cc_final: 0.8504 (pt) REVERT: K 338 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8651 (mtpp) REVERT: K 368 LEU cc_start: 0.9171 (mp) cc_final: 0.8836 (pp) outliers start: 6 outliers final: 0 residues processed: 1046 average time/residue: 0.2233 time to fit residues: 396.9447 Evaluate side-chains 762 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 762 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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: 10.0000 chunk 467 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 394 optimal weight: 30.0000 chunk 375 optimal weight: 5.9990 chunk 400 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 280 optimal weight: 0.0020 chunk 40 optimal weight: 20.0000 overall best weight: 3.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN F 347 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN 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 ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 L 18 ASN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.107297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.096294 restraints weight = 94656.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.099299 restraints weight = 47936.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.101328 restraints weight = 28153.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.102705 restraints weight = 18156.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.103636 restraints weight = 12565.433| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41820 Z= 0.137 Angle : 0.576 11.259 56820 Z= 0.289 Chirality : 0.045 0.200 6216 Planarity : 0.004 0.069 7398 Dihedral : 11.213 179.668 5760 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.09 % Allowed : 1.02 % Favored : 98.88 % 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: -1.07 (0.12), residues: 5130 helix: 0.10 (0.11), residues: 2214 sheet: -0.90 (0.17), residues: 852 loop : -1.42 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 123 TYR 0.019 0.001 TYR A 185 PHE 0.024 0.001 PHE G 385 TRP 0.016 0.002 TRP L 21 HIS 0.007 0.001 HIS D 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (41820) covalent geometry : angle 0.57602 / 0.29 (56820) hydrogen bonds : bond 0.03604 / 2.44 ( 1368) hydrogen bonds : angle 4.53833 / 3.16 ( 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 1006 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1002 time to evaluate : 1.699 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 59 TYR cc_start: 0.8712 (m-80) cc_final: 0.8412 (m-10) REVERT: F 164 MET cc_start: 0.8419 (tpp) cc_final: 0.8180 (mmm) REVERT: F 256 ASN cc_start: 0.7980 (m-40) cc_final: 0.7513 (t0) REVERT: F 264 HIS cc_start: 0.7716 (p-80) cc_final: 0.6959 (p-80) REVERT: F 297 LYS cc_start: 0.9326 (mtpt) cc_final: 0.9001 (mmtt) REVERT: F 300 MET cc_start: 0.8357 (mmm) cc_final: 0.7951 (mtt) REVERT: F 334 GLN cc_start: 0.9112 (tt0) cc_final: 0.8556 (tm-30) REVERT: F 356 ILE cc_start: 0.9296 (mm) cc_final: 0.8760 (tt) REVERT: F 362 LYS cc_start: 0.8474 (tttm) cc_final: 0.8128 (tttm) REVERT: F 363 MET cc_start: 0.8469 (pmm) cc_final: 0.8126 (pmm) REVERT: A 3 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 69 ASP cc_start: 0.8031 (t0) cc_final: 0.7553 (t0) REVERT: A 90 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7326 (tp30) REVERT: A 120 ASP cc_start: 0.8422 (t0) cc_final: 0.8169 (t0) REVERT: A 154 MET cc_start: 0.9150 (mmm) cc_final: 0.8750 (mmm) REVERT: A 241 SER cc_start: 0.7978 (p) cc_final: 0.7699 (p) REVERT: A 254 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7278 (mt-10) REVERT: A 407 TRP cc_start: 0.9081 (m100) cc_final: 0.8597 (m100) REVERT: G 4 ILE cc_start: 0.9633 (mt) cc_final: 0.9369 (mm) REVERT: G 12 CYS cc_start: 0.6879 (t) cc_final: 0.6675 (t) REVERT: G 147 MET cc_start: 0.8812 (tpt) cc_final: 0.8551 (tpp) REVERT: G 203 ASP cc_start: 0.8224 (t0) cc_final: 0.7951 (t0) REVERT: G 213 ARG cc_start: 0.8276 (ptp-170) cc_final: 0.7860 (ttp-110) REVERT: G 264 HIS cc_start: 0.7409 (p-80) cc_final: 0.6323 (p-80) REVERT: G 300 MET cc_start: 0.8462 (mtt) cc_final: 0.8133 (mtm) REVERT: G 323 MET cc_start: 0.8491 (mmm) cc_final: 0.8187 (tpp) REVERT: G 406 MET cc_start: 0.6971 (mmp) cc_final: 0.5925 (tpp) REVERT: D 65 LEU cc_start: 0.8783 (tp) cc_final: 0.8400 (tt) REVERT: D 222 TYR cc_start: 0.7937 (m-80) cc_final: 0.7341 (m-80) REVERT: D 256 ASN cc_start: 0.8119 (m110) cc_final: 0.7619 (t0) REVERT: D 264 HIS cc_start: 0.7906 (p-80) cc_final: 0.7303 (p-80) REVERT: D 312 THR cc_start: 0.8361 (p) cc_final: 0.8155 (p) REVERT: D 329 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8440 (mt0) REVERT: D 409 THR cc_start: 0.9097 (m) cc_final: 0.8719 (p) REVERT: D 426 GLN cc_start: 0.8403 (tp40) cc_final: 0.7857 (tp40) REVERT: I 4 ILE cc_start: 0.9677 (mt) cc_final: 0.9430 (mm) REVERT: I 178 THR cc_start: 0.8372 (m) cc_final: 0.8161 (p) REVERT: I 203 ASP cc_start: 0.8542 (t0) cc_final: 0.8199 (t70) REVERT: I 247 ASN cc_start: 0.8918 (m-40) cc_final: 0.8388 (m110) REVERT: I 257 MET cc_start: 0.7514 (mmm) cc_final: 0.6521 (mmt) REVERT: I 264 HIS cc_start: 0.7807 (p90) cc_final: 0.6983 (p-80) REVERT: I 293 MET cc_start: 0.8342 (mtm) cc_final: 0.8012 (mtm) REVERT: I 310 TYR cc_start: 0.8745 (m-80) cc_final: 0.8500 (m-10) REVERT: I 355 ASP cc_start: 0.8673 (m-30) cc_final: 0.8261 (m-30) REVERT: B 25 SER cc_start: 0.9439 (m) cc_final: 0.9093 (p) REVERT: B 37 HIS cc_start: 0.8996 (m90) cc_final: 0.8706 (m-70) REVERT: B 101 TRP cc_start: 0.9056 (t60) cc_final: 0.8783 (t60) REVERT: B 145 SER cc_start: 0.9085 (p) cc_final: 0.8727 (p) REVERT: B 198 GLU cc_start: 0.8687 (pm20) cc_final: 0.8051 (pm20) REVERT: B 203 ASP cc_start: 0.8500 (t0) cc_final: 0.7934 (t0) REVERT: B 263 LEU cc_start: 0.8521 (mp) cc_final: 0.8280 (pp) REVERT: B 264 HIS cc_start: 0.7713 (p-80) cc_final: 0.7289 (p90) REVERT: B 282 ARG cc_start: 0.7256 (ttm-80) cc_final: 0.7055 (ttm-80) REVERT: B 293 MET cc_start: 0.8424 (mtm) cc_final: 0.8188 (mtm) REVERT: B 321 MET cc_start: 0.8499 (pmm) cc_final: 0.7584 (pmm) REVERT: B 388 MET cc_start: 0.8062 (mtp) cc_final: 0.7854 (mtp) REVERT: H 37 HIS cc_start: 0.8842 (m-70) cc_final: 0.8398 (m-70) REVERT: H 57 ASN cc_start: 0.9108 (m110) cc_final: 0.8770 (m110) REVERT: H 74 ASP cc_start: 0.9224 (m-30) cc_final: 0.8999 (m-30) REVERT: H 203 ASP cc_start: 0.7850 (t0) cc_final: 0.7611 (t0) REVERT: H 204 ASN cc_start: 0.8427 (m110) cc_final: 0.8034 (t0) REVERT: H 256 ASN cc_start: 0.8326 (m-40) cc_final: 0.7840 (t0) REVERT: H 264 HIS cc_start: 0.7351 (p-80) cc_final: 0.6938 (p90) REVERT: H 297 LYS cc_start: 0.9330 (ptpp) cc_final: 0.8747 (mtmm) REVERT: H 321 MET cc_start: 0.8271 (ptp) cc_final: 0.7876 (pmm) REVERT: H 412 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8484 (tm-30) REVERT: E 33 ASP cc_start: 0.8595 (m-30) cc_final: 0.7912 (p0) REVERT: E 49 PHE cc_start: 0.7933 (p90) cc_final: 0.7639 (p90) REVERT: E 90 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7574 (tp30) REVERT: E 151 SER cc_start: 0.9321 (m) cc_final: 0.8716 (t) REVERT: E 352 LYS cc_start: 0.8815 (tptp) cc_final: 0.8153 (tttp) REVERT: E 407 TRP cc_start: 0.8827 (m100) cc_final: 0.8061 (m100) REVERT: J 24 TYR cc_start: 0.8526 (m-80) cc_final: 0.8157 (m-80) REVERT: J 33 ASP cc_start: 0.8520 (m-30) cc_final: 0.7804 (p0) REVERT: J 49 PHE cc_start: 0.7751 (p90) cc_final: 0.7494 (p90) REVERT: J 90 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7753 (tp30) REVERT: J 172 TYR cc_start: 0.8489 (t80) cc_final: 0.8127 (t80) REVERT: J 205 ASP cc_start: 0.8055 (t70) cc_final: 0.7532 (m-30) REVERT: J 230 LEU cc_start: 0.9383 (mp) cc_final: 0.8825 (tt) REVERT: J 237 SER cc_start: 0.8493 (m) cc_final: 0.8223 (p) REVERT: J 315 CYS cc_start: 0.7903 (m) cc_final: 0.7503 (m) REVERT: J 368 LEU cc_start: 0.9129 (mp) cc_final: 0.8860 (pp) REVERT: J 398 MET cc_start: 0.7809 (ttm) cc_final: 0.7537 (ttm) REVERT: C 36 MET cc_start: 0.8131 (ppp) cc_final: 0.7893 (ppp) REVERT: C 69 ASP cc_start: 0.6897 (t70) cc_final: 0.6577 (t70) REVERT: C 112 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8923 (ttpp) REVERT: C 169 PHE cc_start: 0.7986 (m-10) cc_final: 0.7581 (m-10) REVERT: C 233 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8607 (mm-40) REVERT: C 241 SER cc_start: 0.8555 (p) cc_final: 0.8116 (t) REVERT: C 285 GLN cc_start: 0.7839 (pt0) cc_final: 0.6967 (mm-40) REVERT: C 291 ILE cc_start: 0.8800 (pt) cc_final: 0.8393 (pt) REVERT: C 368 LEU cc_start: 0.8856 (mp) cc_final: 0.8503 (pp) REVERT: C 398 MET cc_start: 0.8242 (mtt) cc_final: 0.7604 (ttm) REVERT: C 428 LEU cc_start: 0.8597 (tt) cc_final: 0.8025 (mm) REVERT: L 31 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8142 (mt0) REVERT: L 49 PHE cc_start: 0.7850 (p90) cc_final: 0.7486 (p90) REVERT: L 90 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7500 (tp30) REVERT: L 123 ARG cc_start: 0.8057 (ttp-110) cc_final: 0.7839 (ttm110) REVERT: L 154 MET cc_start: 0.9213 (mmm) cc_final: 0.8947 (mmt) REVERT: L 169 PHE cc_start: 0.7900 (m-10) cc_final: 0.7614 (m-10) REVERT: L 213 CYS cc_start: 0.8678 (m) cc_final: 0.8273 (p) REVERT: L 285 GLN cc_start: 0.8231 (pt0) cc_final: 0.7404 (mp10) REVERT: L 315 CYS cc_start: 0.7593 (m) cc_final: 0.7327 (m) REVERT: L 398 MET cc_start: 0.7849 (ttm) cc_final: 0.7513 (ttp) REVERT: K 33 ASP cc_start: 0.8287 (m-30) cc_final: 0.7772 (p0) REVERT: K 36 MET cc_start: 0.8047 (ppp) cc_final: 0.7799 (ppp) REVERT: K 69 ASP cc_start: 0.8355 (t0) cc_final: 0.7956 (t0) REVERT: K 90 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7212 (tp30) REVERT: K 93 ILE cc_start: 0.8625 (mm) cc_final: 0.8372 (mm) REVERT: K 96 LYS cc_start: 0.8608 (tptm) cc_final: 0.8036 (tppt) REVERT: K 154 MET cc_start: 0.9183 (mmm) cc_final: 0.8779 (mmm) REVERT: K 213 CYS cc_start: 0.8224 (m) cc_final: 0.7927 (p) REVERT: K 221 ARG cc_start: 0.9097 (mmt90) cc_final: 0.8798 (mmt90) REVERT: K 230 LEU cc_start: 0.9121 (mp) cc_final: 0.8812 (tt) REVERT: K 233 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8635 (mm-40) REVERT: K 291 ILE cc_start: 0.8781 (pt) cc_final: 0.8553 (pt) REVERT: K 338 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8683 (mtpp) REVERT: K 368 LEU cc_start: 0.9203 (mp) cc_final: 0.8820 (pp) outliers start: 4 outliers final: 0 residues processed: 1005 average time/residue: 0.2383 time to fit residues: 405.8779 Evaluate side-chains 738 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 738 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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: 1.9990 chunk 278 optimal weight: 10.0000 chunk 200 optimal weight: 20.0000 chunk 309 optimal weight: 6.9990 chunk 301 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 289 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 405 optimal weight: 0.2980 chunk 264 optimal weight: 6.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 347 ASN G 375 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS B 191 GLN B 334 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** 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 ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.106166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095366 restraints weight = 95224.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.098332 restraints weight = 47809.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.100322 restraints weight = 27929.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.101663 restraints weight = 17953.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.102601 restraints weight = 12433.912| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 41820 Z= 0.154 Angle : 0.586 9.655 56820 Z= 0.297 Chirality : 0.046 0.265 6216 Planarity : 0.004 0.075 7398 Dihedral : 11.167 179.029 5760 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.11 % Allowed : 0.80 % Favored : 99.09 % 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: -0.95 (0.12), residues: 5130 helix: 0.24 (0.11), residues: 2166 sheet: -1.02 (0.17), residues: 864 loop : -1.29 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 221 TYR 0.019 0.001 TYR A 185 PHE 0.024 0.001 PHE D 367 TRP 0.018 0.002 TRP C 21 HIS 0.009 0.001 HIS F 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (41820) covalent geometry : angle 0.58626 / 0.30 (56820) hydrogen bonds : bond 0.03689 / 2.49 ( 1368) hydrogen bonds : angle 4.63883 / 3.23 ( 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 978 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 973 time to evaluate : 1.555 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: F 59 TYR cc_start: 0.8786 (m-80) cc_final: 0.8195 (m-10) REVERT: F 256 ASN cc_start: 0.8062 (m-40) cc_final: 0.7597 (t0) REVERT: F 264 HIS cc_start: 0.7653 (p-80) cc_final: 0.6888 (p-80) REVERT: F 299 MET cc_start: 0.8682 (mmm) cc_final: 0.8199 (mmm) REVERT: F 334 GLN cc_start: 0.9116 (tt0) cc_final: 0.8527 (tm-30) REVERT: F 356 ILE cc_start: 0.9334 (mm) cc_final: 0.8843 (tt) REVERT: F 362 LYS cc_start: 0.8529 (tttm) cc_final: 0.8144 (tttm) REVERT: F 367 PHE cc_start: 0.8447 (t80) cc_final: 0.7867 (t80) REVERT: F 426 GLN cc_start: 0.7834 (tt0) cc_final: 0.7627 (tp40) REVERT: A 3 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7503 (mm-30) REVERT: A 69 ASP cc_start: 0.8073 (t0) cc_final: 0.7574 (t0) REVERT: A 90 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7391 (tp30) REVERT: A 120 ASP cc_start: 0.8487 (t0) cc_final: 0.8223 (t0) REVERT: A 154 MET cc_start: 0.9200 (mmm) cc_final: 0.8813 (mmm) REVERT: A 241 SER cc_start: 0.8018 (p) cc_final: 0.7740 (p) REVERT: A 291 ILE cc_start: 0.8710 (pt) cc_final: 0.8508 (pt) REVERT: A 407 TRP cc_start: 0.9063 (m100) cc_final: 0.8665 (m100) REVERT: A 413 MET cc_start: 0.8116 (tpt) cc_final: 0.7841 (tpp) REVERT: G 4 ILE cc_start: 0.9604 (mt) cc_final: 0.9323 (mm) REVERT: G 21 TRP cc_start: 0.8922 (m100) cc_final: 0.8221 (m100) REVERT: G 25 SER cc_start: 0.8476 (t) cc_final: 0.7985 (p) REVERT: G 147 MET cc_start: 0.8842 (tpt) cc_final: 0.8500 (tpp) REVERT: G 203 ASP cc_start: 0.8333 (t0) cc_final: 0.7983 (t0) REVERT: G 213 ARG cc_start: 0.8190 (ptp-170) cc_final: 0.7875 (ttp-110) REVERT: G 263 LEU cc_start: 0.8940 (mt) cc_final: 0.8737 (mt) REVERT: G 264 HIS cc_start: 0.7399 (p-80) cc_final: 0.6393 (p-80) REVERT: G 300 MET cc_start: 0.8486 (mtt) cc_final: 0.8129 (mtm) REVERT: G 323 MET cc_start: 0.8567 (mmm) cc_final: 0.8231 (mmm) REVERT: G 406 MET cc_start: 0.7020 (mmp) cc_final: 0.6023 (tpp) REVERT: D 222 TYR cc_start: 0.7961 (m-80) cc_final: 0.7507 (m-80) REVERT: D 256 ASN cc_start: 0.8234 (m110) cc_final: 0.7824 (t0) REVERT: D 257 MET cc_start: 0.7379 (mmm) cc_final: 0.7073 (mmm) REVERT: D 349 VAL cc_start: 0.8862 (t) cc_final: 0.8628 (t) REVERT: D 409 THR cc_start: 0.9114 (m) cc_final: 0.8756 (p) REVERT: D 426 GLN cc_start: 0.8460 (tp40) cc_final: 0.7848 (tp40) REVERT: I 4 ILE cc_start: 0.9662 (mt) cc_final: 0.9397 (mm) REVERT: I 178 THR cc_start: 0.8630 (m) cc_final: 0.8350 (m) REVERT: I 203 ASP cc_start: 0.8708 (t0) cc_final: 0.7788 (t0) REVERT: I 257 MET cc_start: 0.7405 (mmm) cc_final: 0.6469 (mmt) REVERT: I 264 HIS cc_start: 0.7854 (p90) cc_final: 0.7016 (p-80) REVERT: I 310 TYR cc_start: 0.8747 (m-80) cc_final: 0.8481 (m-10) REVERT: I 348 ASN cc_start: 0.8801 (p0) cc_final: 0.8591 (p0) REVERT: I 355 ASP cc_start: 0.8700 (m-30) cc_final: 0.8222 (m-30) REVERT: I 356 ILE cc_start: 0.9114 (mm) cc_final: 0.8593 (tt) REVERT: B 26 ASP cc_start: 0.9130 (m-30) cc_final: 0.7846 (t70) REVERT: B 37 HIS cc_start: 0.9000 (m90) cc_final: 0.8732 (m-70) REVERT: B 101 TRP cc_start: 0.9128 (t60) cc_final: 0.8603 (t60) REVERT: B 145 SER cc_start: 0.9148 (p) cc_final: 0.8755 (p) REVERT: B 198 GLU cc_start: 0.8731 (pm20) cc_final: 0.8059 (pm20) REVERT: B 203 ASP cc_start: 0.8555 (t0) cc_final: 0.7946 (t0) REVERT: B 264 HIS cc_start: 0.7680 (p-80) cc_final: 0.7258 (p90) REVERT: B 299 MET cc_start: 0.8865 (mmp) cc_final: 0.8332 (mmm) REVERT: B 321 MET cc_start: 0.8528 (pmm) cc_final: 0.8197 (pmm) REVERT: B 359 ARG cc_start: 0.7591 (mtp180) cc_final: 0.7198 (mtm180) REVERT: B 403 MET cc_start: 0.8322 (mmm) cc_final: 0.7894 (tpp) REVERT: H 37 HIS cc_start: 0.8841 (m-70) cc_final: 0.8438 (m-70) REVERT: H 57 ASN cc_start: 0.9118 (m110) cc_final: 0.8777 (m110) REVERT: H 74 ASP cc_start: 0.9242 (m-30) cc_final: 0.9014 (m-30) REVERT: H 203 ASP cc_start: 0.7988 (t0) cc_final: 0.7644 (t0) REVERT: H 204 ASN cc_start: 0.8419 (m110) cc_final: 0.8144 (t0) REVERT: H 264 HIS cc_start: 0.7324 (p-80) cc_final: 0.6929 (p90) REVERT: H 297 LYS cc_start: 0.9324 (ptpp) cc_final: 0.8717 (mtmm) REVERT: H 403 MET cc_start: 0.7754 (mmp) cc_final: 0.6939 (mmt) REVERT: H 406 MET cc_start: 0.7537 (mmm) cc_final: 0.7014 (mmm) REVERT: H 407 GLU cc_start: 0.7276 (tt0) cc_final: 0.6686 (tt0) REVERT: H 412 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8511 (tm-30) REVERT: E 24 TYR cc_start: 0.8567 (m-80) cc_final: 0.8288 (m-80) REVERT: E 49 PHE cc_start: 0.7972 (p90) cc_final: 0.7651 (p90) REVERT: E 90 GLU cc_start: 0.8696 (mm-30) cc_final: 0.7515 (tp30) REVERT: E 151 SER cc_start: 0.9234 (m) cc_final: 0.8676 (t) REVERT: E 205 ASP cc_start: 0.7847 (t0) cc_final: 0.6888 (m-30) REVERT: E 352 LYS cc_start: 0.8830 (tptp) cc_final: 0.8554 (tttp) REVERT: J 24 TYR cc_start: 0.8486 (m-80) cc_final: 0.8180 (m-80) REVERT: J 49 PHE cc_start: 0.7747 (p90) cc_final: 0.7493 (p90) REVERT: J 90 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7775 (tp30) REVERT: J 172 TYR cc_start: 0.8485 (t80) cc_final: 0.8184 (t80) REVERT: J 205 ASP cc_start: 0.8139 (t70) cc_final: 0.7497 (m-30) REVERT: J 230 LEU cc_start: 0.9332 (mp) cc_final: 0.8818 (tt) REVERT: J 237 SER cc_start: 0.8474 (m) cc_final: 0.8268 (p) REVERT: J 272 TYR cc_start: 0.8736 (t80) cc_final: 0.8289 (t80) REVERT: J 285 GLN cc_start: 0.8448 (pm20) cc_final: 0.8237 (pm20) REVERT: J 352 LYS cc_start: 0.8768 (tptt) cc_final: 0.8013 (tppt) REVERT: J 368 LEU cc_start: 0.9169 (mp) cc_final: 0.8844 (pp) REVERT: J 398 MET cc_start: 0.7803 (ttm) cc_final: 0.7467 (ttm) REVERT: C 90 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7691 (tp30) REVERT: C 169 PHE cc_start: 0.8068 (m-10) cc_final: 0.7629 (m-10) REVERT: C 203 MET cc_start: 0.8629 (mmm) cc_final: 0.8374 (mmm) REVERT: C 221 ARG cc_start: 0.8952 (mtt-85) cc_final: 0.8586 (mmm-85) REVERT: C 233 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8358 (mm-40) REVERT: C 241 SER cc_start: 0.8567 (p) cc_final: 0.8082 (t) REVERT: C 285 GLN cc_start: 0.8007 (pt0) cc_final: 0.7108 (mm-40) REVERT: C 291 ILE cc_start: 0.8777 (pt) cc_final: 0.8409 (pt) REVERT: C 398 MET cc_start: 0.8375 (mtt) cc_final: 0.7644 (ttm) REVERT: C 402 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.8044 (mmm160) REVERT: C 417 GLU cc_start: 0.7890 (tp30) cc_final: 0.7494 (tp30) REVERT: L 31 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8245 (mt0) REVERT: L 90 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7510 (tp30) REVERT: L 123 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7864 (ttm110) REVERT: L 169 PHE cc_start: 0.7943 (m-10) cc_final: 0.7647 (m-10) REVERT: L 213 CYS cc_start: 0.8717 (m) cc_final: 0.8301 (p) REVERT: L 285 GLN cc_start: 0.8260 (pt0) cc_final: 0.7424 (mp10) REVERT: L 315 CYS cc_start: 0.7612 (m) cc_final: 0.7377 (m) REVERT: L 372 GLN cc_start: 0.8224 (tp-100) cc_final: 0.7944 (tt0) REVERT: L 398 MET cc_start: 0.7918 (ttm) cc_final: 0.7419 (ttp) REVERT: K 36 MET cc_start: 0.8058 (ppp) cc_final: 0.7746 (ppp) REVERT: K 69 ASP cc_start: 0.8302 (t0) cc_final: 0.7918 (t0) REVERT: K 90 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7450 (tp30) REVERT: K 93 ILE cc_start: 0.8630 (mm) cc_final: 0.8361 (mm) REVERT: K 96 LYS cc_start: 0.8560 (tptm) cc_final: 0.7979 (tppt) REVERT: K 154 MET cc_start: 0.9207 (mmm) cc_final: 0.8849 (mmm) REVERT: K 213 CYS cc_start: 0.8347 (m) cc_final: 0.8054 (p) REVERT: K 230 LEU cc_start: 0.9150 (mp) cc_final: 0.8818 (tt) REVERT: K 233 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8661 (mm-40) REVERT: K 338 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8667 (mtpp) REVERT: K 368 LEU cc_start: 0.9166 (mp) cc_final: 0.8833 (pp) outliers start: 5 outliers final: 1 residues processed: 976 average time/residue: 0.2269 time to fit residues: 378.5268 Evaluate side-chains 736 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 735 time to evaluate : 1.810 ------------------------------------------------------------------------------- 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: 10.0000 chunk 75 optimal weight: 0.8980 chunk 397 optimal weight: 20.0000 chunk 410 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 480 optimal weight: 30.0000 chunk 454 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 350 optimal weight: 20.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 8 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 375 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 ASN H 347 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 ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN L 18 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.106945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.095928 restraints weight = 95019.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.098909 restraints weight = 48178.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.100923 restraints weight = 28343.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.102240 restraints weight = 18352.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.103235 restraints weight = 12890.991| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41820 Z= 0.134 Angle : 0.584 12.310 56820 Z= 0.292 Chirality : 0.045 0.248 6216 Planarity : 0.004 0.072 7398 Dihedral : 11.049 179.861 5760 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.05 % Allowed : 0.48 % Favored : 99.48 % 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: -0.84 (0.12), residues: 5130 helix: 0.31 (0.11), residues: 2184 sheet: -0.91 (0.17), residues: 852 loop : -1.24 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 123 TYR 0.020 0.001 TYR B 222 PHE 0.021 0.001 PHE D 367 TRP 0.044 0.002 TRP B 397 HIS 0.014 0.001 HIS B 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (41820) covalent geometry : angle 0.58401 / 0.29 (56820) hydrogen bonds : bond 0.03535 / 2.38 ( 1368) hydrogen bonds : angle 4.56896 / 3.19 ( 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 984 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 982 time to evaluate : 1.618 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 12 CYS cc_start: 0.6691 (t) cc_final: 0.6239 (t) REVERT: F 25 SER cc_start: 0.9157 (m) cc_final: 0.8709 (p) REVERT: F 256 ASN cc_start: 0.7957 (m-40) cc_final: 0.7588 (t0) REVERT: F 334 GLN cc_start: 0.9082 (tt0) cc_final: 0.8500 (tm-30) REVERT: F 356 ILE cc_start: 0.9319 (mm) cc_final: 0.8910 (tt) REVERT: F 363 MET cc_start: 0.8675 (pmm) cc_final: 0.8409 (pmm) REVERT: F 367 PHE cc_start: 0.8207 (t80) cc_final: 0.7847 (t80) REVERT: A 69 ASP cc_start: 0.8105 (t0) cc_final: 0.7576 (t0) REVERT: A 90 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7291 (tp30) REVERT: A 120 ASP cc_start: 0.8457 (t0) cc_final: 0.8237 (t0) REVERT: A 154 MET cc_start: 0.9215 (mmm) cc_final: 0.8788 (mmm) REVERT: A 168 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7453 (tt0) REVERT: A 320 ARG cc_start: 0.8044 (ptm160) cc_final: 0.7693 (ptm160) REVERT: A 407 TRP cc_start: 0.9027 (m100) cc_final: 0.8654 (m100) REVERT: A 428 LEU cc_start: 0.8141 (tt) cc_final: 0.7742 (mm) REVERT: G 4 ILE cc_start: 0.9599 (mt) cc_final: 0.9335 (mm) REVERT: G 21 TRP cc_start: 0.8924 (m100) cc_final: 0.8297 (m100) REVERT: G 147 MET cc_start: 0.8806 (tpt) cc_final: 0.8514 (tpp) REVERT: G 203 ASP cc_start: 0.8263 (t0) cc_final: 0.7902 (t0) REVERT: G 213 ARG cc_start: 0.8276 (ptp-170) cc_final: 0.7876 (ttp-110) REVERT: G 264 HIS cc_start: 0.7432 (p-80) cc_final: 0.6401 (p-80) REVERT: G 300 MET cc_start: 0.8469 (mtt) cc_final: 0.8167 (mtm) REVERT: G 323 MET cc_start: 0.8458 (mmm) cc_final: 0.8239 (tpp) REVERT: G 406 MET cc_start: 0.7039 (mmp) cc_final: 0.6087 (tpp) REVERT: D 65 LEU cc_start: 0.8898 (tp) cc_final: 0.8300 (tt) REVERT: D 147 MET cc_start: 0.8670 (tpp) cc_final: 0.8407 (mmp) REVERT: D 222 TYR cc_start: 0.7921 (m-80) cc_final: 0.7386 (m-80) REVERT: D 256 ASN cc_start: 0.8141 (m110) cc_final: 0.7808 (t0) REVERT: D 257 MET cc_start: 0.7441 (mmm) cc_final: 0.7222 (mmm) REVERT: D 290 THR cc_start: 0.8737 (m) cc_final: 0.8498 (m) REVERT: D 321 MET cc_start: 0.8117 (pmm) cc_final: 0.7666 (pmm) REVERT: D 426 GLN cc_start: 0.8335 (tp40) cc_final: 0.7877 (tp40) REVERT: I 4 ILE cc_start: 0.9657 (mt) cc_final: 0.9413 (mm) REVERT: I 178 THR cc_start: 0.8579 (m) cc_final: 0.8278 (m) REVERT: I 203 ASP cc_start: 0.8586 (t0) cc_final: 0.7750 (t0) REVERT: I 257 MET cc_start: 0.7425 (mmm) cc_final: 0.6427 (mmm) REVERT: I 264 HIS cc_start: 0.7792 (p90) cc_final: 0.6993 (p-80) REVERT: I 297 LYS cc_start: 0.9405 (mtmt) cc_final: 0.8906 (mtmt) REVERT: I 310 TYR cc_start: 0.8743 (m-80) cc_final: 0.8476 (m-10) REVERT: I 355 ASP cc_start: 0.8687 (m-30) cc_final: 0.8224 (m-30) REVERT: I 356 ILE cc_start: 0.9103 (mm) cc_final: 0.8605 (tt) REVERT: B 26 ASP cc_start: 0.9116 (m-30) cc_final: 0.8804 (t70) REVERT: B 37 HIS cc_start: 0.8961 (m90) cc_final: 0.8691 (m-70) REVERT: B 101 TRP cc_start: 0.9139 (t60) cc_final: 0.8852 (t60) REVERT: B 145 SER cc_start: 0.9109 (p) cc_final: 0.8690 (p) REVERT: B 198 GLU cc_start: 0.8713 (pm20) cc_final: 0.7926 (pm20) REVERT: B 203 ASP cc_start: 0.8500 (t0) cc_final: 0.7837 (t0) REVERT: B 264 HIS cc_start: 0.7379 (p-80) cc_final: 0.6926 (p90) REVERT: B 321 MET cc_start: 0.8620 (pmm) cc_final: 0.8342 (pmm) REVERT: B 406 MET cc_start: 0.6938 (mmp) cc_final: 0.6592 (tpp) REVERT: H 37 HIS cc_start: 0.8975 (m-70) cc_final: 0.8706 (m-70) REVERT: H 57 ASN cc_start: 0.9104 (m110) cc_final: 0.8789 (m110) REVERT: H 74 ASP cc_start: 0.9229 (m-30) cc_final: 0.9001 (m-30) REVERT: H 203 ASP cc_start: 0.7963 (t0) cc_final: 0.7626 (t0) REVERT: H 204 ASN cc_start: 0.8358 (m110) cc_final: 0.8096 (t0) REVERT: H 233 MET cc_start: 0.8490 (ttp) cc_final: 0.8263 (ttp) REVERT: H 255 VAL cc_start: 0.8858 (p) cc_final: 0.8653 (p) REVERT: H 264 HIS cc_start: 0.7384 (p-80) cc_final: 0.6968 (p90) REVERT: H 297 LYS cc_start: 0.9325 (ptpp) cc_final: 0.8707 (mtmm) REVERT: H 321 MET cc_start: 0.8453 (ptp) cc_final: 0.8060 (pmm) REVERT: H 406 MET cc_start: 0.7689 (mmm) cc_final: 0.7187 (mmm) REVERT: H 407 GLU cc_start: 0.7283 (tt0) cc_final: 0.7067 (tt0) REVERT: H 412 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8499 (tm-30) REVERT: H 425 TYR cc_start: 0.8989 (m-80) cc_final: 0.8664 (m-10) REVERT: E 49 PHE cc_start: 0.7948 (p90) cc_final: 0.7616 (p90) REVERT: E 90 GLU cc_start: 0.8677 (mm-30) cc_final: 0.7520 (tp30) REVERT: E 151 SER cc_start: 0.9166 (m) cc_final: 0.8771 (t) REVERT: E 205 ASP cc_start: 0.7705 (t0) cc_final: 0.6713 (m-30) REVERT: E 352 LYS cc_start: 0.8845 (tptp) cc_final: 0.8306 (tttp) REVERT: J 24 TYR cc_start: 0.8511 (m-80) cc_final: 0.8202 (m-80) REVERT: J 49 PHE cc_start: 0.7596 (p90) cc_final: 0.7394 (p90) REVERT: J 90 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7789 (tp30) REVERT: J 172 TYR cc_start: 0.8481 (t80) cc_final: 0.8178 (t80) REVERT: J 205 ASP cc_start: 0.8059 (t70) cc_final: 0.7455 (m-30) REVERT: J 230 LEU cc_start: 0.9335 (mp) cc_final: 0.8809 (tt) REVERT: J 237 SER cc_start: 0.8491 (m) cc_final: 0.8174 (p) REVERT: J 398 MET cc_start: 0.7734 (ttm) cc_final: 0.7445 (ttm) REVERT: J 413 MET cc_start: 0.8159 (tpp) cc_final: 0.7954 (tpp) REVERT: C 90 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7633 (tp30) REVERT: C 169 PHE cc_start: 0.8073 (m-10) cc_final: 0.7607 (m-10) REVERT: C 203 MET cc_start: 0.8643 (mmm) cc_final: 0.8431 (mmm) REVERT: C 221 ARG cc_start: 0.8958 (mtt-85) cc_final: 0.8745 (mmm-85) REVERT: C 233 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8585 (mm-40) REVERT: C 241 SER cc_start: 0.8547 (p) cc_final: 0.8056 (t) REVERT: C 285 GLN cc_start: 0.8053 (pt0) cc_final: 0.7030 (mm-40) REVERT: C 291 ILE cc_start: 0.8775 (pt) cc_final: 0.8423 (pt) REVERT: C 368 LEU cc_start: 0.8892 (mm) cc_final: 0.8532 (pp) REVERT: C 402 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.7983 (mmm160) REVERT: C 417 GLU cc_start: 0.7779 (tp30) cc_final: 0.7446 (tp30) REVERT: C 428 LEU cc_start: 0.8535 (tt) cc_final: 0.7978 (mm) REVERT: L 31 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8363 (mt0) REVERT: L 90 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7491 (tp30) REVERT: L 123 ARG cc_start: 0.8102 (ttp-110) cc_final: 0.7839 (ttm110) REVERT: L 169 PHE cc_start: 0.7941 (m-10) cc_final: 0.7698 (m-10) REVERT: L 213 CYS cc_start: 0.8607 (m) cc_final: 0.8226 (p) REVERT: L 285 GLN cc_start: 0.8230 (pt0) cc_final: 0.7382 (mp10) REVERT: L 291 ILE cc_start: 0.8980 (pt) cc_final: 0.8717 (pt) REVERT: L 315 CYS cc_start: 0.7714 (m) cc_final: 0.7495 (m) REVERT: L 368 LEU cc_start: 0.9107 (mm) cc_final: 0.8689 (pp) REVERT: L 372 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7956 (tt0) REVERT: L 398 MET cc_start: 0.7924 (ttm) cc_final: 0.7422 (ttp) REVERT: K 69 ASP cc_start: 0.8272 (t0) cc_final: 0.7908 (t0) REVERT: K 90 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7417 (tp30) REVERT: K 93 ILE cc_start: 0.8593 (mm) cc_final: 0.8328 (mm) REVERT: K 96 LYS cc_start: 0.8535 (tptm) cc_final: 0.7951 (tppt) REVERT: K 154 MET cc_start: 0.9196 (mmm) cc_final: 0.8838 (mmm) REVERT: K 213 CYS cc_start: 0.8319 (m) cc_final: 0.8050 (p) REVERT: K 230 LEU cc_start: 0.9161 (mp) cc_final: 0.8842 (tt) REVERT: K 233 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8668 (mm-40) REVERT: K 291 ILE cc_start: 0.8772 (pt) cc_final: 0.8559 (pt) REVERT: K 338 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8653 (mtpp) REVERT: K 368 LEU cc_start: 0.9140 (mp) cc_final: 0.8821 (pp) outliers start: 2 outliers final: 0 residues processed: 983 average time/residue: 0.2251 time to fit residues: 376.6844 Evaluate side-chains 746 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 746 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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: 7.9990 chunk 441 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 460 optimal weight: 6.9990 chunk 357 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 329 optimal weight: 20.0000 chunk 471 optimal weight: 30.0000 chunk 108 optimal weight: 0.1980 chunk 192 optimal weight: 4.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN G 375 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 L 192 HIS ** L 197 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.108056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097040 restraints weight = 93999.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.100055 restraints weight = 47743.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.102069 restraints weight = 28029.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.103433 restraints weight = 18147.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.104407 restraints weight = 12623.025| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41820 Z= 0.121 Angle : 0.578 9.655 56820 Z= 0.288 Chirality : 0.045 0.236 6216 Planarity : 0.004 0.074 7398 Dihedral : 10.893 179.185 5760 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.66 % 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: -0.80 (0.12), residues: 5130 helix: 0.39 (0.11), residues: 2184 sheet: -0.99 (0.17), residues: 888 loop : -1.22 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 123 TYR 0.018 0.001 TYR B 208 PHE 0.017 0.001 PHE G 385 TRP 0.039 0.002 TRP B 397 HIS 0.012 0.001 HIS B 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (41820) covalent geometry : angle 0.57751 / 0.29 (56820) hydrogen bonds : bond 0.03509 / 2.37 ( 1368) hydrogen bonds : angle 4.49372 / 3.14 ( 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 989 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 986 time to evaluate : 1.444 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 37 HIS cc_start: 0.8799 (m-70) cc_final: 0.8526 (m170) REVERT: F 59 TYR cc_start: 0.8511 (m-10) cc_final: 0.8168 (m-10) REVERT: F 256 ASN cc_start: 0.7909 (m-40) cc_final: 0.7513 (t0) REVERT: F 264 HIS cc_start: 0.7476 (p-80) cc_final: 0.6917 (p-80) REVERT: F 293 MET cc_start: 0.8692 (ptm) cc_final: 0.7903 (ptt) REVERT: F 300 MET cc_start: 0.8112 (mmm) cc_final: 0.7894 (mtt) REVERT: F 334 GLN cc_start: 0.9049 (tt0) cc_final: 0.8472 (tm-30) REVERT: F 356 ILE cc_start: 0.9330 (mm) cc_final: 0.8878 (tt) REVERT: F 363 MET cc_start: 0.8606 (pmm) cc_final: 0.8192 (pmm) REVERT: F 367 PHE cc_start: 0.8045 (t80) cc_final: 0.7520 (t80) REVERT: A 3 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 69 ASP cc_start: 0.8054 (t0) cc_final: 0.7541 (t0) REVERT: A 90 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7267 (tp30) REVERT: A 120 ASP cc_start: 0.8451 (t0) cc_final: 0.8235 (t0) REVERT: A 154 MET cc_start: 0.9224 (mmm) cc_final: 0.8753 (mmm) REVERT: A 241 SER cc_start: 0.8022 (p) cc_final: 0.7822 (p) REVERT: A 254 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7484 (mt-10) REVERT: A 291 ILE cc_start: 0.8639 (pt) cc_final: 0.8425 (pt) REVERT: A 320 ARG cc_start: 0.8023 (ptm160) cc_final: 0.7641 (ptm160) REVERT: A 407 TRP cc_start: 0.8993 (m100) cc_final: 0.8576 (m100) REVERT: A 428 LEU cc_start: 0.8195 (tt) cc_final: 0.7895 (mm) REVERT: G 4 ILE cc_start: 0.9598 (mt) cc_final: 0.9343 (mm) REVERT: G 21 TRP cc_start: 0.8828 (m100) cc_final: 0.8282 (m100) REVERT: G 147 MET cc_start: 0.8754 (tpt) cc_final: 0.8498 (tpp) REVERT: G 203 ASP cc_start: 0.8244 (t0) cc_final: 0.7904 (t0) REVERT: G 213 ARG cc_start: 0.8153 (ptp-170) cc_final: 0.7629 (ttm170) REVERT: G 264 HIS cc_start: 0.7341 (p-80) cc_final: 0.6564 (p-80) REVERT: G 300 MET cc_start: 0.8461 (mtt) cc_final: 0.8177 (mtm) REVERT: G 323 MET cc_start: 0.8452 (mmm) cc_final: 0.8221 (tpp) REVERT: G 406 MET cc_start: 0.6991 (mmp) cc_final: 0.5944 (tpp) REVERT: D 65 LEU cc_start: 0.8622 (tp) cc_final: 0.8161 (tt) REVERT: D 101 TRP cc_start: 0.9170 (t60) cc_final: 0.8943 (t60) REVERT: D 147 MET cc_start: 0.8634 (tpp) cc_final: 0.8401 (mmp) REVERT: D 222 TYR cc_start: 0.7879 (m-80) cc_final: 0.7343 (m-80) REVERT: D 257 MET cc_start: 0.7497 (mmm) cc_final: 0.7227 (mmm) REVERT: D 267 MET cc_start: 0.8440 (mtp) cc_final: 0.8223 (mtt) REVERT: D 321 MET cc_start: 0.8050 (pmm) cc_final: 0.7177 (pmm) REVERT: D 426 GLN cc_start: 0.8337 (tp40) cc_final: 0.7858 (tp40) REVERT: I 4 ILE cc_start: 0.9667 (mt) cc_final: 0.9429 (mm) REVERT: I 178 THR cc_start: 0.8521 (m) cc_final: 0.8219 (p) REVERT: I 203 ASP cc_start: 0.8576 (t0) cc_final: 0.7996 (t0) REVERT: I 257 MET cc_start: 0.7641 (mmm) cc_final: 0.6761 (mmm) REVERT: I 264 HIS cc_start: 0.7713 (p90) cc_final: 0.6900 (p-80) REVERT: I 297 LYS cc_start: 0.9367 (mtmt) cc_final: 0.8976 (mtmt) REVERT: I 310 TYR cc_start: 0.8703 (m-80) cc_final: 0.8468 (m-10) REVERT: I 321 MET cc_start: 0.8272 (pmm) cc_final: 0.8024 (pmm) REVERT: I 348 ASN cc_start: 0.8629 (p0) cc_final: 0.8405 (p0) REVERT: I 355 ASP cc_start: 0.8611 (m-30) cc_final: 0.8162 (m-30) REVERT: I 356 ILE cc_start: 0.9052 (mm) cc_final: 0.8517 (tt) REVERT: B 25 SER cc_start: 0.9446 (m) cc_final: 0.8999 (p) REVERT: B 26 ASP cc_start: 0.9054 (m-30) cc_final: 0.8811 (t70) REVERT: B 37 HIS cc_start: 0.8970 (m90) cc_final: 0.8688 (m-70) REVERT: B 101 TRP cc_start: 0.9180 (t60) cc_final: 0.8701 (t60) REVERT: B 145 SER cc_start: 0.9136 (p) cc_final: 0.8736 (p) REVERT: B 198 GLU cc_start: 0.8653 (pm20) cc_final: 0.7871 (pm20) REVERT: B 203 ASP cc_start: 0.8004 (t0) cc_final: 0.7717 (t0) REVERT: B 257 MET cc_start: 0.7277 (mmm) cc_final: 0.6865 (mmt) REVERT: B 264 HIS cc_start: 0.7383 (p-80) cc_final: 0.6949 (p90) REVERT: B 321 MET cc_start: 0.8536 (pmm) cc_final: 0.7874 (pmm) REVERT: B 388 MET cc_start: 0.8243 (mtp) cc_final: 0.8017 (mtp) REVERT: B 406 MET cc_start: 0.6940 (mmp) cc_final: 0.6404 (tpp) REVERT: H 37 HIS cc_start: 0.8878 (m-70) cc_final: 0.8647 (m-70) REVERT: H 57 ASN cc_start: 0.9117 (m110) cc_final: 0.8798 (m110) REVERT: H 74 ASP cc_start: 0.9213 (m-30) cc_final: 0.8986 (m-30) REVERT: H 255 VAL cc_start: 0.8801 (p) cc_final: 0.8517 (p) REVERT: H 256 ASN cc_start: 0.8227 (m110) cc_final: 0.7654 (t0) REVERT: H 264 HIS cc_start: 0.7345 (p-80) cc_final: 0.7001 (p90) REVERT: H 293 MET cc_start: 0.8345 (mtm) cc_final: 0.8092 (ptp) REVERT: H 297 LYS cc_start: 0.9310 (ptpp) cc_final: 0.8689 (mtmm) REVERT: H 356 ILE cc_start: 0.9035 (mp) cc_final: 0.8777 (tt) REVERT: H 406 MET cc_start: 0.7679 (mmm) cc_final: 0.7245 (mmm) REVERT: H 412 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8471 (tm-30) REVERT: H 425 TYR cc_start: 0.8932 (m-80) cc_final: 0.8637 (m-10) REVERT: E 24 TYR cc_start: 0.8326 (m-80) cc_final: 0.7867 (m-80) REVERT: E 49 PHE cc_start: 0.7932 (p90) cc_final: 0.7625 (p90) REVERT: E 90 GLU cc_start: 0.8667 (mm-30) cc_final: 0.7514 (tp30) REVERT: E 151 SER cc_start: 0.9212 (m) cc_final: 0.8929 (p) REVERT: E 254 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7739 (mt-10) REVERT: E 352 LYS cc_start: 0.8775 (tptp) cc_final: 0.8335 (tttp) REVERT: J 24 TYR cc_start: 0.8441 (m-80) cc_final: 0.8208 (m-80) REVERT: J 69 ASP cc_start: 0.7696 (t70) cc_final: 0.7202 (t70) REVERT: J 90 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7705 (tp30) REVERT: J 172 TYR cc_start: 0.8490 (t80) cc_final: 0.8173 (t80) REVERT: J 205 ASP cc_start: 0.8026 (t70) cc_final: 0.7393 (m-30) REVERT: J 230 LEU cc_start: 0.9269 (mp) cc_final: 0.8842 (tt) REVERT: J 398 MET cc_start: 0.7758 (ttm) cc_final: 0.7419 (ttm) REVERT: C 90 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7554 (tp30) REVERT: C 170 SER cc_start: 0.8831 (m) cc_final: 0.8308 (p) REVERT: C 203 MET cc_start: 0.8713 (mmm) cc_final: 0.7932 (mmm) REVERT: C 221 ARG cc_start: 0.8919 (mtt-85) cc_final: 0.8701 (mmm-85) REVERT: C 233 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8599 (mm-40) REVERT: C 241 SER cc_start: 0.8553 (p) cc_final: 0.8072 (t) REVERT: C 285 GLN cc_start: 0.7926 (pt0) cc_final: 0.7181 (mm110) REVERT: C 291 ILE cc_start: 0.8745 (pt) cc_final: 0.8347 (pt) REVERT: C 368 LEU cc_start: 0.8914 (mm) cc_final: 0.8537 (pp) REVERT: C 372 GLN cc_start: 0.8238 (tp-100) cc_final: 0.7787 (tt0) REVERT: C 398 MET cc_start: 0.7859 (ttm) cc_final: 0.7629 (ttm) REVERT: C 402 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.8024 (mmm160) REVERT: C 417 GLU cc_start: 0.7632 (tp30) cc_final: 0.7162 (tp30) REVERT: C 428 LEU cc_start: 0.8536 (tt) cc_final: 0.7955 (mm) REVERT: L 31 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8276 (mt0) REVERT: L 90 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7401 (tp30) REVERT: L 123 ARG cc_start: 0.8067 (ttp-110) cc_final: 0.7797 (ttm110) REVERT: L 169 PHE cc_start: 0.7902 (m-10) cc_final: 0.7656 (m-10) REVERT: L 213 CYS cc_start: 0.8630 (m) cc_final: 0.8280 (p) REVERT: L 285 GLN cc_start: 0.8216 (pt0) cc_final: 0.7383 (mp10) REVERT: L 291 ILE cc_start: 0.8948 (pt) cc_final: 0.8695 (pt) REVERT: L 313 MET cc_start: 0.7178 (mmm) cc_final: 0.6916 (mtp) REVERT: L 368 LEU cc_start: 0.9097 (mm) cc_final: 0.8679 (pp) REVERT: L 372 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7962 (tt0) REVERT: L 398 MET cc_start: 0.7894 (ttm) cc_final: 0.7387 (ttp) REVERT: L 407 TRP cc_start: 0.8951 (m100) cc_final: 0.8462 (m100) REVERT: K 33 ASP cc_start: 0.8202 (m-30) cc_final: 0.7641 (p0) REVERT: K 69 ASP cc_start: 0.8202 (t0) cc_final: 0.7837 (t0) REVERT: K 90 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7448 (tp30) REVERT: K 93 ILE cc_start: 0.8656 (mm) cc_final: 0.8381 (mm) REVERT: K 96 LYS cc_start: 0.8559 (tptm) cc_final: 0.7959 (tppt) REVERT: K 154 MET cc_start: 0.9205 (mmm) cc_final: 0.8832 (mmm) REVERT: K 172 TYR cc_start: 0.8102 (t80) cc_final: 0.7720 (t80) REVERT: K 213 CYS cc_start: 0.8299 (m) cc_final: 0.8077 (p) REVERT: K 230 LEU cc_start: 0.9076 (mp) cc_final: 0.8830 (tp) REVERT: K 291 ILE cc_start: 0.8735 (pt) cc_final: 0.8386 (pt) REVERT: K 338 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8618 (mtpp) outliers start: 3 outliers final: 0 residues processed: 989 average time/residue: 0.2269 time to fit residues: 383.5182 Evaluate side-chains 749 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 749 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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: 10.0000 chunk 443 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 280 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 438 optimal weight: 6.9990 chunk 503 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 8 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 ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS G 191 GLN G 375 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 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 ** 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 301 GLN ** 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 = 0.3646 r_free = 0.3646 target = 0.102914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.092077 restraints weight = 97114.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.095009 restraints weight = 49288.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.096988 restraints weight = 28975.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.098305 restraints weight = 18775.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.099235 restraints weight = 13120.017| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41820 Z= 0.199 Angle : 0.645 9.606 56820 Z= 0.326 Chirality : 0.048 0.237 6216 Planarity : 0.004 0.083 7398 Dihedral : 11.071 179.332 5760 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.09 % Allowed : 0.16 % 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: -0.96 (0.12), residues: 5130 helix: 0.25 (0.11), residues: 2178 sheet: -1.07 (0.17), residues: 858 loop : -1.28 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 282 TYR 0.023 0.002 TYR B 222 PHE 0.021 0.002 PHE G 408 TRP 0.033 0.002 TRP B 397 HIS 0.012 0.001 HIS B 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (41820) covalent geometry : angle 0.64506 / 0.33 (56820) hydrogen bonds : bond 0.03849 / 2.58 ( 1368) hydrogen bonds : angle 4.79869 / 3.35 ( 4032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8130.42 seconds wall clock time: 141 minutes 5.61 seconds (8465.61 seconds total)